CA2335240A1

CA2335240A1 - Cyanine dyes and synthesis methods thereof

Info

Publication number: CA2335240A1
Application number: CA002335240A
Authority: CA
Inventors: Malcolm Harry Randall; Philip Richard Buzby; Thomas Joseph Erickson; Joseph David Trometer; Joseph John Miller Jr.; David George Ahern; Mark N. Bobrow
Original assignee: Nen Life Science Products, Inc.; Malcolm Harry Randall; Philip Richard Buzby; Thomas Joseph Erickson; Joseph David Trometer; Joseph John Miller Jr.; David George Ahern; Mark N. Bobrow
Current assignee: PerkinElmer Health Sciences Inc
Priority date: 1999-04-19
Filing date: 2000-04-19
Publication date: 2000-10-26
Anticipated expiration: 2020-04-19
Also published as: US6204389B1; AU767368B2; US6114350A; CA2335240C; US6224644B1; AU4363100A; WO2000063296A2; WO2000063296A3; EP1112254B1; US20010020098A1; EP1112254A4; EP1112254A2; JP2002542365A; US6437141B2; US6197956B1

Abstract

A cyanine dye having formula (II), wherein R1-R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, and C0-C4 alkyl group having a hydrophilic substituent thereon. R11 and R12 are chosen to include a free or protected thiol, amine or hydroxyl substituent capable of reacting with a target molecule through a nucleophilic displacement mechanism.
The dye is useful in labeling a variety of target molecules. Processes are described for synthesizing suitable heterocyclic and indole derivatives as precursors for the aforementioned cyanine dyes.

Description

WO 00/63296 PCTlUS00/10533 CYANINE DYES AND SYNTHESIS METHODS THEREOF
Field of the Invention This invention relates to the synthesis of cyanine dyes having nucleophilic reactive groups. Further, the present invention includes synthetic methods to produce free reactive thiol, amine or hydroxyl groups from protected substituents, the nucleophilic groups capable of nucleophilic additiion to target molecules.
Background of the Invention Cyanine dyes are now recognized to have widespread application as fluorescent probes which can be conjugated to a variety of biological molecules, thus finding applications in DNA sequencing, flow cytometry and immunoassays.
Cyanine dyes are characterized by strong spectral absorption bands with the absorption being tunable over a large spectral range by synthetic design.
In addition to the spectral characteristics of a cyanine dye, a practical dye is characterized by also being stable during isolation and purif cation, yet be reactive for covalent bonding with a target molecule wader conditions which will not degrade the target molecule. Prior art cyaniine dyes having reactive groups capable of covalently bonding a target molecule have all been limited in their utility either by structural stability or the reaction condiitions required for coupling of the dye and target molecules.
An iodo acetyl moiety attached to a cyanine dye is capable of covalently reacting with a sulfhydryl group of a target molecule. The iodo acetyl group is limited in its utility by the sulfhydryl groups being present in only a small class of proteins. Other reactive moieties have included sulfonic acid, carboxylates, and sulfonates (for example see, Anal. Biochem. 243,15-27: 1996; Bioconj. Chem. 4, 105-111: 1993; 8, 751-756: 1997; Cytometry 10, 3-10: 1989; 10, 11-19: 1989;
U.S. Patent 5,106,990; and J. Chem. Soc. Perkin Transactions 1, 143-7: 1998).
Such moieties remain reactive during the course of subsequent chemical transformations and purification or are limited by the reaction conditions for bonding to a target molecule.
U.S. Patent 5,627,027 is directed to a method for labeling proteins, cells, nucleic acid and DNA with a cyanine dye, as well as the reaction therebetween.
The cyanine dye specified is limited in the position of a reactive group within the dye and its identity is limited to isothiocyanate, isocyanate, monochlorotriazine, dichlorotriazine, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, aziridine, sulfonyl halide, acid halide, hydroxy succinimide ester, hydroxy sulfosuccinimide ester, imido ester, gl;yoxal and aldehyde. The method still further requires forming a covalent bond between the reactive group i 5 on the dye, and an amine or hydroxyl group on the material being labeled utilizing an electrophilic mechanism for coupling the dye and material being labeled.
U.S. Patent 5,486,616 is directed to particular cyanine dye structures which are water soluble, and capable of reacting with amino, hydroxy or sulfhydryl groups through a reactive moiety. The dye strictures including at least one sulfonic acid or sulfonate moiety attached directly to a benzyl portion of the dye utilizing an electrophilic mechanism for coupling the dye and material being labeled.

