CA2123133C - Hybridization of polynucleotides conjugated with chromophores and fluorophores to generate donor-to-donor energy transfer system - Google Patents

Hybridization of polynucleotides conjugated with chromophores and fluorophores to generate donor-to-donor energy transfer system Download PDF

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CA2123133C
CA2123133C CA002123133A CA2123133A CA2123133C CA 2123133 C CA2123133 C CA 2123133C CA 002123133 A CA002123133 A CA 002123133A CA 2123133 A CA2123133 A CA 2123133A CA 2123133 C CA2123133 C CA 2123133C
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donor
chromophore
polynucleotide
acceptor
chromophores
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CA2123133A1 (en
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Michael J. Heller
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Nanogen Inc
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Nanogen Inc
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Abstract

The present invention contemplates chromophore-containing polynucleotides having at least two donor chromophores operatively linked to the polynucleotide by linker arms, such that the chromophores are positioned by linkage along the length of the polynucleotide at a donor-donor transfer distance, and at least one, fluorescing acceptor chromophore operatively linked to the polynucleotide by a linker arm, such that the fluorescing acceptor chromophore is positioned by linkage at a donor-acceptor transfer distance from at least one of the donor chromophores, to form a photonic structure for collecting photonic energy and transferring the energy to an acceptor chromophore, and methods using the photonic structures.

Description

;;~, . . . .: _.. ,. , , . ' :, , . :. . w .;., ,., , ..- ... ' , ,.. .
owo ~~io~~zs ~~rms9zio9sz7 _. ~~~~.~
HYBRIDIZATION OF POLYNUCLEOTIDES CONJUGATED WITH
~HROMOPHORES AND FLUOROPHORES TO GENERATE DONOR-TO-DONOR ENERGY
TRANSFER SYSTEM
s s DESCRIPTION
Technical Field This invention relates to design and synthesis of modified synthetic nucleic acid polymers/oligomers with directly incorporated electronic/photonic transfer properties. In particular, it relates to the property of extended directional non-radiative energy.
transfer. These unique components can be programmed to self°assemble and arganize into larger more complex structures. The directly incorporated 15? electronic/photonic functional properties allow con~iections and novel mechanisms to be formed within the organized structures. The combination of the properties allowswltimately for the creation of useful photonic and photovoltaic devices, DNA bio-20 sensors, and DNA diagnostic assay systems.
Backaround of the Tnvention The fields o~ molecular electronics/photonics and nanotechnology offer immense technological promise for r.
25 the future. Nanotechnology is defined~as a projected technology based on 'a generalized ability to build objects to complex atomic specifications. Drexler, Proc. Natl. Acad. Sci USA, 78:5275-5278, (1981).
Nanotechnology means an atom-by-atom or molecule-by-30 molecule control for organizing and building complex structures all the way to the macroscopic level.
~Nalnotechnolpgy is a bottom-up approach, in contrast to x a top-down strategy like present lithograpric techniques used in the semiconductor and integrated 35 circuit industries The success of nanotechnology ., wo 9~io9~z~ PCT/1JS92109~327 ~~.~~ t 33 -2-will be based on tt~e development of programmable self-assembling molecular units and molecular level machine tools, so-called assemblers, which will enable the construction of a wide range of molecular structures awd devices. Drexler, in "Engines of Creation°', Doubleday Publishing Co., New York, NY (1986). 'I~ius, one of the first and most important goals in nanotechnology is the development of programmable self-assembling molecular construction units.
present molecular electronic/photonic technology includes numerous efforts from diverse fields of .
scientists and engineers. Carter, ed. in "Molecular Electronic Devices TI", Marcel Dekker, Inc,_New York, N.Y (198?). Those fields include organic polymer based rectifiers, Met~ger et al., in "Molecular Electronic: ' ;
Devices II°', Carter,,ed:, Marcel Dekker, New York, NY, pp. 5-25, (1987), conducting conjugated polymers, MacDiarmid et al., Synthetic Metals, 18°285, (1987), electrpnic properties of organic thin films or Langmuir-Blogett films; Watanabe et al., Synthetic Metals, 28:C473, (1989), molecular shift registers based on electron transfer, Hopfield e~. al., Science, 241:817, (1988), and a self-assembly system based on . , synthetically modified lipids which farm a variety of different '"tubular" microstructures. Singh et al., in "Applied B~.oactive Polymeric Materials, Plenum Press, New York, NY, pp. 239-249. (1988). Molecular optical or phatonic d~:vices based, on conjugated organic polymers, Baker et al., Synthetic Metals, 28>D639,.
~;
3Q (l~gg); and nonlinear organic materials;have also been described. Potember et al., Proc. Annual Conf. IEEE
Part 4/G:1302-1303, (1989).
in Medicine and Bioloay', , However, none of the cited references describe a ' sophisticated or programmable level of self- y .
..
3-5 organization er self-assembly. Typically the actual '''-i~VO 93/09128 ~ ~ , :. ~ ~ 1PC_°T/LJS92109827 f ~ -3-molecular component whic'~ carries out the electronic and/or photonic mechanism is a natural biological protein or other molecule. Akaike et al., Proc.
Annual Canf IEEE in Medicine and Bioloay, Part 4/ 6:1337-1338, (1989). There are presently no examples of a totally synthetic programmable self-assembling molecule which produces an efficient electronic or photonic structure, mechanism or device.
Progress in understanding self-assembly in biological systems is relevant to nanotechnology.
Drexler, Proc. Natl. Acad. Sci USA, 78:5275-5278, (1981). Drexler, in "Engines of Creation", Doubleday Publishing Co., New .York, NY (1986). Areas of significant progress include the organization of the light harvesting photosynthetic systems, the energy transducing electron.transport systems, the visual ' process, nerve conduction and the structure and function of the protein components which make up these systems. The so called bio-chips described the use of synthetically or biologically modified proteins to construct molecular electronic devices. ~iaddon et al., Proc. Natl. Acad. Sci. USA, 82:1874-1878 (1985).
(McAlear et al:, in "Molecular Electronic Devices II", Carter ed., Marcel Dekker, Inc., New Yark NY, pp. 623--633, (1987). Some work on synthetic pro*~eins (polypeptides) has been carried out with the objective of developing conducting networks. McAlear et al., in "Molecular Electronic Devices", Carter ed., Marcel ' pekker, New York, NY, pp. 175-180, (1982). Other workers have speculated that nucleic acid based bio-dips may be more promising. Robinson et aT., "The Design of a Biochip: a Self-Assembling Molecular-Scale Memory .Device", Protein Engineering, 1:295-300, (1987).

'VV~ 9.~,~'09128 PC.T/US92109~27 -~ _ r,. .., Great strides have also been made in our understanding of the structure and function of the nucleic acids, deoxyribonucleic acid or DNA, Watson, et al., in "Molecular Biology of the Gene°', Vol. 1, Benjamin Publishing Co., Menlo Park, CA, (1987), which is the carrier of genetic information in all living , organisms. Tn ~7NA, information is encoded in the linear sequence of nucleotides by their base units adenine, guanine, cytosine, and thymidine (A, G, G, and T). Single strands of DNA (or polynucleotides) have the unique property o~ recognizing and binding, by hybridization, to their complementary sequence to form a double stranded nucleic acid duplex structure.
This is possible because of the inherent base-pairing properties of the nucleic acids; A recognizes T, and G
recognizes C. This property leads to a very high degree of specificity, since any given polynucleotide sequence will hybridize only to its exact complementary sequence.
2n addition to the molecular biology of nucleic acids, great progress has also been made in the area of the chemical synthesis of nucleic acids (16). This technology has developed so automated.instruments can a now efficiently synthesize sequences over 100 nucleotides in length, at synthesis rates of 15 nucleotides per hour. Also, many techniques have been developed for the modification of nucleic acids with functional groups, including; fluorophores, chromophares, affinity labels, metal chelates, chemically reactive groups and enzymes. Smith et al., y Nature, 321:674-679, (1986); Agarawal et al., Nucleic Acids Research, 14:6227-625, (1986); Chu et al., , °
Nucleic Acids Research; 16:3671-3691, (1988)~
An impetus for developing both the synthesis and z mod~.fication of nucleic acids has been the potential I
i~~0 93/09128 ~ ~ ~ ~ ,,, ~ ~ PCTlUS92I09827 i (,..,. - ~ - .
for their use in clinical diagnostic assays, -n area also referred to as DNA probe diagnostics. Simple i photonic mechanisms have been incorporated into modified oligonucleotides in an effort to impart sensitise fluorescent detection properties into the DNA probe diagnostic assay systems. This approach ; , involved fluorophore and chemiluminescent-labelled oligonucleotides which carry out Forster non-radiative energy transfer. Heller et al., in "Rapid Detection and Identification of Infectious Agents", 7Kingsbury et al,, eds., Academic Press, New York, NY pp. 345- , 356, (1985). Forster non-radiative energy transfer is a prpcess by which a fluorescent donor (D) group , excited at one wavelength transfers its absorbed energy by a resonant dipole coupling process to a suitable fluorescent acceptor (A) group. The efficiency of energy transfer between a suitable donor and acceptor group has a 1/rb distance dependency (see Lakowicz et al., in "Principles of Fluorescent Spectroscopy",, Plenum Press, New York, NY, Chap. 10, . pp. 305-337, (1983)).
In the work of Heller et al., supra, ttao fluorophore labelled oligonucleatzdes,are designed to f bind or hybx'idize to adjacent positions of a complementary target nucleic acid strand and then produce efficient fluorescent energy transfer in terms of re-emission by the acceptor. The first oligonucleatide is labelled in the 3' terminal position with a suitable donor group, and the second is labelled in the 5' terminal position with a suitable acceptor group: The binding or hybridization to the complementary sequence positions the fluorescent donor group and fluorescent acceptor groups so they are at optimal distance (theoretically) for most efficient Fprster non-radiative energy N~~ 93/09128 PC.T/Ua92/09827 -6_ i:_ ~1~3 X33 transfer. However; the observed energy transfer efficiency in terms of re-emission by the acceptor was relatively low (-20%) for this particular arrangement.
In later work (Heller et al., European Patent Application No. EPO 0229943, 1987. and Heller et al., US Patent 4,99,1.43, Feb. 26, 1991), the advances in synthetic chemistry provided methods for the attachment of fluorophores at any position within an oligonucleotide sequence using a linker arm modified nucleotide. Also, with this synthetic linkage technique it was possible to incorporate both a donor and an acceptor fluorophore within the same oligonucleotide. Using the particular linker arm, it was found that the mast efficient energy transfer (in terms of re-emission by the acceptor) occurred when the donor and acceptor. were spaced by 5 intervening nucleotide units; or approximately 2.7 nanometers (nm) apart: Heller et al., US Patent 4,996,143 also showed that as the nucleotide spacing decreases from 4 to 0 units ('1:4 nm to 0 rim), the energy transfer efficiency also decreases; which is not in accordance with ForS'ter theory. As,the nucleotide spacing was increased from 6 to 12 units (2 nm to, 4.1 nm), the energy transfer efficiency was also found to decrease;
which is in accordance with Forster theory. At the time, it was not explained nor understood why the more closely spaced donor and acceptor arrangements had reduced'energy transfer efficiency and were not in agreement with F~rster theory. In particular, the teachings of Hellex et al. did not address multiple ~doriar r~sonarice and extended energy transfer from ~
danors beyond. Forster'distances of > 5 nm.
Fluorescent energy transfer has been utilized in other areas which include immunodiagnostics and liquid chromatography analysis. Morrison et al., Anal.

s Bio~, 174:101-120, (1988); and Garner et al., Anal. Chem., 62:2193-2198, (1990). Also, some of the initial demonstrations of simple fluorescent donor/acceptor energy transfer in nucleic acids were later corroborated by other workers. Cardullo et al., roc. Natl. Acad. Sci. USA, 85:8790-8794, (1988): and Morrision et al., Anal. Hiochems, 183:231-244, (1989).
In the Cardullo et al. work, an arrangement is studied where two short (12-mere oligonucleotide sequences, each terminally labelled with rhodamine acceptors and ~h?~bridized to a complementary 29-mer sequence, are associated with several intercalating donors (acridine orange). The arrangements described by Cardullo show some added energy transfer due to the additional donors. However, this.increase in energy transfer efficiency is entirely consistent with direct donor to acceptor transfer, as none of the donors were described as functioning beyond the Forster distance necessary for efficient transfer. To date, there has been no descriptions of an organized structure capable of extended energy transfer from multiple donors and to an acceptor beyond normal Forster distances.
Summate of the ~nve~tion This invention relates to the design and synthesis of modified synthetic nucleic acid polymers/oligomers into which functional electronic/nhotonic properties are d~rectly incorporated. In particular, it concerns incorporating the property of an extended non' radiative energy transfer process into arrangements of synthetic nucleic acids.

-7a-According to one aspect of the present invention, there is provided a polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, and at least one acceptor chromophore wherein all said chromophores are linked to said polynucleotide by linker arms, wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance.
According to another aspect of the present invention, there is provided an extended photonic energy transfer system able to communicate with an electronic circuit, said transfer system comprising: a polynucleotide having a terminal donor chromophore, at least one intermediate donor chromophore, and at least one acceptor chromophore linked to said polynucleotide by linker arms;
wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore;
and wherein at least one said chromophore is adapted to convert electronic energy to photonic energy.
According to still another aspect of the present invention, there is provided an extended photonic energy transfer system able to communicate with an electronic circuit, said transfer system comprising: a polynucleotide having a terminal donor chromophore, at least one intermediate donor chromophore, and at least one acceptor chromophore linked to said polynucleotide by linker arms;
wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore;
and wherein at least one said chromophore is adapted to convert photonic energy to electronic energy.

-7b-According to yet another aspect of the present invention, there is provided a diagnostic assay system for photonic detection of a preselected nucleotide sequence comprising, in an amount sufficient for at least one assay, a polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, all said chromophores are and at least one acceptor chromophore linked to said polynucleotide by linker arms, wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance.
According to a further aspect of the present invention, there is provided a duplex nucleic acid structure capable of extended photonic energy transfer, said structure comprising: a first polynucleotide; a second polynucleotide hybridized to said first polynucleotide; a terminal donor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide; at least one intermediate donor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide;
and at least one acceptor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide; wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore spaced from said terminal donor chromophore by a donor-donor transfer distance; and wherein said donor and said acceptor chromophores are alternately positioned on said first polynucleotide and said second polynucleotide such that said photonic energy transfer crosses between said first and said second polynucleotides of said duplex.