U.S. Patent 5,268,486 discloses water soluble dyes which contain reactive moieties including isothiocyanate, isocyanate, monochlorotriazine, dichlorotriazine, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, maleimide, aziridine, sulfonyl halide, acid halide, hydroxysuccinimide ester, hydmxysulfosuccinimide ester, imudo ester, hydrazine, azidonitrophenyl, azide, 3-(2-pyridyl dithio)-proprionamide, glyoxal and aldehyde. These dyes are chosen to Label target moaecules containing amino-, hydroxy- and sulfhydryl groups.
In view of the prior art, it is apparent that there exists a need for a wider range of indole derivatives which will allow the facile synthesis of stable cyanine dyes with suitably positioned reactive groups for covalent attachment to target molecules. The cyanine dyes should allow covalent bonding to target molecules under conditions which will not degrade the target miolecules. They should be stable, easily formed, purified and reactive under conditions of attachment to target molecules. This invention describes the facile synthesis of new, stable indole precursors derived from indoles. These precursors allow the facile synthesis of cyanine dyes with protected thiol, amine or hydroxyl groups. The protected groups can be deprotected to yield free thiol, amine or hydroxyl groups which can be covalently attached to target molecules via a nucleophilic mechanism.
In view of the prior art, it is apparent that there exists a need for a cyanine dye having a mare generic utility. A need exists for a cyanine dye which is water soluble and contains at least one reactive moiety capable of labeling a range of substances in addition to compounds containing amino, hydroxy and sulfhydryls through covalent bonding with target molecules under conditions which will not degrade a target molecule.
Prior coupling reactions have been carried out by an electrophilic mechanism. Thus, there further exists a need for a generic class of cyanine dyes which are capable of coupling to a target molecule by a nucleophilic mechanism.
Detailed Description of the Invention The present invention relates to a class ofnitrogen containing heterocyclics of the formula:
--~cH3 (1) wherein Y, is selected from a group consistirAg of \ ~~° ~ s Rg R;o -°' /
~,o -~) ~o wherein Rl, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, a Co-~C4 alkyl group having a hydrophilic substituent selected from a group consistuig of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines, optionally, at least one ofR~-Ra is the Co-C4 alkyl group having the hydrophilic substituent;
wherein R9, R9', Rto and Rlo' are each independently selected from a group consisting of Ct-C3o alkyl, and a heteroatom substituted C~-C3o alkyl wherein the 5 heteroatom is O, N or S; and wherein Rt ~ is selected from a group consisting of _ H
-Rt N~ .
-Rt3-Q R~t3 ~ -Rt3~S NHp , ~ R t3-NHy H H
-Rt N~ ~N R~~t3 Rty~Q
R t3 O S R t3 .
/Q
-Rta S NOZ
'-Rta rR~ N~
/S~~/ .
-Rta "'-Rts .
S- 'O ~ ~
S/ \ H~ .

WO 00!63296 PCTIUS00110533 Y
~H~OCth , /S S' . /S~-'S
_. ".".R~a '-Rt3.
H
/ N ~ /, O

R~~ . and R~3 O~--Si(CH~;3 wherein R,3, R',3, R"13 and R"'13 are each independently CI-C3o alkyl. Q
is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen.
Prior to the present invention it has been difficult to synthesize N
substituted heterocyclics and indoles in particular with hydrocarbon moieties containing protected nucIeophilic groups. The present invention describes a facile reaction between bifunctional hydrocarbons containing the moiety XR, 3Q where X is chlorine, bromine or iodine, 8,315 CI-C3o alkyl and Q is sulfur, nitrogen or oxygen; and nitrogen containing heterocyclics which leads to heterocyclics having protected nucleophilic groups in the primary position on the new N-substituent or a moiety which can be converted to a protected nucleopihilic group such as a thiol, amine or alcohol. The new reaction proceeds by heating a solid mixture of the precursors at elevated temperature for a short period of time. The product is purified using conventional chromatography. Alternatiively the reaction proceeds by heating a suitable suspension of solid nitrogen containing heterocyclic in a suitable reagent solution. The product from the latter method can be purified using conventional methods.