-7c-According to yet a further aspect of the present invention, there is provided a biosensor for detecting the presence of an analyte in solution, said analyte comprising a target DNA sequence, said biosensor comprising: an excitation source for delivering emitting photonic energy; a donor sequence comprising a first polynucleotide having a terminal donor chromophore and at least one intermediate donor chromophore linked to said first polynucleotide by linker arms, wherein said first polynucleotide is complementary to a first region of said target DNA sequence;
an acceptor sequence comprising a second polynucleotide having at least one acceptor chromophore linked to said second polynucleotide by linker arms, wherein said second polynucleotide is complementary to a second region of said target DNA sequence; wherein the distance between one said donor chromophore and one said acceptor chromophore is such that they are in an energy transfer relationship; and an associated photon sensing means to detect photonic energy emitted from said acceptor.
According to still a further aspect of the present invention, there is provided a biosensor for detecting the presence of an analyte in solution, said analyte comprising a target DNA sequence, said biosensor comprising: an excitation source for delivering emitting photonic energy; a donor sequence comprising a first polynucleotide having a terminal donor chromophore and at least one intermediate donor chromophore linked to said first polynucleotide by linker arms, wherein said first polynucleotide is complementary to a first region of said target DNA sequence;
an acceptor sequence comprising a second polynucleotide having at least one acceptor chromophore linked to said second polynucleotide by linker arms, wherein said second polynucleotide is complementary to a second region of said -7d-target DNA sequence; and an associated photon sensing means to detect photonic energy emitted from said acceptor;
wherein said first polynucleotide and said second polynucleotide are able to hybridize with said target DNA
sequence to form a complex wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore.
According to another aspect of the present invention, there is provided a method for detecting the presence of a preselected nucleic acid target sequence in a nucleic acid-containing sample comprising the steps of:
(a) admixing; (i) a polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, and at least one acceptor chromophore, said chromophores are linked to said polynucleotide by linker arms, all wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance, and (ii) said nucleic acid-containing sample to form a hybridization reaction admixture, said polynucleotide having a preselected nucleic acid sequence adapted to hybridize to said target sequence;
(b) subjecting said hybridization reaction admixture to hybridization conditions for a time period sufficient for said polynucleotide to hybridize to said preselected nucleic acid base sequence and form a donor chromophore containing-and acceptor chromophore containing-hybridized nucleic acid duplex; (c) exciting said donor chromophores in said nucleic acid duplex formed in step (b) by exposing said donor chromophores to sufficient photonic energy to induce emission of photonic energy from said acceptor chromophore;
and (d) detecting the presence of photonic energy re-emitted -7e-from said acceptor chromophore using a photon sensing means, thereby detecting the presence of said preselected nucleic acid target sequence in said sample.
According to yet another aspect of the present invention, there is provided a method for detecting the presence of a preselected nucleic acid target sequence in a nucleic acid-containing sample comprising the steps of:
(a) admixing; (i) a first polynucleotide having a terminal donor chromophore and at least one intermediate donor-acceptor chromophore, said donor and donor-acceptor chromophores are linked to said first polynucleotide by linker arms; and (ii) a second polynucleotide having at least one acceptor chromophore liked to said second polynucleotide by a linker arms, and (iii) said nucleic acid-containing sample to form a hybridization reaction admixture, said first and second polynucleotides having preselected nucleic acid sequences adapted to hybridize to said target sequence and thereby position said terminal donor chromophore on said first polynucleotide and one said acceptor chromophore on said second polynucleotide at a distance which is greater than 5 nm, and wherein there is at least one said intermediate donor chromophore within said distance; (b) subjecting said hybridization reaction admixture to hybridization conditions for a time period sufficient for said polynucleotide to hybridize to said preselected nucleic acid base sequence and form a donor chromophore containing- and acceptor chromophore containing-hybridized nucleic acid duplex; (c) exciting said donor chromophores in said nucleic acid duplex formed in step (b) by exposing said donor chromophores to sufficient photonic energy to induce emission of photonic energy from said acceptor chromophore; and (d) detecting the presence of photonic energy re-emitted from said acceptor chromophore -7f-using a photon sensing means, thereby detecting the presence of said preselected nucleic acid target sequence in said sample.
It has now been discovered that multiple chromophore donor groups which are located beyond the normal Forster distance (> 5 nm) can be arranged to I.
W~ 9310912 PCflU~92149827 _g_ a sorb and transfer photonic energy to a terminal acceptor group, thereby acting as a light antenna or photonic conductor. This property involves ~.he ability of an array of donor groups to absorb photonic energy at one wavelength (hv~) ; and directionally transfer it, via a coupled resonance pracess, to an , acceptor group, where it is then re-emitted as photonic energy at a longer w«velength (hv2). The selection and relative positioning of special donor I
1,0 chromophore graups, which include non-fluorescent chromophores, with appropriate acceptor fluorophores, leads to an efficient extended energy transfer process with unigue properta:es. Additionally, appropriate I
designs for oligonucleotides and polynucleotides have found which allow a primary donor group to be placed :, in close proximity with an acceptor group.
Since the relative positions of the functional molecular components (chromophores) can be programmed, via their placement upon nucleotide sequences,wucleic acid containing the chromophores can be designed to self=assemble and organize into larger and more complex defined' structures. The programmability and functional eleatronic/photonic properties of the molecular components enable connections, amplifica~ion mechanisms, and antenna arrays to be made within the ' nucleic acid structures. The combination of properties ultimate3.y leads tc the creation of i pho'tonic devices, photovoltaic devices, biosensors, and homogeneous and heterogeneous DNA diagnostic assay . ' , , .
The present invention therefore describes'a ~
polynucleotide having at bast two (multipl,e) donor , inked to the of r~ucleptide 'chromophores operatively 1 p y by linker arms, such that the chrcmopr~oi'es are r;
positioned by the linkage along;the length of the WO 93109128 P~1'1US92109827 av polynucleotide at a donor-donor transfer distance.
Typically the donor chromophores are non-fluorescing chromophores.
The polynucleotide can further contain a ;
fluorescing acceptor chromophore operatively linked to the polynucleotide by a linker arm, wherein the fluorescing acceptor chromophore is positioned by the .
linkage at a donor-acceptor transfer distance from the donor chromophares such that the multiple donors can collect excitation light and transfer it to the acceptor which then re-emits the collected light.
In another embodiment the donor chromophores and acceptor chromophores can be displaxed upon more than , one polynucleotide such that upon their hybridization, the acceptor fluorescing chromophore is brought into donor-acceptor transfer distance to at least one of the donor chromophores. Thus, combinations of polynucleotides are contemplated containing preselected sequences and the requisite donor and acceptor chromophores that can be adapted for a .
variety of uses as described herein. , example, a diagnostic assay system is described that contains a polynucleotide capable of <:
donor--donor transfer as described above. The system can utilize an acceptor;chromophore that is present on .
a separate polynucleotide, or the acceptpr chromophore can b~ present on the same polynucleotide as the donor chromophores.
The sequences of the polynucleotides can be selected for purposes of complementary hybridization to facilitate assembly of larger structures capable of y donor-donor transfer and ultimate donor-acceptor transfer. Alternatively, the sequences of the t0 golynucleotides can be selected to be complementary tar et nucleic acid sequences such that the wo ~3io~ax~ ~~.-r>us9z~o9sz~
~~.23 X33 , .. ..
-~o-polynucleotides are used diagnostically to detect the target sequences in samples.
In another embodiment, the invention describes, structures in the form of a nucleic acid duplex that , are comprised of at last two polynucleotides hybridized together by ~onventianal complementary , nucleotide base hybridization. Multiple polynucleotides can be hybridized to farm the duplex as is represented in Figure 3. The.polynucleotides contain operatively linked donor and acceptor chramophares to provide a larger structure upon which the disclosed donor-donor and donor-acceptor energy transfers can occur. The chromophores can be arranged along a single strand of the duplex structure, but are 25 preferably positioned such that the energy transfer alternates between the strands of the duplex.
Also contemplated is a biosensor device comprising a photonic energy sensing means and a palynucleatide of this invention having at leash two 2Q~ donor chromophares operatively linked to the palynucleotide by linker arms; wherein the chromaphares are positioned by~the linkage along the length of the palynucleotide at a donor-donor transfer disrtance. The biosensor has at least one fluorescing 25 acceptor chromophore operatively linked to the polynucleotide by a linker arm such that the fluorescing acceptor chromophore is positioned by the linkage at a donor-acceptor transfer distance from at bast one of the donor chromaphores. Furthermore, the 30 polynucleotide is detestably positioned adjacent to ~ ~ the sensing means sucta that the sensing''means can detect photonic energy emitted from the acceptor chromophore upon excitation of the donor chromophores.
In another embodiment, the invention contemplates >°' 35' a method for detecting the presence of a preselected WO 9/09128 PCT/U~92/09827 1 nucleic acid sequence in a nucleic acid--containing sample that involves the use of one,or more polynucleotides of this invention as a probe, and relying upon the energy transfer systems described herein far producing a detectable fluorescent acceptor emission to indicate a hybridization event.
Other embodiments will be apparent based on the disclosures herein:
Brief Description of the Drawincts In the drawings forming a portion of this disclosure:
FIGURE l illustrates haw two chromophore-labelled - oligonucleotides (donor oligomer SEQ ID rdO 1 and acceptor oligomer SEQ ID NO 2) are designed to bind or hybridize to adjacent positions on a complementary target nucleic acid strand (target sequence SEQ ID NO
3). The binding or hybridization to the target sequence approximates the fluorescent donor group and fluorescent acceptor group at a preselected donor-aGCeptor transfer distance so that when the system is irradiated by photonic energy at hv~ the donor group absorbs the energy arid transfers it by non-radiative energy trans~~r (----->) to the acceptor group which re-emits it at hv2. Irradiating and emitting photons are ~:ndicated by the wavy-lined arrows. The exact nucleotide sequence and position of d~nor and acceptor groups is shown for the un-hybridized (or disassociated system) in the upper portion of the figure. The hybridized figure (or associated system) is'x°epresented schematically for purposes o~
simplicity in the lower portion of the figure. v FIGURE 2'illustrates in Panel (a) a schematic representation of multiple donors groups (D) and a ~5 single acceptor group (A) incorporated into a single .WC? 93/09128 - PCT/US92/09827 ,? . r~ a ~, ~ ~
V
.~ ~. i,~ .l -12 -DNA polynucleotide strand hybridized or associated to a template DNA aligomer. Panel (b) illustrates a multiple danor DNA palymer and an acceptor DNA Polymer assembled into an organized structure on a template , DNA polymer.

FTGURE 3; in the upper portion, illustrates schematically the exemplary 14 nm photonic antenna structure described in Example 1 that is assembled and organized :from four oligonucleotides: the l6-mer acceptor unit (AU), the 30-mer interznedza~e donor 1 unit (ID1), the 29-mer intermediate donor 2 unit (ID2), and the terminal donor unit (TD)o The lower .

portion of the figure illustrates extended energy trans~'er when the assemb~.ed structure is ,illuminated wit light at 495 nm: The wavy lines indicate irradiating or emittzng photons and the dashed arrow' (.-- ->) shows the direction o~ the extended energy transfer process. .

FIGURE 4 illustrates a homogeneous DNA

hybrid'ization,assay method based an extended energy transfer as described in Example 3. The polynualeotides shown include the multiple donor- ' containing oligomer (MDO), the acceptor oligomer (AO), the, quencher oligomer (Qo) and a target DNA. Panel (a) shows the homogeneous system before. the target DtA

is denatured. Note that the acceptor group is :proximal to the quencher group, and therefor emission from the acceptor ~.s' quenched. Panel (b) shocas the homogeneous system after the target DNA is denatured whereupon the multiple donor and acceptor oligomers ~have'hybxid'ize'd to the target DNA at specific, programmed, complementary sites to produce a structure s capable of extended energy 'transfer.

" r. ; r r .v .. ., .. ~ ::.., ,. . . . .
C > , . . , . , . . . c W~ 93/0912 P~T/US92/09~27 ~1~ ~ ). 3 3 Detailed Description of the Invention A. Chramophore-Containing Palynucleotides This invention relates to the design and synthesis of modified synthetic nucleic acid polymers/oligomers into which functional electranic/photonic properties are directly incorporated. Synthetic nucleic acids having inherent recognition properties (i.e., complementary hybridization} and are ideal materials for constructing molecular components which can self-organize into electronic and photonic structures and devices.
In one embodiment, the invention contemplates polynucleotide(s} having an acceptor chromophore group and one or more primary donor chromophores within Forster distance (< 5 nm), and at least two donor chromophores, or preferably mult~.ple chromophores located beyond normal Fnrster distance (> 5 nm).
Operatively acceptor and donor chromophores are linked to the polynu~cleotide(s) by linker arms, such that the chromophores are positioned along the length of the polyx~ucleotide at donor-donor transfer distance (1'.4 nm.to 6.1 nm) effective for resonant energy transfer as described by the present discoveries.
The polynucleotides described herein can be formatted and used in a variety of configurations.
The donor chromophores can be present on a single polynucleatide and the acceptor chromophore can be present on a separate polynucleotide that is only brought into donor~acceptor transfer distance by a preselected hybridization event. Alternatively, acceptor chromophores can be present on the same polynucleotide together with orie or more of the donor chromophores. s BCD 93/0912$ . PCTf US92/09~27 ~~.~3 x.33 In one embodiment, a polynucleotide has at least two donor chromophores operatively linked to the polynucleotide by linker arms such that the donor chromophores are positioned by the linkage along the .
length of the polynucleotide at a donor-donor transfer distance as defined herein. A preferred donor-donor transfer distance is about 1.4 to about 6.1 nanometers.
The polynucleotide(s) have a predetermined sequence selected to be complementary to other nucleic acid sequences, so that the chromophore containing polynucleotides can be programmed (1) to self-assemble with each other by the hybridization process, forming organized photonic or electronic structures on solid supports or thin films such as glass, silicon, 'germanium, gallium arsonide, polymers, resists, Langmuir Blodgett fluids and the like or (2) to bind td preselected target~nucleic acid~sequenc~s in solution or attached to solid supports or thin film materials.
In one embodiment, a terminal or central polynucleotide further contains at least one fluorescing acceptor chromophore operatively linked to the polynucleotide by a linker arm, such that the fluorescing acceptor chromophore is positioned by linkage at a donor-acceptor transfer distance of from about 0.1 nm to about 1.7 nm from at least one primary or main coupling donoL chror~ophore,: These configurations provide the organized structures ~ ; , 30 ~ ,qapable c~f extended non-radiative :,energy transfer described by the present invention.
For purposes cf thi.s invention and unless otherwise stated, the terms "oligonucleotide"
oligomer" or "polynucleotide" will rifer generally to nucleic acids in the form of single-stranded nucleic w~ ~~io~~zs 3 ~ 1'CT/U~92f09~z7 i ° 15 _ i.
acid polymers, comprised of DNA, RNA, or modified sequences produced by totally synthetic procedures.
Technically, the shorter sequences from 2 to 50 nucleotides in length are referred to as oligonucleotides or oligomers, and the longer sequences (> 50 nucleotides) are referred to as polynucleotides. However, for this invention the terms are used somewhat interchangeably insofar as they bath denote nucleic acid polymers..
Important advantages of synthetic DNA as the support structure for providing the array to orient multiple donors and acceptor in a transfer structure are: (1) rapid synthesis with automated instruments, in lengths from 2 to 150 nucleotide units (0.? nm to 50 nm); (2) programmable recognition with high specificity, via their nucleotide sequence; (3) easily modified with, fluorophores, chromophores, affinity labels, metal chelates, and enzymes; (4) modifiable at any position in their sequence, and at several~places within the base unit; (5) modifiable backbone structure to'produce.different properties (example; ' normally.negatively charged DNA can be made in a neutral form) (6) sinkable both covalenthy and non°
covalently to solid surfaces: glass; metals, silicon, organic polymers, and bio-polymers; (7) reversible organizational properties; (8) ability to form three dimensional and brandhed structures; and (g) well understood an3 easily modelled structural and organizational properties.
~ ' 1, Extended Enera~Y Transfer The particular functional electronic/photonic property which concerns this invention, is an extended non-radiative (Forster) energy transfer process. The basic Forster energy transfex process involves the 2 . P('f/US92/09827 -16_ c.;.:.
. .
ability of a donor group to absorb photonic energy at one wavelength (hv~) and transfer it, via a non-radiative dipole coupling process, to an acceptor group which re-emits the photonic energy at a longer , wavelength (hv2). Energy transfer efficiency ~is dependent upon the parameters which are given in the equations below:
E - R~6 Ro + rb Ro = 9.8 x 103 (kz n~4 Od J) (in A) (2) where E = the. transfer efficiency, r = the distance between the donor and acceptor, k is a dipole orientation factor, n is the refractive index of the medium, Od is the quantum yield of the donor, and J is the overlap integral which express the degree of overlap between the donor~emissian and the acceptor absorption. All other parameters being optimal, the 1/r6 dependency requires a donor to acceptor distance of less than 2 nm (20 A) for high efficient energy transfer to occux. Table 1 shows the theoretical energy transfer efficiencies by conventional Forster energy transfer (ET) when the donor (D) to acceptor (A) distance range is from 0 to ~:5 nm.

~A Distance (nm ~ Theoretical ET Efficiency (o) ~0 0.5 100 ,: , ,. , ..; 1.0 fig;
1.5 98 2s0 9?
2.5 86 ' 3.p ;:;-.: ,;
wo 9~rom zs ~c°rrus9zro9~z7 -m-3.5 50 4.0 28 4.5 < 10 Figure 1 shows haw two fluorophore-labelled oligonucleotides (a donor and an acceptor) are designed to bind ox hybridize to adjacent positions of a complementary target nucleic acid strand and then produce efficient fluorescent energy transfer.
Relative efficiencies for the energy transfer process can be expressed in two simplistic ways. The first is in terms of the ratio of transferred energy to the energy absorbed by the donor; this is determined by measuring the relative amount of donor fluorescence quenching that occurs in the presence of the acceptor.
The second way,expresses relative efficiency in terms of the ratio of energy re-emitted by the acceptor to the energy absorbed by the donor; this is determined by measuring the relative increase zn acceptor fluorescence due to donor group. While both methods are considered rela ive measures of energy transfer effic~.ency, the eff~.cient transfer of energy from the donor to the acceptor (seen as donor quenching), does nat necessarily lead to the same efficiency for re-emission by the acceptor. This acGUrs when secondary processes (acceptor ~uenchingj cause the acceptor to dissipate its energy other than by re-emission.
Extended energy transfer is the process by which multiple donor groups absorb photonic energy at one wavelength' (hv~) forming a coupled resonant structure which can directionally transfer the energy to an ' acceptor group. The resonant energy is then re-ema:ttad as photonic energy at wavelength (hv2). Under conditions'where hv~ is non-saturating, photonic 'd9'~ ~3~~~~8~ ~ , PLT/US92JtD982 i _18_ energy can be collected lay arrays of donor groups and directionally transferred to an appropriate acceptor, greatly enhancing its fluorescent emission at hvz.
This can be considered a molecular antenna or amplifier mechanism. Alternatively, photonic energy (hv~) can be collected at one end of a structure by a donor group arid be transferred by a linear array of ' donors, to an acceptor group at the other end of the structure where it is re-emitted as hvz. This type of molecular photonic transfer mechanism can be considered the equivalent of a photonic wire or connector. These mechanisms can also be used to interconnect different molecular structures, to connect molecular structures to surfaces, and to make molecular connections between surfaces (monolayers).
Thus, distances between donor chramophores are selected to provide a donor-donor transfer distance, which indicates that the transfer is a non-radiative energy transfer. Similarly distances between a.
terminal donor chromophore and the acceptor chromophore are selected to provide a donor-acceptor transfer distance, whidh indicates that the transfer .
by donor is non-radiative and results in the excitation of a fluorescing acceptor chromophore and subsequent emission spectrum from the acceptor.
2. Chromaphores And Fiuoraphores A novel part of this invention relates to the selection and positioning of special chromophore and fluorophore groups to form appropriate donor and 'acceptor pairs'which are capable of energy transfer by dipole coupling.
A chromophore refers to those groups which have favorable absorption characteristics, i.e, are capable of excitation upon irradiation by any of a variety of VVJ 93!09128 P~'f/U~92/09827 photonic sources. Chromophores can be fluorescing or non-fluorescing. Non-fluorescing chromophores v typically do not emit energy in the form of photonic energy (hv2~. Thus they can be characterized as having a low quantum yield, which is the ratio of emitted phatonic energy to adsorbed phatonic energy, typically less than 0.01. A fluorescing chromophore is referred to as a fluorophore, and typically emits photanic energy at medium to high quantum yields of 1.0 0 . 01 to 2 .
Of particular importance to the present invention is the demonstration that non-fluorescent chromophores, such as 4-Dimethylaminophenyl-azophenyl-4'-isothiocyanate (or DAB2TC}, can function as 1.5 effective energy transfer donor groups. When these chromophare donor groups are closely approximated (0:1 nm to 1.7 nm} to a suitable acceptor group they produce a significant fluorescent re-emission by the acceptor. Chromophores capable'of energy transfer to 20 a suitable acceptor chramaphore are referred to herein as donor chromophores or donors.
An acceptor chromaphore for the purposes of the present invention is a fluorophore, that is capable of accepting energy transfer Pram a donor chromophore and 25 producing an emission spectrum. Because energy transfer by dipole coupling can typically occur when there is an overlap in the emission spectrum of the donor and the excitation spectrum of the acceptor, a "suitable" acceptar typically has an excitation 30 spectrum in the longer wavelengths than its ~correspondi,ng';suitable donor. Tn this regard, donors and acceptors can be paired far capacity to transfer energy on the basis of overlapping donox emission and accept~r excitation spectra; Therefore, potentially '.
35 any chromophorc can be paired with another chromophare ~'CT/US92/09827 r' _20- ;.
to form an acceptor-donor pair, so long as the two chromcphores have different emission spectrums, and have sufficiently overlapping donor emission and acceptor excitation spectra to effect energy transfer.
A non-fluorescent donor producing fluorescent re-emission in the acceptor group is an extremely valuable property. The non-fluorescing donor in a composition of the present invention provides the particular advantage of a low ar absent level of emission by the donor, thereby not contributing to background or the detectable emitted light in a donor-acceptor jystem. Thus, non-fluorescent donors allow for very low background and are particularly preferred.
A multiple donor system comprised of such non-fluorescent chromophores would have very little inherent fluorescent background. This property overcomes a major limitation that has severely limited practical uses of fluorescent energy transfer i.n.DNA
diagnostic assay applications. It also opens opportunity to create more useful photonic mechanisms and applications.
With regard to unique properties.in acceptors, most preferred are acceptors with the highest quantum yields, ar with other properties that increase the signal-to-noise ratio between specific acceptor emissions and the background (non-specific) emissions avttributable to the donor. Examples of approaches to reduce the signal-to-noise ratio include using donors hawing lower emission, preferably non-fluorescing ''dbnbrs, selection of acceptor-donor pairs in' which the spectral distance between the emission spectrum of the donor and acceptor is maximized, and preferably selected as to be non-overlapping, and the like approaches described further herein.

~~~~1 W~ 93/09128 P~C'T11J~92109827 _..

Fable 2 lists some of the potential chromophores and fluorophores which can be used as donors, acceptors, and quenchers for the novel extended energy 'transfer mechanisms and applications disclosed in this invention. The list is not meant to be exclusive in that it identifies some specific types or classes of donors, acceptors, and quenchers which can produce these unique and desirable properties.

CHROMOPHORE DERIVATIVES USEFUL AS DONORS, ACCEPTORS, OR QUENCHERS FOR THE EXTENDED'ENERCY TRANSFER PROCESS
AND RELATED FHOTONIC MECHANISMS
DERIVATIVES (EX~ ~ (EM; 3 (Qy) 4, 4,4'-Diisothiocyanatodihydro-stxlbene-2,2'-disulfonic acid 286 none5 < 0.01 4-acetamido-4,'-isothiocyanato-stilb~ne-2,2'-disulfoniC acid 336 438 M

4~4e-Diisothiocyanatostilbene -2,2'-disulfonic acid' ' 342 4T9 M

Suecinimidyl pyrene butyrate 340 375,395 0.6 Acridine isathiocyanate 393 47.9 M

4-Dimethylaminophenylazophenyl -4'isothiocyanate (DABITC) 430 hones 0.01 <

Lucifer Yellow vinyl sulfone 438 540 0.2 r ''?5 Fluorescein isothi.ocyanate 494 520 0.5 Reactive Red 4 (Cibacron Brilliant Red 3B-A) 535 noneS < 0.01 Rhodamine X isothiocyanate 578 604 M-H
Texas Red (Sulforhodamine 101, sulfonyl chloride) 596 615 H
Malachite Green isothiocyanate 629 none5 < 0.01.

~ The fluorophores and chromophores listed abave are shown in derivatized forms suitable for direct coupling to the primary amino group incorporated into the DNA polymer. In many cases other types of derivatives (succinimidyl esters arid haloacetyl) are available for coupling to am~.nes. Also; derivatives specific for coupling to sulfhydryl and aldehyde functional groups are available.
Z EX is the absorption maximum in nanometers (nm).
~ EM is-the emissie~n maximum in nanorneters (nm).
For quantum yields (QY) the approximate ranges ~ , .i 30 , ~ a~'e:, "LoW" , p . pl_p . 1 ~ "Medium".,. 0. 1-;0. 3 : a;nd i "High", p,3-1Ø
5 These are essentially non-fluorescent (QY <0.01) 'organic compounds, with medaum to high molar absorptivity. They are more appropriately called chromophores.
IR144 (Kodak~Laser Dye) is un-derivatized,, and requires modification before it can be coupled to a DNA polymer.
Particularly preferred donor chromophores are selected from the group cons_sting of 4,4'-Diisothiocyanatodihydro-stilbene-2,2'-disulfonic arid, 4-acetamido-4'-isothiacyanato-stilbene-2,.2!-disulfonic acid, 4,4'-Diisothiocyanatostilbene-2,2'-disulfonic acid, Succinimidyl pyrene butyrate, Acridine isothiocyanate, 4-Dimethylaminophenylaaophenyl-4'-isothiocyanate (DAHITC), Lucifer Yellow vinyl sulfone, Fluorescein isothiocyanate, Reactive Red 4 (Cibacron Brilliant Red 3B-A), Rhodamine X isothiocyanate, Texas Red (Sulforhodamine 101, sulfonyl chloride), Malachite Green isothiocyanate and IR1446. Exemplary donor chromophores are descr~bed~ in the Examples.
Particularly preferred fluorescing acceptor chromophores are selected from the group consisting of pyrene, Lucifer Yellow, acridine, riboflavin, fluorescein, rhodamine, Sulforhodamine 101, Texas Red and IR 144. Exemplary fluorescing acceptor chromophores are described in the Examples.
Also contemplated as useful donor or acceptor chromophores for the invention include those chromophores, derivatives of or combinations of, which would allow electronic signals such as excited electrons to enter the donor-donor transfer system and then be transferred as resonant energy to the acceptor and to exit the system as an electronic signal. In other words, the mechanism for input, exit, or both, into and out of the donor-donor-acceptor transfer *Trade-mark ..
'W~ 93/0928 PCT/US92/09827 ' ~~.23 x.33 -24-system of this invention can involve chromophore(s) adapted to convert electronic energy into the resonant energy of the transfer system (and back again) such ' that the transfer system communicates to an electronic , circuit. In this manner, an extended energy transfer !
system of the present invention can function as an electronic connector or signal conduit. Possible convertors between electronic energy and resonant enErgy include but are not limited to luminescent compounds, such as ruthenium complexes, photovaltaic cells, and the like.
3. Donor and Acceptor Pair configurations From the chromophores and fluorophores listed in Fable 2 a number of donor/acceptar configurations or arrangements can be, made that will produce efficient extended energy transfer processes and novel.photonic mechanisms. These arrangements which are shown in Table 2 include:
ZO
(1) Arrangements of multiple donors groups (fluorescent and non-fluorescent) transferring energy to a single or smaller number of acceptor groups.
Geh;erally, multiple donors transfer to a single acceptor group, but under some conditions and for certain photonic mechanisms more than one acceptor group may be used, The preferx°ed arrangements are those involving the non-fluorescent donors, which provide the important advantage of a low background 3Q ', ,e,xtended energy, transfer process. ,Other preferred I , arrangements involves multiple fluorescent donors, exited in the visa.ble-region, which transfer to an acceptors) which re-emits in the infra--red region.
This is a useful mechanism because the infra-red emi:ssian can be de ected by aptoelectronic devices ....,_.. : . . .< .-..:.. .:. ,,; ., . . :~.:. : . .... _ .. . : .- ..:~,... .
... : :.:. .. .-. . , , : _:_: ..,... . : ...._. ... ._... _.

l~V~ 93/09128 ~ P~'f/US92/p9827 -2'- ' which are mueh less sensitive to background fluorescence produced in the visible region.
(2) Arrangements in which multiple donor groups (fluorescent and non-fluorescent) absorb light at hv~, and transfer to an intermediate donor-acceptor, which then transfers to a final acceptor group, which re-emits at hv2. These arrangements have the advantage of producing a large Stokes shift between the excitation wavelength (hv~) and the emission wavelength (hv2) of the system. This is important because the larger the separation between excitation and em~.ssion', the lower the background fluorescence for the system. Exemplary configurations are shown in Table 3, where three chromophores are shown in series.
The preferred arrangements are those which transfer from non-fluorescent or fluorescent donors to an acceptors) which re-emit in the infra-red region.A
preferred embodiment contemplates the use of IR~144 (a Kodak Laser Dxe), a chromophore that accepts excitation energy from donors that are excited in the visible region 'arid then re-emits in the infra-red region.
(3) Special arrangements in which certain chromophore groups with strong quenching properties are used to pre~rent fluorescent emission by the acceptor group. In this embodiment, the present invention contemplates the use of a quencher chromnphore (or quencher), that has the capacity to accept, lice an acceptor, the transfer of energy by dipo~.e coupling, but does not have significant emission. ~;lthough'similar in properties to a non-fluc~re~cing donor, the term quencher refers to a non-fluorescing chromophore that is configured o draw the i i~V~ 93/09128 PCT/U592/09827 '.
2~.~31:33 _ energy potential away from an excited acceptor so that the acceptor does not emit, i.e., the acceptor is quenched. An exemplary configuration utilizing a quencher. chromophore in combination with a multiple , v donor oligonucleotide of the present invention is described in Example 3 and Figure 4. .
The mechanism for energy transfer to a quenching chromophore is the same as for donor-donor or donor-aoceptor transfer, namely dipole coupling, and 20 therefor is subject to the same requirements as descri.bed herein relating to transfer distances and optimum pairing configurations. Exemplary non-fluorescent chromophores suited for quenching are Reactive Red 4 or Malachite Green because they have no 25 detectable emission and they are located at the "red'°;
end of the spectrum, and therefore can be selected relative to a variety of acceptor chromophore to accept (quench) energy from the acceptor before it emits. The preferred arrangements are for the non-20 fluorescent criromophores Reactive Red 4 or Malachite to quench fluorescence in the Texas Red acceptor group.

MULTTPLE DONOR/ACGEPTUR, MULTTPLE' DONOR ./ACCEPTOR
DONOR 2/ACCEPTOR; AND SPECIAL QUENCHING ARRANGEMENTS
~* PREFERRED *), ~0 , ., ,DABITC _-,-> ,Fluorescein * DABTTC ---> Texas Red *,DABTTC -> TeXas Red ---> ZR 144 Lucifer Yellow - ->'Texas Red i - Lucifer Yellow ---> Fluorescein ---> Texas Red 35 * Lucifer Yellow - -> Texas Red - -> TR 1~4 * , j '1'V~ 93/09828 ~ ~ ~ ~ ~: -~ ~~ PCT/US92/09827 _27_ Fluorescein ---> Texas Red Fluorescein --°> IR 144 * Fluorescein ---> Texas Red ---> IR 144 * Texas Red ---> IR 144 * P4alachite Green ...:> Texas Red * Reactive Red 4 ...:> Texas Red *