WO 00/63296 PCT/US00lI0533 Chemicals containing the indole nucleus occur widely throughout the animal and plant kingdoms and are components of chemicals found in the human body. For example, the essential amino acid tryptophan (which occurs in many peptides and bioactive proteins) contains an indole nuc;Ieus and is the biochenucal precursor to serotonin which is the important neurotransmitter involved in learning, memory, depression and feeding behavior. Many naturally occurring alkaloids containing the indole nucleus such as Harmaline, Cinchera, Yohimbine, Rauwolfia and Ergot alkaloids have widely differing impacts on biological activities. Indole containing chemicals have been used in industrial applications as dye components and biochemical labeling reagents..
The new and facile chemistry described in this application enables the synthesis of many new derivatives of indole containing chemicals by providing a vehicle to add a wide variety of chemical groups to an indole nucleus allowing researchers in the life sciences access to a broader va~lety of biologically active 1 S molecules and labeling reagents for target molecules. For example, long chain hydrocarbons may be added to indole chemicals living them hydrophobic qualities or alternatively linker molecules may be added that will enable the various biological activities of the indoles to be covalently attached to reporter systems or to be used as the reporter molecule in various biological systems.
This chemistry can also be used to synthesize new indole derivatives having interesting and beneficial pharmaceutical properties. In research, new derivatives that act as agonists or antagonists to the various sub classes of serotonin receptors may be formed. New derivatives may also lead to new labeling reagents and alternative methods of attaching labeling reagents, such as cyanine dyes, to target molecules.
The new heterocyclic derivatives synthesized lby the above methods can be converted to cyanine dyes using conventional chemistry.
These heterocyclics are operative as precursors for a generic class of cyanine dyes having a protected reactive group for nucleophilic covalent attachment to target molecules. The precursor. (1) is condensed to form a fluorescent cyanine dye through a polymethine linkage.
R,, R2, R3 and R4 are optionally such that two of these adjacent R groups are fused to form a ring structure. The resulting ring structure also optionally being functionalized to modify solubility and spectral properties.
The polymethine linkage being formed by reacting two equivalents of precursor (1) in the presence of a molecule illuslxatively including trialkyl orthoformate, dialkyl amides, and trialkoxy alkene in the presence of a base.
Preferably, the base is an organic base. The linkage reaction proceeds under ambient air in a refluxing organic solvent, although it proceeds at a slower rate without solvent reflux. The organic base illustratively includes pyridine, phenol and an alkoxide, morpholine, piperidine, t-butylamin~e, and triethylamine and an amine. The polymethine linkage is a conjugated system having 3, 5, 7 or more linear carbon atoms therein.
The polymethine linkage between two molecules of precursor (1) is appreciated to include linear chains, as well as also cyclo-aliphatics, substituted aryl and heterocyclic ring structures coupled to thE; conjugate system of the polymethine chain. For instance, a bisaldehyde is more reactive towards the precursors of the present invention than fonnates, amides or alkoxyalkenes and reaction does not require the presence of a base. Instead, reaction occurs in the presence of an alcohol (J. Org. Chem. 60, 2391-2395: 1995). A 1-formyl-3-(hydroxymethylene)cyciohex-1-ene derivative thus yields a heptamethine linkage.
Thus, it is appreciated that modification and extensiam of the conjugate bonding across the chain will affect the absorption characteristics of the dye.
Further, it is appreciated that additional reactive groups or solubility enhancing moieties are readily coupled to the polymethine linkage.
The resulting cyanine dye has the formula:
(2) wherein R1, R2, R3, R4, R5, Rb, R7, and R8 are each independently selected from a group consisting of hydrogen, C,-C3o alkyl soup, a Co-Ca alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein Y, and Y2 are each independently selected from a group consisting of ~, R;o Re Re ~o -~) ~o and wherein R9, R'g, R,o, and R'to are each independently selected from a group consisting of C,-C6 alkyl, and a heteroatom substituted C,-C6 alkyl wherein the heteroatom is O, N or S;
wherein R,1 and RIZ are each independently selected from a group 5 consisting of C~-C3o alkyl, phenyl substituted Ct-C3o, C~-C3o having a protected substituent selected from a group consisting of -Rt N~
-R13~Q X15 . -Rta-S NHZ . ~ Rts-NHZ
_ t \ /N R t3 ., Rt~Q
R to ~S R to / \.
O p Q
Hg S/H . /S ~ N02 -'Rta -R13 ~ ' N02 S o,.~~ , /o~o.
-Rt3 /S- 'O ~
-Ra3 /S~'H' \OCH3 -Rt3 Y
N~ i''~~
~S H OCH3 , ~S-~-S , ~S-S
-Rt3 ._..R13 --Rt3 H
~N~~~ ~N