The ----> indicatPS an energy transfer effect which leads to significant re-emission by the acceptor group. The ...:> indicates an energy transfer effect that significantly quenches the fluorescence of the acceptor group.
It is important to point out that the various arrangements and configurations of donor, acceptor, and quencher groups described above can be achieved by either incorporating them within a single DNA polymer;
or by using a DNA template to assemble variouo combinations of multiple donor DNA polymers., acceptor DNA polymers, .and quencher~DNA polymers; Hoth types of arrangements are shown schematically in Figure 2.
With regard to the optimum positioning or spacing of ~hs primary "donor to acceptor" pair, thereb~r forming the donor-acceptor transfer distance, the basic 1/r6 distance dependency for Forster transfer requires'a spacing of 0 to 5 nm, and.preferably a spacing of about 0.1 nm to about 1:7 nm betweem the groups for efficient ('80--1004) energy transfer to ' pGCUr. In teems of nucleotide spacing in single and double-stranded DIVA polymers, this optimum transfer distance is'roughly equivalent to o~to 5 nucleotide ~
tanits. At the shorter separation distances efficiency can theoretically a~praach l00%. At a distance > 4.0 r' nm or 12 nucleotide units, energy transfer efficiency is less than 20%. For the primary d~nor to acceptor CVO 93109128 PCT/US92/0~9827 r coupling, a close spacing (0, l or 2 base pairs) can be carried out, but requires special linker arm chemistries which orient groups for optimal energy transfer and e~.iminate any secondary quenching mechanisms or excitation traps.
With regard to the optimum positioning or spacing .
of the "donor to donor" pairs in multiple donor arrangements, thereby forming the donor-donor transfer distance, the incorporation of multiple donors at too close a spacing can interfere with the ability of the DNA to hybridize with high specificity. Also, close spacing of donor-donor pairs can sometime introduce secondary quenching mechanisms or excitation traps which can greatly reduce energy transfer efficiency.
Presently, the best available chemistries for modifying a polynucleotide sequence at internal and terminal positions allows donor-donor spacings of about 4 to about l8 nucleotide units (1.4 nm to 6.1 nm) to be achieved over reasonably long distance.
This would mean about 10 donors could be incorporated in a single oligonucleatide sequence of 50 nucleotides. Spacing at the longer intervals from 8 to l8 nucleotide units can be used, when hybridization of a complementary multiple donor polynucleotide produces a double-stranded structure with alternating donors now spaced at 4 to 9 nucleotide units. These alternating donor types of structures maintain reasonable transfer efficiency, reduce secondary donor--donor quenching; and interfere less with hybridization arid stability of the organized structures.
In those case where quenching is a desired .
property, there can be 0 to 5 nucleotide unit (0.1 nm to 1.7 nm) spacing between the quencher groups) and the acceptor group. It should be kept in mind that ~'U 93109128 ~ ~ ~~" ~ ~ ~ ~ ~'~C1'/I1S92/Q9~27 ' ,..
,,. -29-quencher-acceptor, donor-acceptor, as well as donor-donor pairs can also be formed between groups which are located on alternate sides of double--stranded DNA
structures.
4. Synthesis and Labelling of Oliaonucleotides and Pol~nucleotides Synthesis of oligonucleotide and polynucleotide sequences can ba carried out using any of the variety of methods including de novo chemical synthesis of polynucleotides such as by presently available automated DNA synthesizers and standard phasphoramidite chemistry, or by derivation of nucleic , acid fragments from native nucleic acid sequences existing as genes, ar parts of genes, in a genome, plasmid; or ether vector, such as by restriction ~ndarauclease digest of larger double-stranded nucleic acids and strand separation or, by enzymatic synthesis using a nucleic acid template.
2Q De novo chenuical synthesis of a polynucleotide can be conducted using any suitable method, such as, gar example, the phosphotriester or phosphodiester methods. See Narang et al., Meth. Enzymol., 68:90, (19T9); U.S. Patent Na. 4,356,270; Itakura at al., ?5 Ann. Rev. Biochem., 53:323-5G (1989}; and Brown et al., Meth. Enzymol.; 68:109; (1979).
Derivat~.an of a polynucleotide from nucleic acids a.nvolv~s the cloning e~f a nucleic acid into an appropr~.ate host by means of a cloning vector, 30 replication of the vector and therefore multiplication of the amount~of the cloned nucleic acid, and than the is;olation'of subfragments of the cloned'nucleic acids.
For a descriptian of subcloning nucleic acid fragments, see Maniatis et al.; Molecular ~Ionina: A
35 Labaratory Manual, Cold SPring ~Tarbor Laboratory, PP

390-401 (1982); and see U.S. Patents No. 4,416,988 and No. 4,403,036.
In preferred embodiments, automated syntheses using an Applied Biosystems~Model X381 DNA synthesizer and commercially available (Applied Biosystems) 5'-dimethoxytrityl nucleoside b-cyanoethyl phosphoramidite reagents and controlled pore glass synthesis columns were conducted for the work described in this patent application. In addition to the "standard phosphoramidite chemistry" other chemistries including RNA, hydrogen phosphonate, and phosphothioate may also be used.
Modified oligonucleotides with internal or terminal functional groups for subsequent labelling can be obtained in a number of ways. Several particularly useful methods to incorporate functional groups are described below. [For this particular section on synthetic procedures "incorporation of functional groups" means chemically reactive groups (primary amines, sulfhydryl groups, aldehydes, etc.) for subsequent coupling with fluorophores or chromophores. This should not be confused with "incorporation of functional properties" which in the main body of this invention concerns electronic/photonic properties.
Internal functional primary amine groups can be incorporated at selected positions within the seguence and at the 3' and 5' terminal positions as suitably protected linker arm nucleosides (5'-dimethoxytrityl-5[N-(7-trifluoroacetylaminoheptyl)-2'-deoxyuridine 3'-O-phosphoramidite). This linker arm nucleoside (supplied by Glen Research) can be easily incorporated during the automated synthesis procedure. It provides a primary amine group for subsequent coupling *Trade-mark reactions with various activated fluorophores and chromophores (the actual linker arm length is 1.5 nm).
Primary amine functionality can also be incorporated at the 5'-terminal position by using Aminolin~:*'2. Aminolink 2 is a phosphoramidite molecule with a six carbon chain arm (0.9 nm) and a protected amine group (supplied by Applied Biosystems). This suitably protected linker group can be incorporated in the 5'-terminal position at the end of the automated synthetic procedure, providing a primary amine group for subsequent coupling reactions with various activated fluorophozes and chromophores.
A different type of functionality can be incorporated at the terminal position by sta=ting the synthetic procedure using a ribonucleoside, instead of a deoxyribonuclaoside: This provides a ribonucleotide at the 3' terminal position of the oligomer, which subsequently can be oxidized with sodium periodate to form reactive aldehydes groups which can be coupled with a variety of fluorophores and chromophores.
These procedures for functionalizing oligonucleotides are not meant to be exclusive, as other procedures are available or can be developed to further enable the novel concepts of this invention.
At the end of each synthesis the finished oligonucleotide (modified or un-modified) is released from the support and blocking groups removed by treatment with concentrated ammonium hydroxide for 12 hours at 55'C. The dimethoxytrityl group can~be left on the oligonucleotide to aid in the purification.
The 5'-trityl oligonucleotide can be purified by reverse phase high pressure liguid chromatography (HPLC). The purity of each oligonucleotide product can be determined by analytical polyacrylamide gel electrophoresis. At this point the un-modified *Trade-mark W~ 93/89128 PQ_'T/US92/09827 2~.~3133 _32_ oligonucleotides are ready for experimental use. The oligonucleotides with reactive linker arms) can be reacted with the appropriate. activated fluorophore.
Those fluorophore and chromophore derivatives containing isothiocyanate, sulfonyl chloride, succinimidyl ester, or triazine, can be easily coupled to oligonucleotides containing primary am~.ne functional groups. Oligonucleotides containing 3'-terminal aldehydes (from periodate oxidized ribonucleotide) can be reacted with fluorophores and chromop'~ores with primary amino or hydrazide groups.
A wide variety of reagents and procedures exist for incorporating different fluorophores and chromophores into functionalized oligonucleotides [see:
Bioconjugate Chemistry, Vol 1, n3, pp. 165-187 (1990);
Symons, R. H., Nucleic Acid Probes, CRC Press, Inc.
(1989); and Kelley et,al., DNA Probes, Stockton Press, (1989)]. Also, direct fluorescent labelling of oligonucleotides (internal and terminal) can be carried out using fluorescent (fluorescein and acridine) phosphoramidites (Clontech). With this procedure a complete nucleotide is replaced by the fluorescent phosphoramidite derivative,. These derivatives are incorporated during the normal automated DNA synthesis procedure.
5. Mechanisms, Devices and Svstems It is important to emphasize that the programmability of the functional molecular components, via their nucleotide sequence, allows them '' ~ to self-assemble and arganiz~ into'larger and more complex defined structures. This programmability and , the functional electronic/photonic properties of these molecular components enable photonic connections, , amplification mechanisms, and antenna arrays to ~rJ 93/09128 ~ ~. ~ ~ ~ ~ J PC f1L1592/09827 organize within the structures. The combination of properties ultimately leads to the creation of photanic devices, photovoltaic devices, biosensars, and homogeneous and heterogeneous DNA diagnostic a assays.
t Since a large number of DNA polymers each ' containing a number of donor groups can be organized together, it is possible to build relatively large antenna ar amplifier networks., or to make long photonic transfers and connections. With regard to extended energy transfer far amplification or antenna functions; the number of donors to an acceptor in a given molecular structure or system depends on several , factors. These include: (1) the light flux (intensity) impinging on the final systems (2) the overall energy transfer efficiency for the donor arrays, (3) the quantum yield (QY) of the donors and the acceptors, and (4) the life time (tau) of the donor and acceptor excited states. For antenna or photanic amplification applications, at low to intermediate light levels, the number of donors to acceptor could range from the lower limit.of 2 to 1, and preferably 10 to 1, to the upper limit of 106 to 1. Far heterogeneous DNA diagnostic and Biosensar applications, the number of donors to an acceptor could range from the lower limit,of 2. to 1, and preferably 5 to 1, to the upper limit of 105 to 1.
For homogenous DNA diagnostic applications using the typical mercury or xenon light sources found in the standard spectrofluorometers or other instruments for t fluorescent analysis, the number of donors to an x acceptor could range from the lower limit of 2 to 1 to the upper limit of 10'' to Z. Also, far some photonic mechanisms and certain device applications, a multiple donor DNA polymers) may transfer to an acceptor DNA

i:
iV0 93/09128 PC.'T/U~92/09827 212 3 ~t': 3 3 ,.

polymer which has more than one acceptor group. The same basic ratios of donors to acceptor that were , given above apply to the those molecular- structures or systems which have an acceptor DNA polymer with mare .
than one acceptor group.
f A device of this invention can be described in , ' terms of a duplex nucleic acid structure, that is two or more palynucleotides hybridized by conventional camplementarity to form the typical double stranded duplex, except that a "strand" of the duplex can be comprised of two or more adjacent polynucleotides as shown in Figure 3.
A duplex nucleic acid structure of this invention is therefore comprised of at least twa hybridized polynucleotides. The structure has (1) at least two, donor chromophores .operatively linked to the structure by linker arms at~tach~d to a polynucleotide of the structure such that the donor chromophores are positioned by the linkage along the length of the structure at a donor-donor transfer distance. The structure also has (2) at least one fluorescing chrcamophore operatively linked to the structure by a Tinker arm attached to a polynucleotide of the structure such that the fluorescing chromophore is positioned by the linkage at a donor-acceptor transfer distance froze at least one of the donor chromophores.
As suggested by the configuration shown in Figure 3, one embodiment can involves the use of one or more alternating chromophores. That is, the structure contains donor chromophares that are alternately pa~sitioned bn the structure such that said donor-donor transfer distance can cross (alternates) between poTynucleotides of the duplex. The alternating configuration can be such that some donor-donor , WO 93/0912 ~ ~ ~ ~ Ir ~ ~ PC'f/US92/09~27 i ~-35- ' transfers are between adjacent donors on the same polynucleotide and some are between donors on opposite duplex strands (i.e., alternating), or such that all the transfers are alternating. The alternating transfer distance can be expressed in terms of a donor-donor transfer distance, as described herein, or can be expressed in terms of nucleotide base spacing.
Thus, for example, a structure with alternating donor chromophores is contemplated that comprises at least 1J three donor chromophores wherein the donor chromophores are positioned from 4 to 18 nucleotide base units apart on a single polynucleotide.
Another embodiment is the use of the capability of. extended photonic energy transfer across multiple donors as a photonic energy transfer system or circuit. The photonic energy transfer system can have one or more of th'e polynueleotide components described herein. Thus a photonic energy transfer system comprises a polynucleotide having at least two donor chromaphores ,as described before. The polynucleotide may also contain an acceptor chromophore. The system may comprise one or mare additional polynucleotides in the various configurations described herein.
Insofar as the present invention describes structures and systems for extended photonic energy transfer, it is to be understood that one enbodiment contemplates the use of the described structures, polynucleotides, mu~.ti-polynucleotide duplexes, photonic energy transfer systems and the like; in a solid state. That is, a polynucleatide(s) of the 1 system can'be~ operatively limked (attached) to 'a solid support to facilitate the use of the extended energy transfer device. Solid support systems are particularly suited for electronic devices, such as °
i~VO 93/09128 PL f/US92/09827 X123133 _36_ photonic energy collectors, light amplifiers, energy transfer conduits, and the like.
Attachment of a polynucleotide to a solid support ', car, by any of a variety of means and is not to be ~ , g construed as limiting. Exemplary attachment means are described elsewhere herein, and are generally well known to one skilled im the polynucleotide arts.
In one embodiment, a solid support can represent a passive support, that is the support acts passively to only hold the energy transfer polynucleotide in the Bali;'. phase. Ln another embodiment, a solid support can be active, that is the support provides a complementary function such as to donate energy to the , transfer System, or to have the capacity to detect, 1.5 receive, convert, translate or transmit the emitted photonic energy from the acceptor to a second circuit.
An exemplary second circuit is a photosensor,, photovoltaic, and the like de~tice in the solid phase medium.
zo B. . Diagnostic Systems and Methods 1. Diac~",nostic Systems A diagnostic system in kit form of the present invention includes, in an amount sufficient 25 for at least one assay, a chromophore-containing polynucleotide of the present invention, as a separately packaged reagent. Instructions for use of the packaged reagent are also typically included.
°'lnstructions for use'! typically include a 30 tangible expression describing the reagent ~concentrati~on or a~ least one assay method parameter such-as the relative amounts of reagent and'sample to , be admixed, maintenance time periods for reagent/sample admixtures, temperature; buffer .
35 conditions and the like.

WO 93/~9~28 ' ~ PCT/U~92/09827 ,. ....
_37_ Tn one embodiment, the invention contemplates a diagnostic system for photonic detection of a preselected nucleotide sequence comprising, in an amount sufficient for at least one assay, a polynucleotide having at least two donor chromophores operatively linked to the polynucleotide by linker arms, wherein the donor chromophores are positioned by linkage along the length of said polynucleotide at a donor-donor transfer distance. The polynucleotide is designed to hybridize to the preselected nucleotide sequence (i.e., the target nucleic acid sequence), and therefore contains a nucleotide sequence complementary to the target nucleic acid sequence. Target nucleic acid sequence complementarity is well known in the L5 nucleic acid diagnostic arts as it applies to a reagent polynucleotide (i.e., probe), and therefore need not be described in detail.
Tn another embodiment, the polynucleotide of a diagnostic system further contains at least. one fluorescing chromophore operatively linked to the polynucleotide by a linker arm, such that the fluorescing chromophore is positioned by linkage at a donor-acceptor transfer distance from at least one of the donor chromophoxes: Tn this embodiment, both the acceptor and multiple donor chromophores are present on a single polynucleotide. Exemplary is the structure shown in Figure 2(a).
i Tn another embodiment, a diagnostic system includes a second polynucleotide containing at least one fluorescing chromophore operatively linked to said ', ~ec~ond polynucleotide by a linker a'rm. Exemplary is the structure shown in Figure 2(b). 'r In a-further embodiment, a diagnostic system also contains, typically iii a separate container, a WO 93/09128 P~.T/US92/09827 _38_ ~.~.~~~I ~~
quencher polynucleotide of the present invention. The included quencher polynucleotide is complementary to , at least a portion of the acceptor polynucleotide, and preferably is completely complementary to the acceptor .
polynucleotide. A quencher polynucleotide must be shorter in length that an acceptor polynucleotide, typically at least 10 percent shorter, and more preferably at least 50 percent shorter, to assure that the acceptor will preferentially hybridize to a target sequence if present in the hybridization admixture.
The reagent species, i.e., chromophore-containing polynucleotide of the invention, of any diagnostic system described herein can be provided in ' solution, as a liquid dispersion or as a substantially dry power, e.g., in lyophilized form. A solid support as a reaction vessel and one or more buffers can also be included as separately packaged elements in this diagnostic assay system.
The packages discussed herein in.relation to diagnostic systems are those customarily utilized in d~:agnastic systems. The term "package" refers to a solid matrix or material such as gloss, plastic, paper, foil and the like capable of holding within fixed limits a diagnostic reagent of the present invention. Thus, for example, a package can be a glass vial used to contain a contemplated diagnostic reagent.
2. Diactnostic Methods The present invention also oontempl~ates any diagnostic method that results in detecting emitted ph~otoni~ ~nergy'produced by an chromophore-containing structure of the present invention. Insofar as the , emission is a result of excita ion and subsequent energy transfer from the excited donor-chromaphores to W~ 93/09128 PCT/US92/09827 , i , _3g-the acceptor chromophore, the present method comprises at least two steps:
(1) excitation of an organized structure of this invention that contains at least two donor chramophores operatively linked to a support structure by linker arms, such that the donor chromophores are positioned along the length of the support at a donor-donor transfer distance, and also contains at least one fluorescing acceptor chromophore operatively linked to the support structure by a linker arm at a position ow the structure that provides a donor-acceptor transfer distance from at least one of the donor ehromophores. The excitation is an amount of - photonic energy sufficient to induce non-radiative energy transfer between the donor chromophores as a "collecting" event, and to induce non-radiative energy transfer between the donor chromophore and the acceptor chromophore such that the acceptor itself is excited sufficient to result. in emission of photonic energy.
(2) detection of the resulting emitted photonic energy by the use of any of a variety of photonic sensors.
The organized structure containing the chromophores as described above can be any of the various ponfigurations described herein. The particular excitation means and sensing means can vary widely depending on the needs of the system at hand, and depend upon sensitivity required, the excitation and emission characteristics of the incorporated donor and acceptor ctiroz~ophores, and the application of the' structure.
In a particularly preferred diagnostic method, the present invention contemplates a method of photonic detection of preselected nucleic acid ~~D 93/0912 ~CT/US92/09~27 1~~ ~':~~ -40-sequences using chromophore-containing polynucleotides of the present invention as hybridization probes fcr detecting a target sequence in a sample containing I
nu~.leic acids .
~'hus a diagnostic method for detecting the presence of a preselected nucleic acid sequence in a nucleic acid-containing sample is contemplated comprising the steps of:
(a) admixing:
(i) a polynucleotide having (1) at least two donor chramophores operatively linked to a polynucleotide by linker arms, such that the chromophores are positioned by linkage along the - length .of the polynucledtide at a donor-donor transfer distance, and (2} at least one fluorescing acceptor chromophore operatively linked to the polynucleotide~
by a linker arm, such that the fluorescing acceptarv chromophore is positioned by linkage at a domor-acceptor transfer distance from at last one of the 2p donor chromophores, wherein the polynucleotide has a nucleotide sequence that is preselected as to be complementary to the preselected "target'' nucleic acid sequence; with (ii) a nucleic maid--containing sample Gon~ain;ing the preselected nucleic acid base ("target"} sequeince to foam a hybridization reaction admixture;
(b} s~b,jecting the hybridization reaction admixture to hybridization conditions for a time period sufficient for the polynucleotide to hybridize !~d th'e target scquence'and form a donor chromophore containing- and acceptor chromophore containing-hybridized nucleic aqid duplex;'' (c) exciting the'donor chromophore in the nucleic acid duplex formed'in step (b} by exposing the W~ 9/09128 PCT/LJS92/09827 ... ~~~r~J ~~.~J
.. -~ 1-donor chromophore to sufficient photonic energy to induce emission of photonic energy from the acceptor chromophore; and (d) detecting the presence of photonic energy emitted from the excited acceptor chromophore, thereby detesting the presence of the preselected nucleic acid sequence in the sample..
In a related embodiment, the admixing of step (a) differs in that instead of a single polynucleotide containing both the multiple. acceptors any at least one acceptor chromophores, the donars are present on one or more polynucleotides separate from the polynucleotide containing the acceptor chromophore.~
In this embodiment, illustrated in Figure 2(b) and in Figure 3, the positioning of the donors and the acceptor are controlled bath by their linkage position ' . on their respective polynucleotides, and on the proximation of those chromophores upon hybridization to a preselected nucleic acid target sequence.
In another embodiment, the hybridization admixture can contain a quencher polypeptide as described herein, having a nucleic acid sequence designed to compete with the target sequence for hybridization with the polynucleotide containing the target nucleic acid sequence. The embodiment is shown' in Example 3 and Figure 4.
A hybridizat~.ori reaction mixture is prepared by admixing effective amounts of a polynucleoti.de probe or probes of this invention, a target nucleic acid and other components compatible with a hybridization 'r!eaction admixture.
Target nucleic acid sequences to be hybridized in the present methads can be present in any nucleic acid-containing sample so long as the sample is in a form, with respect to purity and concentration, i i W~ 93/09128 PCT/US92/09~27 '' ~~.2~ t ~3 , ;
compatible with nucleic acid hybridization reaction.
Isolation of nucleic acids to a degree suitable for hybridization is generally known and can be, accomplished by a variety of means. For instance, .
nucleic acids can be isolated from a variety of nucleic acid--containing samples including body tissue, , such as skin, muscle, hair, and the like, and body fluids such as bland, plasma, urine, amniotic fluids, cerebral spinal fluids, and the like. See, for 20 example, Maniatis et al., Molecular Cloning: A
Laboratory Manual, Cold Spring Harbor Laboratory (2982)7 and Ausubel et al., Current Protocols in Molecules BioIoaY, John Wiley and Sons (1987).
The hybrid~.zation reaction mixture is maintained 25 in~the contemplated method under hybridizing conditions for a time period sufficient far the polynucleotide probe to hybridize to complementary nucleic acid sequences present in the sample to form a hybridization product; i.a., a complex contafining the ;
?.0 chromophore-containing palynucleotide probes) of this invention and'target nucleic acid.
The phrase "hybridizing conditions" and its :grammatical equivalents, when used with a maintenance time period, indicates subjecting the hybridization 25 reaction admixture, in the context of the concentrations of reactants and accompanying reagents in the admixture, to time, temperature and pH
conditions sufficient to allow the polynucheotide probe to anneal with the target sequence, typically to 30 form a nucleic acid duplex. Such.time,,temperature !~~(d ''pH cond=itions ~-equxred to accompIish' h~rbridizatien depend, as is well. known in the art, on the length of the polynucleot-fide probe to be hybridized, the degree of complementarity between the polynucleotide probe 35 and the target, the guanidine and cytosine content of dV~ 93/09~~128 l'CT/US92/09~27 i _4~-the palynucleatide, the stringency of hybridization desired, and the presence of salts or additional °
reagents in the hybridization reaction admixture as ;
may affect the kinetics of hybridization. Methods for optimizing hybridization conditions for a given hybridization reaction admixture are well known in the art.
Typical hybridizing conditions include the use of solutions buffered to pH values between 4 and 9, and are carried aut at temperatures from 18 degrees C
(18°G) to 75°C, preferably about 37°C to about 65°C, more preferably about 54°C, and for time periods from 0.5 seconds to 24 hours, preferably 2 min.
Hybridization can be carried out in a homogeneous or heterogeneous format as is well known. The homogeneous hybridization reaction occurs entirely in solution, in which both the polynucleatide probe, and the nucleic acid sequences to be hybridized (target) are present in soluble foams in solution. A
heterogeneous reaction involves the use of a matrix that is insoluble in the reaction medium to which either th.e polynucleotide probe or target nucleic acid in bound. For instance, the body sample to be assayed can be affixed to a solid matrix and subjected to in situ hybridization.
In situ hybridization is typically performed on a b~dy sample in the 'form of a slice or section of tissue usually having a thickness in the range of about 1 micron ta'about 100 microns, preferably about 1 micron to about 25 microns and more preferably about '1: micron to, ab'otlt 10 microns. Such sample can be prepared using a commercially available cryostat.
Alternatively, a heterogeneous format widely used is the Southern blot procedure in which genomic DNA'is el2~trophoresed after restriction enzyme digestion, l Wig 93/09~Z8 PCT/US9Z/09$27 ~~.~~~33 --44- ' and the electrophoresed ANA fragments are first denatured and then transferred to an insoluble matrix.
1n the blot procedure, a polynucleotide probe is then i hybridized to the immobilized genomic nucleic acids .
containing complementary nucleic acid (target) sequences.
Still further, a heterogeneous format widely used is a library screening procedure in which a multitude of colonies, typically plasmicl-containing bacteria or lambda bacteriophage-containing bacteria, is plated, cultured and blotted to form a library of cloned nucleic acids on an insoluble matrix. The blotted library is then.hybridized with a polynucleotide probe ' to identify the bacterial colony containing the nucleic acid fragments of interest.
Typical heterogeneous hybridization reactions include the use of glass slides, vitro-cellulose sheets, and the'like as the solid matrix to which target-containing nucleic acid fragments are affixed>
. Also preferred are the homogeneous hybridization reactions such as are conducted far a reverse transcription of isolated mRNA to form cDNA, dideoxy sequencing-and other procedures using primer extension reactions in which polynucleotide hybridization is a first-step. Particularly preferred is the homogeneous hybridization reaction in which a specific nucleic acid sequence is amplified via a polymerase chain reaction (PCR).;
Where the nucleic acid containing a target sequence is in a double-stranded (ds) form, it is 'preferred to first denature the dstiNA; as by heating'' or alkali treatment; prior to conducting the v hybridi~ati~n reaction. The denaturation of the dsDNA
can be carried aut prior to admixture with a polynucleotide to be hybridized, or can be carried out ;'~ :~ ; o ,l CVO 9~/09R28 ~ ~ ~ :.~ .. .s .'. P~/US92/09~27 after the admixture of the dsDNA with the polynucleotide. Where the polynucleotide itself is provided as a double-stranded molecule, it too can be denatured prior to admixture in a hybridization reaction mixture, ar can be denatured concurrently therewith the target-containing dsDNA.
The amounts of polynucleotide admixed to a hybridization reaction admixture can vary widely, and depends an the application, which in turn depends on the sensitivity required for detection of the target sequence. For homogeneous hybridization admixtures, the chromophore-containing polynucleotides can be present in concentrations of about 1 to 1000 nanograms (ng) per milliliter (ml), and preferably about 10 to 100 ug/ml where the polynucleotide of about 20 nucleotides in length.