. and R13-n-Si(CH3)3 wherein Ri3, R'13, R",3 and R"' ~3 are each independently C1-C3o alkyl; Q is sulfur, nitrogen ar oxygen, X is a halogen and Y is a halogen;
L is selected from a group consisting of methine, a methine group having a substituent C,-C6 alkyl group and a substituted C,-C6 alkyl group having a phenyl, hydroxyl, sulfonyl, a halogen atom, a heteroatorn substituted phenyl and a C~-C4 alkoxyl where n is 1, 2, 3 or greater.
RI-Rg are optionally such that two of these adjacent R groups are fused to form a ring structure. The resulting ring structure optionally is functionalized to modify solubility and spectral properties.
in order to increase the water solubility of the resulting dye (2), the Rl, R2, R3, R4, R5, R6, R~, RS, R9, R9', R,o, Rio', Rlt and R12 gxoups are each optionally WO 00/63296 PCTlUS00/10533 selected from well known polar and charged moieties., Preferably, each precursor molecule {1) contains at least one hydrophilic moiety in order to impart water solubility. The hydrophilic moieties illustratively innlude Co-C4 alkyl-hydroxy, -substituted amino, -quaternary amino, -sulfonate and -carboxylate. It is appreciated that hydrophobic or nonpolar precursors are useful in organic solvent systems.
A dye (2) is reactive towards a target molecule upon formation of a thiol, amine or hydroxyl moiety. The thioi, amine or hydroxyl moiety is characterized by a lone pair of electrons stericaily and electronically amenable to bonding with a reactant which is reactive towards target molecules. The reaction of a dye (2) with a deprotecting agent converts the substituent into a reactive thiol, amine or hydroxyl substituent. Deprotecting agents are well known to the art. (Theodora W. Greene and Peter G.M. Wuts, Protective Groups in Organic Synthesis, 2nd edition ( 1991 ) 277-308.) It is appreciated that an amine or hydroxyl substituent in fact optionally need not be protected, but instead <~re stable under synthesis conditions and are isolated as such. Thus, an amine or hydroxyl substituent operates as a reactive nucleophilic substituent without the occurrence of an intermediate deprotecting reaction.
It is appreciated that the dyes of the present invention are also amenable to isolation in deprotected form of free thiols. A free thiol containing dye of the present invention results upon reacting a dye (2) with a deprotecting agent and isolating the free thiol therefrom. The resulting free thiol, depending on its specific identity, has a shelf life of more than one month. As with other reactive thiols, free thiol cyanine dyes of the present invention. are best maintained under conditions suitable to prevent the formation of disulfide linkages. These conditions illustratively include refrigeration, darkness and storage under an inert atmosphere. Alternatively, nitrogen containing heterocyclics identical to ( 1 ) except that R~, is selected from the group consisting of R14SH, RI4NH2 and R,40H
are formed directly wherein R~4 is a C3-C3o alkyl and C3-C3o alkyl having a phenyl, hydroxyl, sulfonyl, or halogen atom or a hete~~oatom substituted phenyl.
The reaction chemistry to produce a free thioI dye precursor analog to (1) proceeds in a similar fashion to the formation ofprotected heterocyclics (1).
For example, a cationic nitrogen-containing heterocyclic and a halogenated thiol are able to react via a metatheses reaction to create a free; thiol dye precursor.
The amine or hydroxyl moiety are produced by analogous type reactions. A free thiol precursor thereafter is reacted in a manner similar to precursor (1) to form a polymethine linkage therebetween. The resulting cyanine dye compound is identical to that of (2) except that Rl ~ and R,2 are each independently R~4SH, R~4NHz or R~40H when R14 is a C3-C3o alkyl or C3-C3o alkyl having a phenyl, hydroxyl, sulfonyl, or halogen atom or a heteroatom substituted phenyl.
A commercial package of the present invention includes a compound of Formula ( 1 ) with instructions and optionally reagents fir converting the precursor (1) to a dye compound (2) and further instructions for the use of the dye compound (2) as a dye or hapten. It is appreciated that a free thiol, amine or hydroxyl analog of a compound (1) is also operative; herein. Alternatively, a commercial package includes a compound (2) as an active ingredient together with instructions for the use thereof as a dye or hapten in labeling a target molecule. It is also appreciated that a free thiol, amine or hydroxyl analog of a compound (2) is also operative herein.
The addition of a reactive form of a dye (2) to a target molecule proceeds under conventional nucleophilic reaction conditions. The solvent for the nucleophilic reaction is dictated by the identity of the target molecule.
Since many target molecules of interest are of a biological nature, water is often the nucleophilic reaction solvent.
A target molecule which is coupled with a dye of the present invention illustratively includes organic molecules, polymers, ;oilaceous materials, natural and synthetic: Iipid vesicles, amino acids, peptide nucleic acids, peptides, nucleic acids, nucleotides; nucleosides, DNA, RNA, proteins, carbohydrates, oligosaccharides, polysaccharides, antibodies, cellular receptors, antigens, haptens, iectins, avidins, streptavidins, lyrnphokines, hormones, metabolites, toxins, virions, bacteria, fungal components, esinophils, eukaryotic cells, and derivatives thereof.
A dye (2) of the present invention in which neither R1I or R,2 is C~-C,~o having a heteroatom containing substituent finds utility as a physi-sorbed, fluorescent dye. Alternatively, a dye of the present invE;ntion lacking a heteroatom within Rl, or Ri2 is coupled to a target molecule through a hydrophilic moiety of RI-R8 or a pendant reactive moiety extending from the polymethine linkage.

In order to more fully demonstrate the advantages arising from the present invention, the following examples are set forth. It is to be understood that the following is by way of example only and not intended. as a limitation on the scope of the invention.
5 Example 1- Dye precursor 1-(3-S-Acetylthioprop;yl]-2,3,3-trimethyl-5-sulfo-3H-indolium, inner salt (5).
To a 250 mL round bottom flask with magnetic stir bar is added 2,3,3-trimethyl-5-sulfo-3H-indolium, potassium salt (3) (7.21 mmol) and 3-bmmo-I-10 thioacetylpropane (4) (25.88 mmol). The mixture is stirred and heated at 165°C
for 20 min. The residue is cooled to 20°C and washed with diethyl ether. The solid is purified by Reversed Phase Chromatography to give 1-(3-S-Acetylthio-propyl]-2,3,3-trimethyl-5-sulfo-3H-indolium, inner salt (5) as a solid.
Example 2 - Dye precursor 1-[3-S-Acetylthiopropyl]-2,3,3-trimethyl-5-IS hydroxyl-6-benzo-3H-indolium, inner salt ('n.
The procedure of Example 1 is repeated except 2,3,3-trimethyl-5-hydroxyl-6-bent-indolium, potassium salt (6) is substituted for (3). A solid product I-[3-S-Acetylthiopropyl]-2,3,3-trimethyl-5-hydroxyl-6-benzo-3H-indolium, inner salt (7) is isolated.
Example 3 - Dye precursor 1-[4-S-benzoylbutyt]-3-.methyl-4-carboxyl benzoxizolium, inner salt (10).
The procedure of Example 1 is repeated except 3-methyl-4-carboxyl benzoxizolium, sodium salt (8) is substituted for (3) and 4-bromo-I-S-benzoylbutane (9) is substituted for (4). A solid product I -[4-S-benzoylbutyl]-3-methyl-4-carboxyl benzoxizolium, inner salt (10) is isolated.