In terms of the amount of acceptor chromophore present on a subject polyucleotide, in,homogeneous liquid hybridization admixtures the l.eVe1 of detection ~ for a single acceptor ~hromophore per palynucleotide i.~ at least about 104 to 105 acceptor chromophare molecules per 100 microliters (ul).
For heterogeneous hybridization admixtures, such as where the target nucleic acid is present in the solid phase, the chromophore-containing polynucleotides are added to the hybridization admixture in amounts of at beast about 106 to 107 molecules of acceptor chromophore per band of nucleic acid to be detected, or per 2 millimeter (mm).dot blot of target nucleic acid. An exemplary application is .
~to~detect nucleic acid segments present on a Southern blot or a DNA sequencing gel using, for example, an ASI sequence reader that detects fluorometrically labelled probes:.

~VCI 93109128 P~CT/U~92/09827 ..
~1~3=~ 33 ~ -~~-C. Photonic Devices The present invention provides for photonic devices such as light collectors and photonic conductors, by virtue ~f the capacity of the multiple . -donor transfer structure to be extended over long distances. Thus the structure can be designed as a linear conductor of photonic energy, or can be configured as an light-sensitive photonic switch, i.e., a biosensor.

pp Thus in one embodiment, the present invention contemplates a biosensor comprising a polynucleotide of the present invention having at least two donor chromaphores operatively linked to said palynucleotide , by linker arms, wherein said chromaphores are positioned by said linkage slang the length of said polynucleotide at a donor-donor transfer. distance.

the polynucleotide also has at least one fluorescing acceptor chromophore operatively linked to said pol,ynucleotide by a pinker arm, wherein said fluorescing acceptor chramophore is positioned by said linkage at a donor-acceptor .transfer distance from at peast one of said donor~chromophores.

Thus thevbiosensor contains a photon collector that can be a varzety of lengths; delivering the collected and transferred photonic energy to the .

acceptor chromophore: Preferably, a biosensor contains multiple acceptor chromophores clustered to provide a brighten photonic output.

Positioned adjacent to the acceptor ar cluster of 34 acceptors is a photon sensing means to detect the ,presence of emitted photonic energy. The sensing means can be any of a variety of light detecting , devices; such as a photomultiplier tube, a fiber optic system that delivers the smitted light to a light .

w ::
.r . . ., ,~ . . . . . J-: . . . . ..
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;~. ;... .. ,: ...., ,: ;.:. ....; : , .;.. .:.:.: , ..,:
°~VO 93/49128 PCf/U592109827 -47- ,, sensitive photomultiplier, and the like sensing means.
EXAMPLES
The following examples are intended to 5, illustrate, but not limit, the present invention.
1. Desian and Synthesis of a Self-Oraanizi.pq Extended Energy Transfer System Five different specific sequence fluorescent oligonucleotides and non-functionalized versions of the same sequences were designed and synthesized far the experimental demonstration of an extended energy transfer system. These include the following:
' (1) An acceptor 16-mer oligonucleotide unit, 5.4 nm in length, labelled with Sulforhodamine 101 (AU).
(2) A first intermediate donor 30-mer oligonucleotide wn~.t, 10.2 nm in length, labelled with two fluoresceins separated by a spacing of 6 nucleotides or 2.4 nm (ZD1).
(3) A second intermediate donor 29-mer o~.igonucleotide unit, 9.9 nm in length, labelled with two fluoresceins separated by a spacing of 6 nucleotides or 2.4 nm (ID2).
(4) A repeater intermediate donor 30-mer oligonueleotide unit, 10.2 nrn in length, labelled with two fluor~sceins separated by a spacing of 7 nucleotides or 2.7 nm; (~tD). The repeater unit is designed sp that the structure can lae extended.
(5) A terminal donor 15-mer oligonucleotide unit, 5.1 nm in length, labelled with a single fluc~rescein ,;
(TD) The un-modified versions of all the above oligonucleot.ides were also synthesized. All of the oligonucleot.ides are designed by their encoded sequence to bind to complementary portions of each other, to form linear double stranded structures. The specific sequence and position of the fluorescent labels) (A = Sulforhodamine 101 (Texas Redj, D =
Fluorescein~ in the five modified oligonucleotide sequences are shown below and labelled as SEQ ID NOs 4-8, respectively:
A
(1) AU 5'-ATGTCTGACTGCAGCT-3' D D
1 i (2) ID1 5'-ACGACCRTAGTGCGAGCTGCAGTCAGACAT-3' D D
i i (3) ID2 5'-CGCACTATGGTCGTGAGTGTTGAGAGGCT-3' D D
i (4) RD 5'-ACGACCATAGTGCGAGCCTCTGAACACTC-3' D
i (5) TD 5'-AGCCTCTGAACACTC-3' The oligonucleotide sequences shown above and the non-functionalized versions were all synthesized on an Applied Biosystems Automated DNA Synthesizer, Model n381, using standard phosphoramidite chemistry on controlled pore glass support. In the case of the functionalized oligonucl~eotides the protected linker arm nucleoside (5'-dimethoxytrityl-5-trifluoroaminoalkyl deoxyuridine) was incorporated at the selected positions) indicated above. This linker arm nucleoside provides a primary amine group for reaction with the activated fluorophores, Sulforhodamine 101 sulfonyl chloride (Texas Red) and fluorescein isothiocyanate (FITC).
*Trade-mark At the end of each synthesis the finished oligonucleotide was released from the support and blocking groups removed by treatment with concentrated ammonium hydroxide for 12 hours at 55'C. The dimethoxytrityl group was left on the oligonucleotide to aid in the purification. The 5'-trityl oligonucleotide was purified by reverse phase high pressure liquid chromatography (HPLC). The purity of each oligonucleotide product was determined by analytical polyacrylamide~gel electrophoresis.
The HPLC-purified and un-modified oligonucleotides were ready for experimental use. The oligonucleotides containing the reactive linker arms) were then reacted with the appropriate activated fluorophore. Fluorescent labelling was carried out by reacting '500 ng of the oligonucleotide containing the reactive linker arm with 1 mg of either Sulforhodamine 101 sulfonyl chloride (Texas Red) or Fluorescein isothiocyanate (both available from Molecular Probes) in 100 ul of 0.1 M sodium bicarbonate (pH 8.5) for 2 hours at 20 C. Afte= the reaction was complete the excess fluorophore reagent was removed by passing the solution through a Sephadex G-25 gel filtration column. The final purification of the fluorescent- labelled oligonucleotides from un- -labelled material was carried out by preparative polyacrylamide gel electrophoresis.
The UV/Visible spectra (240 nm to 600 nm) were obtained (Hewlett Packard 8451A Diode Array Spectrophotometer) for all purified fluorescent and un-modified oligonucleotides. From the spectral data the concentrations, and the degree of fluorescent labelling were determined. The Acceptor Unit (AU) was determined to be > 95~ pure in terms of sulforhodamine 101 (Texas Red) labelling. The Intermediate Donor 1 *Trade-mark ;; ~ . ; . : ;.. ,. ,.: :,. '. , ; . ... ., :. . , ~VE7 93/09128 PC."T/US92/09827 t::
~~.~3 ~ 33 , ..
_50_ j (ID1) was determined to be about 40o pure in terms of the double fluorescein labelled component, the remainder was a mix of the single labelled components.
The Intermediate Donor 2 (ID2) was determined to be .
about 30% pure in terms of the double fluorescein labelled component, the remainder was a mix of the .
single labelled components. The Repeat Donor (RD) unit was determined to be about 25o pure in terms of the double fluorescein labelled component, the remainder a mix of the single labelled components.
The Terminal Donor (TD) was determined to be > 95%
pure in terms of fluorescein labelling. While the Intermediate Donors were not fully doubled labelled .
with fluorescein, they still are suitable for ~,5 demonstrating the extended energy transfer mechanism in a self-organizing system.
The actual experiments designed to show extended energy transfer herein involve. organizing a 14 nm long photonic antenna structure, via hybridization, of the four oligonucleotide units: the acceptor unit (AU), the intermediate donor 1 unit (ID1), the intermediate donor 2 unit (ID2), and one terminal donor unit (TD).
The organized structure and the path for extended energy transfer are show in Figure 3.
The assembled structure of the 14 nm antenna structure was formed by combining the above oligonucleotides at a concentration of 0.5 nanomole/ul in 500 ul of aqueous buffer (0.2 M Sodium chloride/0.02 M sodium phasphate, pH 7.8) at 20°C.
These conditions are optimal for the oligonucleotide units to quickly hybridize (one minute) to their ;
complementary sequences and self-organize (assemble) the 16 nm linear double stranded structures.
A number of experimental control structures were also assembled with the same basic arrangement, except . q Wt~ 93/~9~2~ ~ ~ ~ ~ ~ ~ 1PC'f/US92l09827 -51_ one or more of the donor units utilized was in the un-labelled (NL) form. Fluorescein and Sulforhodamine 101 were picked as the fluorescent donor and acceptor groups because of the potential for reasonably efficient Forster energy transfer. The organized 14 nm antenna structure is designed to have a 6 base pair (2.4 nm) spacing (acceptor-donor transfer distance) between the Sulforhodamine group in the acceptor unit AU) and the first fluorescein group in the intermediate donor 1 unit (ID1), and to have a 6 base pair spacing (donor-donor transfer distance) between each of .the fluorescein donors in the rest of the array. , - Fluorescein has its absorption (excitation) maximum at 495 nm wavelength (EX495,), its emission maximum at 520:nm wavelength (EMSZO), and an extinction coefficient of '72,000. Sulforhodamine 101 (Texas Red) has its absorption (excitation) maximum at 595 nm 1 wavelength (EXSSS), its emission maximum at 615 nm wavelength (EM6~5); and an extinction coefficient of '8,000. Fluorescein's broad emission band spans from 500 nm out to 600 nm, and has gaod overlap with sulforhodamine's broad.absorption band which spans from 520 nm to 600 nm. This overlap of the emission and adsorption bands and high quantum yield of each of the fluorophores make them a good pair for energy transfer.
The demonstration o~ extended energy transfer in the assembled photonic antehna structure was' carried out by exciting the fluorescein donor units with radiation et 495 nm, and measuring the re-emission of radiation at 615 nm by the sulforhadamine 101 acceptor unit. The base Texas Red fluorescent emission at 615 nm was determined by exciting at 595 nm (an Aminco°
Bowmen Spectrophotofluorometer was used to carry out '!~O ~3/091z~ ; F'c"flu~9z~o9sz~ , -52- ,,:..
these experiment). The relative energy transfer efficiency (ET eff.) is the ratio of the 615 nm emission when the system is excited at 495 nm to the i 615 nm emission when excited at 495 nm multiplied by , 100, and can be represented by the formula:
ET eff. - EM6~5(EX49s)/EM4~5(EXs9s) X 100, (3}
Demonstration of reversibility of self-organization of the 1G nanometer photonic antenna structure was carried out by first assembling the organized structure at 20°C, then heating it to 90°C
for ane minute, and then cooling the system.back to 20°G (one minute). Excitation arid emission measurements were conducted as before for each condition after the processes of assembly (initial), ' heating (heated) and cooling (cooled). The results for the experimental demonstrations of extended energy transfer in the various arrangements, and for the reversible self-assembly are given in Table 4.

RESULTS OF EXTENDED ENERGY TRANSFER EXPERIMENTS
_STRUCTUREt TEMP(C) EX(nml E.T.Eff. l o) AU/xD1/ID2(NL}/TD(IvL) 20 495 46 AU/ID1(NL)/ID2/TD . 20 ~ 495 8 AU/ID1(NL)/ID2(NL)/TD(NL) 20 495 4 ' !AU/ID1 (NL) j,ID2 (NL~)/TD(NL) 20 595 100 AU/ID1/ID2/TDz (~.nitial) 20 495 73 AU~ID1/ID2/TDz (heated} 90 4g5 6 A.U/ID1/ID2/TD~ (cooled} 20 495 77 ~crms9zm~sz~
wo ~~~09'zs EAU = acceptor unit with Sulf~rhodamine 101a ID1 = the intermediate donor 1 with two fluoresceins; ID2 = the intermediate donor 2 with two fl.uoresceins; TD = the terminal donor with one fluorescein; NL means the oligomer was not labelled (no fluorescein donor groups ) .
2Exp~riments demonstrating reversible self--assembly, initially at 20°C, heat to 90°C, and cooled back to 2a°c.
Extended energy transfer is shown in Table 4 to be occurring in the organized (AU/ID1/ID2/TD) antenna structure producing about a ?6% energy transfer .
efficiency to the acceptor unit (AU) when all the donor units present. When just the ID1 unit is fluorescent, in the AU/ID1/ID2(NL)/TD(NL) system, energy transfer is 4Go. This indicates that 30% of the transferred energy was coming from the ID2 unit;
which has its first donor group located 20 base. pairs 20- or G.8 nm frpm the acceptor group. This is well beyond the Forster distance necessary to account for any significant level of energy transfer. When only the ID2 and TD units are fluorescent,;in the (AU/:LD1(NL)/ID2/TD) system, the energy transfer drops to about 8%. .This is an important result, because it corroborates the other results showing that the ID2 and TD units were transferring through the ID1 unit to Jthe AU unit. The AU/ID1(NL)/ID2(NL)/:D(NL) system result at 495 nm excitation simply shows the level of Texas Red background fluorescence for AU; and the ' res~zlt at '595nm excitation gives the normal ors bases level of Texas Red fluorescence for AU.
The-assembly, heating and cooling experi:~ent clearly demonstrates the reversible organization properties of the system; by showing complete loss of S' W,d 93/0912 . PCT/U~92/09827 ~~~3~~..33 energy transfer at 90°C when the system is completely disassembled, and the return of energy transfer i capability when the system is, cooled.
2. Demonstration of Non-Fluorescent Donor to Fluorescent Acceptor Enerrsy Transfer With , Significant Re-Emission Several oligonucleotides were designed and synthesized to demonstrate that certain non-fluorescent donor groups which energy transfer to Texas Red can lead to significant re-emission. The same basic procedures that, were described in the Synthesis and Labelling Section and in Example 1 were ' used to synthesize and label two complementary 18-mer 25 sequences. Oligonucleotide (A) below was functionalized (derivatized) with a primary amino group on the sixth nucleotide from its 3'-terminal position. Oligonucleoti.de (B) below was - functionalized with a 5'-terminal amino group using the Aminolink,2 chemistry. Oligonucleotide (A) was then labelled with Fluorescein, DABITC (Molecular Probes), Reactive Red (Sigma Chemical), or Malachite Green (Molecular Probes). DABTTC, Reactive Red ~, and Malachite Green ara non-fluorescent chromophore groups. Oligonucleotide (B) was labelled with Texas Red. The oligonucleotide sequences are shown below and labelled as SEQ ID NOs 9-10, respectively:
(A)' S'-CCTGCTCATGAGTCTCTC-3' i A , i ~
(B) 5'-GAGAGACTCATGAGCAGG-3' where D = Fluoresc~in, DABTTC, Reactive Red 4 or Malachite Green; and A _ Texas Red.

PCT/U~92109827 w~ 93ro9~2~ ~ ~ ~ ~ '; s~ 3 _5g_ ', When hybridized together oligonucleotide (A) and (B) produce a 5 base pair spacing (2.0 nm) between the donor and acceptor groups. Tire hybridized arrangement for Texas Red (A) and Fluorescein (B) oligomers is shown below and labelled as SEQ ID NOs 9-°10, respectively:
D
a 5'-CCTGCTCATGAGTCTCTC-3 3'-GGACGAGTACTCAGAGAG-5' A
Oligonucleotides corresponding to oTigonucleotide (A) but having one of fluorescein, DABITC, Reactive Red 4, or Malachite Green were independently tested to , determine their respective energy transfer capacity to the Texas Red acceptor group on oligonucleotide (B).