Example 4 - Dye precursor 1-[3-S-t-butylpropyl]-3-methyl-5-sulfo-benzoimidazolium, inner salt (13).
The procedure of Example I is repeated except 3-methyl-5-sulfo benzoimidazolium (11) and 3-bromo-1-S-t-butyl propane {12) is substituted for (4). A solid product 1-[3-S-t-butylpropyI]-3-methyl-5-sulfo-benzoimidazolium, inner salt (13) is isolated.
Example 5 - Cyanine-3 dyes derived from (5).
A solution of (5) (2.68 rnmol) and I-ethyl-2,3,3-trirnethyl-5-sulfa-3H-indolium, inner salt (14) {2.68 mmol) is heated to reflex in pyridine (70 mL) and triethyl orthoformate (24.0 rnmol) is added via syrin~;e over 1 hour in four equal portions. The suspension is then heated to reflex for an additional 3 hours and cooled to room temperature. The solvents are removed under reduced pressure and the solid is azeotroped two times with methanol. The solid is purified by Reversed Phase Chromatography and the isolated products are passed over an AGSOW-X4, 200-400 mesh K+ form, column to give I-[3-S-acetylthiopropyl]-2-[3-[ I -ethyl-I,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1-propenyl]-3,3-dirnethyl-5-sulfo-3H-indolium, potassium salt (15;1,1-[3-S-AcetylthiopropylJ-2-[3-[I-[3-S-acetylthiopropyl]-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylideneJ-1-propenylJ-3,3-dimethyl-5-sulfa-3H-indoli~un, potassium salt (16), and 1-ethyl-2-[3-[1-ethyl-1, 3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-I-propenyl]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (17) as solids.

Examples 6-10 - Cyanine-3 dyes derived from (7)" (10) and (13).
The procedure of Example 5 is repeated with ( 7), ( 10) and ( I 3) substituted for (5) and the 1-ethyl-analogs of (7), {IO) and (13) substituted for (14).
The resulting solid compounds which are isolated in purified form are summarized in Table I.
Example 11- Cyanine-5 dyes derived from (5).
A solution of (5) (1.60 mmol), (14) (1.60 mmol) and potassium acetate (3.56 mmol) in.methanol {50 mL) is heated to reflux and 1,3,3-trimethoxypropene (21.0 mmol) is added via syringe over I hour in four equal portions. The IO suspension is then heated to reflux for an additional :3 hours and cooled to room temperature. The methanol is removed under reducE;d pressure and the solid is purified by Reversed Phase Chromatography to give I-[3-S-Acetylthiopropyl]-2-[5-[1-ethyl-1,3-dihydro-3,3-dimethyl-5-suIfo-2H-indol-2-ylideneJ-I,3-pentadienyl]-3,3-dimethyl-S-sulfo-3H-indolium, potassium salt (29), 1-[3-5-Acetylthiopropyl]-2-[3-[1-[5-S-acetylthiopropyl]-1,3~-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylideneJ-1,3-pentadienyl]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (30) and 1-ethyl-2-[5-[I-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadienylJ-3,3-dimethyl-5~-sulfo-3H-indolium, potassium salt (31) as solids.
Example 12 - Dye precursor S-(3-Iodopropyl)isothiourea (32).
Thiourea (14 mmol) is added to a solution of 1,3-diiodopropane (340 mmol) in anhydrous methanol (300 mL) and stirred under an atmosphere of nitrogen at 60°C for 4 hours. The solution is cooled to 4°C
overnight during WO 00!63296 PCT/US00/10533 which time excess 1;3-diiodopropane separates to the bottom of the flask as a colorless oil. The excess 1,3-diiodopropane is rernoved by pipette and the remaining methanol solution is evaporated in vacuo and the residue is suspended in dichloromethane, filtered, and washed with additional dichloromethane to give S S-{3-Iodopropyl)isothiourea (32) as a powder.
Example i3 - Dye precursor 1-[3-Isothiouronylpropyl)-2,3,3-trimethyl-5-sulfo-3H-indolium, inner salt (33).
A solution of (32) (0.36 mmol) and 2,3,3-trimethylindoleninium-5-, sulfonate, potassium salt (3) (0.46 mmol) are placed in a flask and heated to 148°C with stirring for 15 minutes under an atmosphere ofnitrogen. The reaction mixture is cooled to room temperature and the re:~idue is crystallized from methanol to give 1-[3-isothiouronylpropyl]-2,3,3-trime;thyl-5-sulfo-3H-indolium, inner salt (33) as a powder.
Example 14 - Cyanine-3 dyes derived from (33).
A solution of (33) (0.022 mmoi) and 1-ethyl-2,3,3-trimethyl-5-sulfo-3H-indolium, inner salt {14) (0.022 mmol) are dissolved ir.~ N,N-dimethylformamide containing 50 uL of triethylamine and the mixture is heated to 60°C as triethylorthoformate (4 x 10 uL, 4 x 0.06 mrn~ol) is addled in four portions over 3 hours. The solution is heated at 60°C for an additional hour, cooled to room temperature, washed 3 times with diethyl ether, and the resulting precipitate is purified by reverse phase HPLC to give isolated 1-j3-I;>othiouronylpropyl]-2-[3-[ 1-ethyl-I,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-.ylidene]-1-propenyl]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (34),1-[3-Isothiouronylpropyl]-2-[3-[I-[3-isothiouronylpropyl]-1,3-dihydro-3,3-dimetlryl-5-sulfo-2H-indol-2-ylideneJ-1-propenylJ-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt {35) and 1-ethyl-2-[3-[1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1-propenylJ-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (17) as solids.
Example 15 - Bonding of dye (15) to a target nucleotide derivative.
To a 2 mL vial with a stir bar is added ( I S) ( 1.58 ptnol), 5-[3-[3-[2,5-dihydro-2,5-dioxo-1 H-pyrrole)propanamidoJ-1-propynylJ-2'-deoxycytidine triphosphate (36) (S.0 pmol) in 50 mM sodium dihydrogenphosphate pH 7.0 - 7.5 (250 p,I,). To the stirred solution is added 1M hydroxylamine pH 7.0 - 7.5 (250 p,L) and the resulting solution is stirred at room temperature for 1 hour. The reaction mixture is purified to give 5-[3-[3-[3-[1-[3-thiopropylJ-2-[3-[1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylideneJ-1-propenylJ-3,3-dimethyl-5-sulfo-3H-indoliumJ-2,5-pyrrolidindione]propanamidoJ-1-propynylJ-2'-deoxycytidine triphosphate (37).
Example 16 - Bonding of dye (28) to a target nucleotide derivative.
The procedure of Example 15 is repeated with. (28) substituted for (15).
The reaction mixture is purified to give S-[3-[3-[3-[I-[3-thiopropylJ-2-[3-[1-ethyl 3-methyl-5-sulfo-bent-imidazol-2-ylideneJ-1-propenylJ-3,3 dimethyl-5-hydroxyl 6-Benz-indoliumJ-2,5-pyrrolidindione]propanamidoJ-1-~propynylJ2'-deoxycytidine triphosphate (38).
Example 17 - Bonding of dye (29) to a target nucleotide derivative.
The procedure of Example 15 is repeated with (29) substituted for (15).