The structures were formed by combining the above oligonucleotides (A) and (B) ~t a concentration of 0.5 nanomole/ul in 500 u~. of aqueous buffer (0..1 M sodium chloride/0.02 M sodium phosphate, pH '7.8) at 20°C.
These conditions are optimal for the oligonucleotide units to quickly hybridize (one minute) ~o~their complementary sequences. The fluorescent analysis experiments were carried out using.the equipment and 2a procedures as described in Example 2.
The following results were obtained:
~1) Fluorescein-labelled oliga (A) when hybridized to Texas Red-labelled (B) produced. about i: i i, , ,, i i , , 55% energy transfer as re-emission at 615 nm w2ien the arrangement was'excited at 495 nm (the fluorescein excitation maximum);. This is reasonably good efficiency,for this system. However, significant background fluorescence is still present from the dV~ 93I09~2R ~ . lP~f/US92/09~27 ~ ~. 2 3 ~: 3 3 _56_ donor group. That is, 45% of the fluorescent emission ("500 nm to 600 nm) from fluorescein is still present.
(ii) -DABI'rC-labelled olicso (A) when hybridized to Texas Red-labelled oligo (B) produced about 5% to 100 energy transfer as re-emission at 615 nm when the arrangement was excited at 430 nm (the DABITC
excitation maximum). However, there was no detectable fluorescent emission form just beyond the excitation of DABITC at.~440 nm, to the beginning of the Texas Red fluorescent emission at 600 nm. In this same arrangement DABITC appears to produce little or no quenching of tre Texas Red fluorescent emission (615 nm), when the arrangement was excited at 595 nm (the Texas Red excitation maximum).
(iii) Reactive Red 4-labelled oligo (A) when hybridized to Texas Red-labelled oligo (B) produced no positive energy transfe-r as re-emission at 610 rim when the arrangement was excited at 535 nm (the Reactive Red 4 excitat,zon maximum). Reactive Red 4 produced over 80o quenching of Texas Red fluorescent emission (615 nm) wk:en the arrangement was excited at 595 nm z5 (the Texas Red excitation maximum).
(iv)' Malachit a Green-labelled olzgo (A) when hybridized to Texas Red-labelled oligo (B) produced over 60% quenching of Texas Red fluorescent emission (615 nm) when the arrangement was excited at 595 nm (the Texas~Red excitation maximum). Malachite Green's excitation maximum is at 629 nm. , ~'he results described above in (i) and (ii) , clearly demonstrate that DABITC, a non-fluorescent i~IYO 93/09128 ~'9E ', ~':~~ ~'~ PCT'/US92/09827 -57_ chromophore group, at a 5 base pair spacing (2.0 nm) can produce significant fluorescent re-emission in a Texas Red acceptor. Also, DABITC produces no .
detectable background fluorescence in the same range where fluorescein produces significant background (45%). with regard to multiple donor systems, this is much more important than the fact that the re-emission produced by transfer from DABITC (5% to 100) is lower than from fluorescein (55%). In a multiple donor system, the additive effect of background fluorescence .from the fluorescent donors can very quickly limit it.s performance and usefulness. Thus, DABITC andsimilar chromophpres are more ideal for use in multiple donor systems.
The result described above in (iii) and (iv) demonstrate that other non-fluorescent chromophore groups (Reactive Red and Malachite Green) at a spacing of 5 base pairs (2.0 nm) can significantly quench the fluorescent emission of a Texasl red acceptor. These strong quencher groups can be useful in devising mechanisms which would allow amplified phatonic emiss~.ons to be. switched on and o:~f. Thus, they help tp create a more navel and useful pho~tonic mechanism or device. An example of a useful system a,n which a . 25 quencher group is utilized to reduce background is de cribed in Example 4 and shown in Figure 4.
3. A Homogen~ous DNA Hybridization Assay Method Based On Extended Energy Transfer The Following describes a homogeneous DNA
,. , . i , , , i hybridization assay method which utilizes a low fluore~eent background extended ensrgy transfer process: ;The system involves a multiple donor, an acceptor and a quencher oligo:~ucleotide.

,... . . ~: w,;y: , ; -:~,~, .;, v~ , : - . ; ;. , .:. ~~ :,.
I
t.. .
~'O 93/0912 ~~.T/U~92l09$27 .._ , ~ ~ z ~ ~ ~ ~ -5~-A multiple donor oligonucleotide (MDO) of 20 to 100 nucleotides in length is labelled with DABITG
(non-fluorescent) donor groups at spaci.ngs of from 3 to t~ base pairs. The multiple donor system could also _ !
be an arrangement c:f a number of multiple donor t probes, similar to the arrangement discussed in .
Example 1. A portion of at least 10 to 50 nucleotides of multiple donor oligomer is complementary to a specific portion of a target DNA sequence.
14 An acceptor oligonucleotide (AO) of 15 to 50 nucleotides in length, is labelled with Texas Red at or near its 5'-terminal position, and is complementary to that portion of the DNA target sequence continuous with the target sequence specific for the multiple donor oligomer. .
A quencher oligonucleotide (QO) of 10 to 45 nucleotides in length, is labelled with Reactive Red 4 near its 3'~terminal position. The quencher oligomer is made complementary to the acceptor oligomer, but is 5 to 10 bases shorter. The Quencher oligomer is constructed so that when it is hybridized to the acceptor oligomer; the Reactive Red 4 group is within 1 to 5 bases of the Texas Red group, causing complete quenching of the Texas Red fluorescence.
Figure 4 shows the homogeneous assay procedure.
This procedures can be carried using aqueous buffers common to the art of hybridization. Initially the multiple donor oligomer is provided into the homogeneous system as an un-hybridized (single-stranded) oligomer and the quencher oligomer is ' p~ov'ided to~th~ system hybridized to the acceptor oligomer. The target DNA is either already present or now added to the assay system. The system is then heated to a temperature which causes denaturation of the target DNA. The systeri is then cooled to allow L

i WO 93/09128 PC,°T/US92/09827 i -59 ~.~~ k~~
the new specific hybridizations to take place. The ' donor oligomer then hybridizes to its complementary f sequence on the target DNA and the acceptor oligomer also hybridizes to the target DNA, adjacent to the multiple donor. Both oligamers are constructed relative to a preselected target sequence so that upon programmed assembly (hybridization) the terminal donor group is located,within 3 to G base pairs of the acceptor group: The quencher oligomer is designed to be shorter in length than the acceptor and therefor cannot effectively compete with target sequences for hybridization to the target bound acceptor oligomer.
Any un-hybridized acceptor oligomer re-hybridizes with quencher oligomer. The target DNA has now organized the danor oligomer and the acceptor oligomer for efficient extended energy transfer to the Texas Red' group. Target DNA.can be quantitatively determined by fluorescent analysis.
The above assembled system is then excited at 430 nm and the fluorescent emission at 615 nm is determined. This homogeneous sys~:em has the unique advantages of having no fluorescent background from the any of the multiple donor groups as well as from ax~y of the non-'target hybridized acceptar oligomer.
This particular procedure represents just one of a number of possible homogeneous and heterogeneous DNA
assay systems that car, be developed based on novel extended energy transfer mechanisms: ' Demonstration of Efficient EneraY Transfer ' 'In A~Closely Approximated Donor Acceptor Arr~anaement The following describes the demonstration of efficient energy transfer in an aligonucleotide in which the terminal acceptor (Texas Red) is separated i wo ~~romz~ ~crrus~2ro~sZ~
,, :. , -60- ;
by one nucleotide unit (0.34 nm) from its primary donor (Fluorescein). The arrangement of the fluorescein donor and Texas Red acceptor in the nucleotide sequence is shown below (SEQ ID NO Z1): , 5'-(TR)-G-(F}-GAGACTCATGAGCAGGGGCTAGC-3' , The above fluorescent modified aligonucleotide was made synthetically using the previously described techniques, except that a fluorescein (F}
phosphoramidite (Clontech) replaced the second nucleotide in from the 5' terminus of the oligonucleotide. This second nucleotide position was -. functionalized with standard C6 linker amine (Aminolink 2), which was subsequently reacted with Texas Red. The resulting oligonucleotide derivative was purified by polyacrylamide gel (150}
electrophoresis.
Fluorescent energy transfer far this fluorescent ;
phosphorami.dite derivative oligonucleotide was carried out after first hybridizing the derivative to a complementary oligonucleotide. The concentration for , both the oligonucleotides was 25 ug/ml;, and hybridization was carried out at room temperature in 1X SSC (pH 7.0). When excited at 490 nm, this derivative pradL~~ed > 50% energy transfer, in terms of 610 nm re-emission by the Texas Red acceptor. This clearly,demonstrates a closely spaced donor-acceptor arrangement in which secondary quenching mechanisms have been reduced, and higher energy transfer in terms of ~aCCeptar '~re-emission is observed:
The foregoing is intended as.illustrative of the present, invention but not linviting. Numerous , variations and mcadificatians can be effected without WO 931U9128 PC1'/iJS92/09827 ~~.23r1-33 ~~1~
departing Pram the true spirit and scope of the invention.

iY0 93/09128 ~1~3~1 ~~

SEQUENCE LISTING
(1) GENERAL INFORMATION:
a 1 ,1 .
(i) APPLICANT. Heller, Micha (ii) TITLE OF INVENTION: SELF-ORGANIZING MOLECULAR PHOTONIC
STRUCTURES BASED ON CHROMUPHORE- AND FLUOROPHORE-CONTAINING
POLYNUCLEOTIDES AND METHODS OF THEIR USE
(iii) NUMBER OF SEQUENCES: 11 (iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: Thomas Fitting (B) STREET: 12526 High Bluff Drive, Suite 300 (G) CZZ1': San Diego (D) STATE: California {E) COUNTRY: USA
(F) ZIP: 9213(1 (v) COMFUTER READABLE FORM: ' (A) MEDIUM T'YFE: Floppy disk (B) COMFUTE~t: IBM FC compatible (C) OPERATING SYSTEM: PC°D0S/MS-DOS
(D) SOFTWARE: Paten~In Release ~~1.0, Version ~~1.25 (vi) Cx APPLICATION DATA:
(A) APPLICATION NUMBER: PCT/US92 (B) FILING DATE: 06-NOV-1992 (C) CLASSIFICATION:
(vii) PRTOR APPLTGATION DATA:
(A) APPLICATION NUMBER: US 07/790,262 (B) FILING DATE: 07-N0V°1992 (vi:ii) ATTORNEY/AGENT INFORMATION: .
(A) NAME: Fitt~,ng, Thomas , (B) REGISTRATION NUMBER: 34,163 (C)-REFERENCE/DOCKET NUMBER: rIEL0005P
(ix) TELECOMMUNICATION INFORMATION:
(A) TELEPH0:1E: 619-792-3680 (B) TELEFAX: 619-792-84.77 (2) INFORMATTON FOR SEQ ID NO:1:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 10 base pairs (B~ TYPE: nucleic acid .. ;;, ,....: , .. , ._; , .... ; .- , , . ,.-. " , ,.. ;,. :. , -... ~ : . -, . , ;, ._ , .. _.. . . , . . . ..

W~ 93/09y2~ ~ ~ ~ ''' ~ ~ ~ PC'f/US92/09827 (C) STRANDEDNESS: single (D) TOPOLOGY: linear (~:i) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(ix) FEATURE:
(A) NAME/KEY: misa~feature (B) LOCATION: 10 (D) OTHER INFORMATION: /note- "Donor chromophore at the 3' T nucleotide"
{xi) SEQUENCE DESCRIPTION: SEQ ID N0:1: , (2) INFORMATION FOR SEQ ID N0;2:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 10 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(ix) FEATURE:
(A) NAME/KEY: masc~feature {B) LOCATTON: 1 (D) OTHER INFORMATION: /note "Acceptor chramophore at the S' T nucleotide"
(xi) SEQUENCE DESCRIPTION: SEQ ID ri0:2:

(2) INFORMATION FCR SEQ ID NO:3:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs (B)'~yPE: nucleic acid W~ 93109128 ;
.. . , (G) STRANDEDNESS: single (D) TOPOLOGY: linear enomic) (ii) MOLECULE TYPE: DNA (g , i I
(iii) HYPOTHETICAL: N0 (iv) ANTI-SENSE: NO
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:3:
ATCGTACTGA ACGTATGCAT
(2) INFORMATION FOR SEQ ID N0:4:
(i) SEQUENCE CHARACTERISTICS: , (A} LENGTH: 16 base pairs (E) TYPE: nucleic acid (C) STRANDEDNESS: single (D} TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: N0 (iw) ~NTZ-SENSE: NO
(ix) FEATURE: .
(A) NAME/KEY: misc_~sature (B) LOCATION: 6 .
(D) OTHER INFORMATION: /note~ "Sul~orhodamine 101 (Texas Red)-libelled T nucleotide"
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:4:
ATGTCTGACT GGAGCT
(2) INFORMATION FOR'SEQ ID N0:5:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 30 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) .TOPOLOGY: linear .
(ii) MOLECULE TYPE'. DNA (genomic) (iii) HYPOTHETICAL: NO

i~'~ 93/U9128 ~ ~ ? ~,. ,~ 3 1'~/US92/09827 (iv) ANTI-SENSE: NO
(ix) FEATURE:
(A) NAME/KEY: misc,feature (B) LOCATTON: I1 (D) OTHER INFORMATION: /note- "Fluorescein-labelled T
nucleotide"
(ix} FEATURE:
(A) NAME/KEY: mist feature (B) LOCATION: 18 (D) OTHER INFORMATION: /note- "Fluorescein-labelled T
nucleotide"
(xi) SEQUENCE DESCRIPTION: SEQ,ID N0:5: , (2) INFORMATION FOR SEQ ID N0:6:
(i) SEQUENCE CHARPrCTERISTICS:
(A} LENGTH: 29 base pairs (B} TYPE: nucleic acid (C) STRANDEDNESS: single .
(D) TOPOLOGY: linear ' (ii} MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE:'NO
(ix) FEATURE:
(A) NAME/KEY: mist~feature (B) LOCATION: 11 (D) OTHER INFORMATION: /note- "Fluorescein-labelled T
nucleotide"
(ix) FEATURE:
., ~ ~ (A) .NAME/KEY': misc~feature ;
(B) LOCATION: 18 (A) OTHER INFORMATION: /note- "Fluorescein-labelled T
n~zcleotide~~
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:6:

f dVCD 931U9~28 PC1'/US92/09827 ;

i (2) INFORMATION FOR SEQ ID N0:7:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 29 base pairs ' (E) TYPE: nucleic acid (C) STRANDEDNESS: single _ (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) _iYPOTHETICAL: NO
(iv) ANTI-SENSE:~NO
ix ) FE,ATURE
(A) NAME/KEY: misc~feature .
(B) LOCATION: 11 (D) OTHER INFORMATION: /note "Fluorescein-labelled T
nucleotide"
(ix) FEATURE:
(A) NAME/KEY: misc feature (B) LOCATION: 19 (D) OTHER INFORI~tATION: /note- "Fluorescein-labelled T
nualeotide'°
(xi) SEQUENCE DESCRIPTLON: SEQ ID N0:7:
ACGACCATAG 'TGCGAGGCTC TGAACACTC 29 (2) INFORMATION FOR SEQ ID N0:8:
(i) SEQUENCE CHARACTERISTICS:
(.A) LENGTH: 1S base pairs (:~) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (uii) HYPOTHETICAL:'NO
(iv) AN".~I-SENSE: N0 ( ix ) FEATURE
(A~ NAME/KEY: misc feature (FS) LOCATION: 5 (D) OTHER INFORMATION: /note "Fluarescein-labelled T

WO 93109128 1'CT/US92/09827 :.
6~ i nucleotide"
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:8:
i i (2) INFORMATION FOR SEQ ID N0:9: .
(i) SEQUENCE CH.4R.A,CTERISTICS:
(A) LENGTH: 18 base pairs (B} TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO , (iv) ANTI-SENSE: NO
(ix) FEATURE:
(A) NAME/KEY: misc feature (B) LOCATION: 13 (D) OTHER INFORMATION: /note= "Fluorescein-labelled T
nucleotide"
(xi) SEtaUENCE DESCRIPTION: SEQ ID N0:9:

(2} INFORMATION FOR SEQ ID N0:10: ' (i) SEC~UENCE CHARACTERISTICS:
(A} ~NGTH: 18 base pairs (.~S) TYPE: nucleic acid (C:) STRANDEDNESS: single (D) TOPOLOGY; linear (ii) MOLECULE TYPE: DNA (genomic) ._ ~~.ii) HYPOTHETICAL:''NO ' i (iv} ANTI-SENSE: NO
:i (i~) FEATURE:
(A) NAME/KEY: misc Feature (B) LC)CA~'ION: I ' (D} OTHER INFORMATION: /notem "Texas Red-labelled G

~'O 93/Q9128 PC.T/~JS92/09827 ~~.23~~.3~

nucleotide" a (xi) SEQUENCE DESCRIPTION: SEQ ID N0:10:

(2) INFORMATION FOR SEQ ID N0:11:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 2~+ base pairs (:B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HY:~OTHETIGAL: NO , (iv) AN'.CI-SENSE: NO
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION: 1 (D) OTHER TNFORMATION: /note "The 5' G nucleotide separates the terminal Texas Red (TR) acceptor from its pri.mar~r donor, fluroescein (F)"
(xi) SEQUENCE DESCRIPTION: SEQ ID N0:11:
GGAGACTCAT GAGCAGC;GGC TAGC 2~

Claims (45)

CLAIMS:
1. ~A polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, and at least one acceptor chromophore wherein all said chromophores are linked to said polynucleotide by linker arms, wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance.
2. ~The polynucleotide of claim 1, wherein at least one said acceptor chromophore is able to re-emit light.
3. ~The polynucleotide of claim 1 or claim 2, wherein light transferred from at least one said donor chromophore produces an increase in acceptor re-emission.
4. ~The polynucleotide of any one of claims 1 to 3 wherein said donor chromophore is selected from the group consisting of 4,4'-diisothiocyanatodihydro-stilbene-2,2'-disulfonic acid, 4-acetamido-4'-isothiocyanato-stilbene-2,2'-disulfonic acid, 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid, succinimidyl pyrene butyrate, acridine isothiocyanate, 4-dimethylaminophenylazophenyl-4'-isothiocyanate, Lucifer Yellow vinyl sulfone, fluorescein isothiocyanate, Cibacron Brilliant Red 3B-A, Rhodamine X isothiocyanate, Sulforhodamine 101 acid chloride, Malachite Green isothiocyanate and IR144.
5. ~The polynucleotide of any one of claims 1 to 4 wherein said terminal donor chromophore and said at least one intermediate donor chromophore are non-fluorescing chromophores.
6. ~The polynucleotide of any one of claims 1 to 5 wherein said terminal donor chromophore and said at least one intermediate donor chromophore comprise 2 to 100 chromophores.
7. ~The polynucleotide of any one of claims 1 to 6 wherein the acceptor chromophore is a fluorescing acceptor chromophore.
8. ~The polynucleotide of claim 7 wherein said fluorescing chromophore is selected from the group consisting of pyrene, Lucifer Yellow vinyl sulfone, acridine isothiocyanate, riboflavin, fluorescein isothiocyanate, Rhodamine X isothiocyanate, Sulforhodamine 101 acid chloride and IR144.
9. ~An extended photonic energy transfer system able to communicate with an electronic circuit, said transfer system comprising:
a polynucleotide having a terminal donor chromophore, at least one intermediate donor chromophore, and at least one acceptor chromophore linked to said polynucleotide by linker arms;
wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore; and wherein at least one said chromophore is adapted to convert electronic energy to photonic energy.
10. ~The transfer system of claim 9, wherein the chromophore adapted to convert electronic energy to photonic energy is selected from the group consisting of luminescent compounds, ruthenium complexes, and photovoltaic cells.
11. ~An extended photonic energy transfer system able to communicate with an electronic circuit, said transfer system comprising:
a polynucleotide having a terminal donor chromophore, at least one intermediate donor chromophore, and at least one acceptor chromophore linked to said polynucleotide by linker arms;
wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore; and wherein at least one said chromophore is adapted to convert photonic energy to electronic energy.
12. ~The transfer system of claim 11, wherein the chromophore adapted to convert photonic energy to electronic energy is selected from the group consisting of luminescent compounds, ruthenium complexes, and photovoltaic cells.
13. ~A diagnostic assay system for photonic detection of a preselected nucleotide sequence comprising, in an amount sufficient for at least one assay, a polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, all said chromophores are and at least one acceptor chromophore linked to said polynucleotide by linker arms, wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance.
14. ~The diagnostic system of claim 13 wherein at least one of said terminal donor chromophore, said at least, one intermediate donor chromophore, and said at least one acceptor chromophore is a fluorescing chromophore operatively linked to said polynucleotide by a linker and, wherein said fluorescing chromophore is positioned by said linkage at a donor-acceptor transfer distance from at least one of said non-fluorescing chromophores.
15. ~The diagnostic system of claim 13 or claim 14, further comprising a second polynucleotide containing at least one fluorescing acceptor chromophore linked to said second polynucleotide by a linker arm.
16. ~A duplex nucleic acid structure capable of extended photonic energy transfer, said structure comprising:
a first polynucleotide;
a second polynucleotide hybridized to said first polynucleotide;
a terminal donor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide;
at least one intermediate donor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide; and at least one acceptor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide;
wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore spaced from said terminal donor chromophore by a donor-donor transfer distance; and wherein said donor and said acceptor chromophores are alternately positioned on said first polynucleotide and said second polynucleotide such that said photonic energy transfer crosses between said first and said second polynucleotides of said duplex.
17. ~The structure of claim 16, wherein said donor-donor transfer distance is 1.4 to 6.1 nm.
18. ~The structure of claim 16 or claim 17, wherein said donor chromophores are selected from the group consisting of 4,4'-diisothiocyanatodihydro-stilbene-2,2'-disulfonic acid, 4-acetamido-4'-isothiocyanato-stilbene-2,2'-disulfonic acid, 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid, succinimidyl pyrene butyrate, acridine isothiocyanate, 4-dimethylaminophenylazophenyl-4'-isothiocyanate (DABITC), Lucifer Yellow vinyl sulfone, fluorescein isothiocyanate, Reactive Red 4 (Cibacron RTM Brilliant Red 3B-A) rhodamine X
isothiocyanate, Sulforhodamine 101, Malachite Green isothiocyanate and IR144.
19. ~The structure of claim 16 or claim 17, wherein said donor chromophores are non-fluorescing chromophores.
20. ~The structure of any one of claims 16 to 19, wherein said at least one intermediate donor chromophore comprises 1 to 99 chromophores.
21. ~The structure of any one of claims 16 to 20, further comprising at least one fluorescing acceptor chromophore operatively linked by linker arms to one of said first polynucleotide and said second polynucleotide, wherein .gamma.

said at least one fluorescing accepting chromophore is positioned by said linker arms at a donor-acceptor transfer distance from at least one of said donor chromophores.
22. The structure of claim 21, wherein said donor-acceptor transfer distance is 0.1 to 1.7 nm.
23. The structure of claim 21 or claim 22, wherein said fluorescing acceptor chromophore is selected from the group consisting of pyrene, Lucifer Yellow, acridine, riboflavin, fluorescein, rhodamine, sulforhodamine 101, and IR144.
24. The structure of any one claims 16 to 23, wherein at least one of said first polynucleotide and said second polynucleotide is linked to a solid support.
25. The structure of claim 24, wherein the solid support is selected from the group consisting of glass, metals, silicon, organic polymers, membranes, and bio-polymers.
26. A biosensor for detecting the presence of an analyte in solution, said analyte comprising a target DNA
sequence, said biosensor comprising:
an excitation source for delivering emitting photonic energy;
a donor sequence comprising a first polynucleotide having a terminal donor chromophore and at least one intermediate donor chromophore linked to said first polynucleotide by linker arms, wherein said first polynucleotide is complementary to a first region of said target DNA sequence;

an acceptor sequence comprising a second polynucleotide having at least one acceptor chromophore linked to said second polynucleotide by linker arms, wherein said second polynucleotide is complementary to a second region of said target DNA sequence; wherein the distance between one said donor chromophore and one said acceptor chromophore is such that they are in an energy transfer relationship; and an associated photon sensing means to detect photonic energy emitted from said acceptor.
27. The biosensor of claim 26, wherein said analyte, upon hybridization, is sufficiently close to permit detection by said photon sensing means.
28. The biosensor of claim 26 or claim 27, wherein at least one of said first polynucleotide, said second polynucleotide, and said target DNA sequence is bound to a solid support or matrix that is insoluble in the analyte solution.
29. The biosensor of claim 28, wherein said solid support or matrix is selected from the group consisting of glass, metals, silicon, organic polymers, membranes, and bio-polymers.
30. The biosensor of any one of claims 26 to 29, wherein said associated photon sensor means is selected from the group consisting of a photodiode, photodiode array, photomultiplier tube, and a fiber optic detection system.
31. A biosensor for detecting the presence of an analyte in solution, said analyte comprising a target DNA
sequence, said biosensor comprising:

an excitation source for delivering emitting photonic energy;
a donor sequence comprising a first polynucleotide having a terminal donor chromophore and at least one intermediate donor chromophore linked to said first polynucleotide by linker arms, wherein said first polynucleotide is complementary to a first region of said target DNA sequence;
an acceptor sequence comprising a second polynucleotide having at least one acceptor chromophore linked to said second polynucleotide by linker arms, wherein said second polynucleotide is complementary to a second region of said target DNA sequence; and an associated photon sensing means to detect photonic energy emitted from said acceptor;
wherein said first polynucleotide and said second polynucleotide are able to hybridize with said target DNA
sequence to form a complex wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore.
32. The biosensor of claim 31, wherein said analyte, upon hybridization, is associated in close proximity to said photon sensing means.
33. The biosenor of claim 31 or claim 32, wherein at least one of said first polynucleotide, said second polynucleotide, and said target DNA sequence is bound to a solid support or matrix that is insoluble in the analyte solution.
34. The biosensor of claim 33, wherein said solid support or matrix is selected from the group consisting of glass, metals, silicon, organic polymers, membranes, and bio-polymers.
35. The biosensor of any one of claims 31 to 34, wherein said associated photon sensor means is selected from the group consisting of a photodiode, photodiode array, photomultiplier tube, and a fiber optic detection system.
36. A method for detecting the presence of a preselected nucleic acid target sequence in a nucleic acid-containing sample comprising the steps of:
(a) admixing;
(i) a polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, and at least one acceptor chromophore, said chromophores are linked to said polynucleotide by linker arms, all wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance, and (ii) said nucleic acid-containing sample to form a hybridization reaction admixture, said polynucleotide having a preselected nucleic acid sequence adapted to hybridize to said target sequence;
(b) subjecting said hybridization reaction admixture to hybridization conditions for a time period sufficient for said polynucleotide to hybridize to said preselected nucleic acid base sequence and form a donor chromophore containing- and acceptor chromophore containing-hybridized nucleic acid duplex;

(c) exciting said donor chromophores in said nucleic acid duplex formed in step (b) by exposing said donor chromophores to sufficient photonic energy to induce emission of photonic energy from said acceptor chromophore;
and (d) detecting the presence of photonic energy re-emitted from said acceptor chromophore using a photon sensing means, thereby detecting the presence of said preselected nucleic acid target sequence in said sample.
37. The method of claim 36 wherein said terminal donor chromophore and said at least one intermediate donor chromophore are excited by photonic energy at a wavelength corresponding to the excitation maximum of the donor, and wherein the photonic energy re-emitted from said acceptor is detected at its emission wavelength.
38. The method of claim 36 or claim 37, wherein at least one of the polynucleotide and the nucleic acid target sequence is attached to a solid support or matrix.
39. The method of claim 38, wherein the solid support or matrix is selected from the group consisting of glass, metals, silicon, organic polymers, membranes, and bio-polymers.
40. The method of claim 38 or claim 39, wherein the photon sensing means is closely associated with said solid support or matrix.
41. A method for detecting the presence of a preselected nucleic acid target sequence in a nucleic acid-containing sample comprising the steps of:
(a) admixing;

(i) a first polynucleotide having a terminal donor chromophore and at least one intermediate donor-acceptor chromophore, said donor and donor-acceptor chromophores are linked to said first polynucleotide by linker arms; and (ii) a second polynucleotide having at least one acceptor chromophore liked to said second polynucleotide by a linker arms, and (iii) said nucleic acid-containing sample to form a hybridization reaction admixture, said first and second polynucleotides having preselected nucleic acid sequences adapted to hybridize to said target sequence and thereby position said terminal donor chromophore on said first polynucleotide and one said acceptor chromophore on said second polynucleotide at a distance which is greater than nm, and wherein there is at least one said intermediate donor chromophore within said distance;
(b) subjecting said hybridization reaction admixture to hybridization conditions for a time period sufficient for said polynucleotide to hybridize to said preselected nucleic acid base sequence and form a donor chromophore containing- and acceptor chromophore containing-hybridized nucleic acid duplex;
(c) exciting said donor chromophores in said nucleic acid duplex formed in step (b) by exposing said donor chromophores to sufficient photonic energy to induce emission of photonic energy from said acceptor chromophore;
and (d) detecting the presence of photonic energy re-emitted from said acceptor chromophore using a photon sensing means, thereby detecting the presence of said preselected nucleic acid target sequence in said sample.
42. The method of claim 41, wherein said donor chromophores are excited by photonic energy at a wavelength corresponding to the excitation maximum of the donor, and wherein the photonic energy re-emitted from said acceptor is detected at its emission wavelength.
43. The method of claim 41 or claim 42, wherein at least one of the first polynucleotide, the second polynucleotide, and the nucleic acid target sequence is attached to a solid support or matrix.
44. The method of claim 43, wherein the solid support or matrix is selected from the group consisting of glass, metals, silicon, organic polymers, membranes, and bio-polymers.
45. The method of claim 43 or claim 44, wherein the photon sensing means is closely associated with said solid support or matrix.
CA002123133A 1991-11-07 1992-11-06 Hybridization of polynucleotides conjugated with chromophores and fluorophores to generate donor-to-donor energy transfer system Expired - Fee Related CA2123133C (en)

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US6395492B1 (en) * 1990-01-11 2002-05-28 Isis Pharmaceuticals, Inc. Derivatized oligonucleotides having improved uptake and other properties
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