The reaction mixture is purified to give 5-[3-[3-[3-I-[3-thiopropylJ-2-[5-[ 1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene;]-1,3-pentadienyl]-3,3-dimethyl-5-sulfo-3H-indolium]-2,5-pyrrolidindione]propanarnido]-1-propynyl]-2'-deoxycytidine triphosphate (39).
Example 18 - Dye precursor 1-[3- Isothiouronylpropyl]-2,3,3-trimethyl-3H-5 indolium iodide {41).
To a 50 mL round bottom flask is added 2,3,3-trimethylindolenine (14.4 mmol} and 1,3-diiodopropane (72.7 mmol) and the mixture is stirred at 60°C
under an atmosphere of nitrogen for 16 hours. The resulting solid is recrystallized 10 from ethanol to give 1-[3-iodopropyl]-2,3,3-trimethyl-3H-indolium iodide (40) as crystals.
To a 100 mL round bottom flask is added (40) {4:38 mmol), thiourea (4.5 mmol), and methanol (30 mL). The solution is stirred at 60°C for 5 hours, evaporated in vacuo, the residue is dissolved in water (20 mL) and washed with 15 dichloromethane (3 x 6 mL) and cooled to 4°C overnight; and the resulting crystals are filtered and washed with acetone to give 1-[3-isothiouronylpropyl]-2,3,3-trimethyl-3H-indolium iodide (41).
Example i9 - Cyanine-3 dyes derived from (41).
To a 25 mL round bottom flask is added (41) (1.0 mmol), (14) (1.5 mmol), 20 and pyridine (10 rnL). The solution is heated to reflu~i: and triethyl orthoformate (4 x 166 uL, 4 x 1.0 mmol) is added in four portions over one hour. The solution is heated at reflux far an additional hour, cooled to room temperature, the evaporated in vacuo, and the residue is washed with ethyl ether (3 x 25 mL), and purified by Ci8 reverse phase chromatography to give isolated 1-[3-isothiouronylpropyl]-2-[3-[ 1-ethyl-1,3-dihydro-3,3-dvnethyl-S-sulfo-2H-indol-ylidene]-1-propenyl]-3,3-dimethyl-3H-indolium, izmer salt (42), 1-[3-isothiouronylpropyl]-2-[3-[1-[3-isothiouronylpropyl]~-I,3-dihydro-3,3-dimethyl-2H-indol-2-ylidene]-1-propenyl]-3,3-dimethyl-3H-indolium iodide (43) and 1-S ethyl-2-[3-[1-ethyl-1,3-dihydro-3,3-dirnethyl-S-sulfo-2H-indol-2-ylidene]-1-propenyl]-3,3-dimethyl-S-sulfo-3H-indolium, potassivum salt (17) as solids.
Example 20 - Cyanine-5 dyes derived from (41).
A solution of (41) (0.28 mmol) and (14) (0.28 mmol) and potassium acetate (0.28 mmol) in methanol (2 mL) is heated to reflux and 1,3,3 trimethoxypropene 1160 uL, 1.17 mmol) is added via ;syringe over 2 hour in four equal portions. A suspension is then heated to reflux for an additional 3 hours and cooled to room temperature. The methanol is removed under reduced pressure and the solid is purified by C18 Reversed Phase Chromatography to give 1-[3-isothiouronylpropyl]-2-[S-[I-ethyl-1,3-dihydro-3,3-dirnethyl-S-sulfo-2H-indol-1S ylidene]-1,3-pentadienyl)-3,3-dirnethyl-3H-indolium, inner salt (44), the related di-isothiouronyl-propyi and diethyl inner salts as solids.
Example 21 - Bonding of dye~(42) to,a target nucleotide derivative.
To a 2 mL vial with a stir bar is added 1-[3-isothiouronylpropyl]-2-[3-[1-ethyl-1,3-dihydro-3,3-dimethyl-S-sulfo-2H-indol-2-yIidene]-1-propenyl]-3,3-dimethyl-3H-indolium, inner salt (42) (8 wmol) in 0.1 ll~ipotassium hydroxide (1.0 rnL). The solution is stirred at room temperature for 1 hour to form the free thiol of (42). Thereafter, (36) (1 S lcmol) is added to the thiolL in aqueous solution. The reaction mixture is purified to give S-[3-[3-[3-[I-[3-thiopropyl]-2-[3-[I-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene)-1-propenyl]-3,3-dimethyl-3H-indoiium]-2,5-pyrrolidindione]pmpanamido]-1-propynyl]-2'-deoxycytidine triphosphate (45).
Example 22 - Bonding of dye {44) to a target nucleotide derivative.
The procedure of Example 21 is repeated with (44) substituted for (42).
The reaction mixture is purified to give 5-[3-[3-[3-[1-[ 3-thiopropyl]-2-[5-[1-ethyI-1,3-dihydro-3,3-dimethyl-5-sulfo-ZH-indol-2-ylidene]-1,3-pentadienyl]-3,3-dimethyl-3H-indolium]-2,5-pyrrolidindione]propanamido]-1-propynyt]-2'-deoxycytidine triphosphate (46).
I O Example 23 - Bonding of dye {15) to a target nucleotide derivative.
To a 5 mL vial with a stir bar is added (15) (19 pmol), 5-[3-[iodoacetamido]-1-propynyl]-2'-deoxycytidine triphosphate (47) (30.0 Eunol) in mM sodium dihydrogenphosphate pH 7.0 - 7.5 (250 IrL). To the stirred solution 1M hydroxyiamine pH 7.0 - 7.5 (250 ~,L) is added. The resulting solution is IS stirred at room temperature for 4 hours to react the free thiol of {15) with (47).
The reaction mixture is purified to give 5-j3-[1-[3-thio~propyl]-2-[3-[1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylideneJ-1-propenyl]-3,3-dimethyI-5-sulfo-3H-indoliumJacetamido-1-propynyI]-2'-deoxyc5~tidine triphosphate (48).
Example 24 - Bonding of dye (29) to a target nucleotide derivative.
20 The procedure of Example 23 is repeated with (29) substituted for (15).
The reaction mixture is purified to give 5-[3-[1-[thiopropyl]-2-[5-[1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-yiidene]-1,3-pentadienyl]-3,3-dimethyl-5-sulfo-3H-indoIium]acetamido-I-propynyl]-2'-deoxycytidine triphosphate (49).

Example 25 - Dye precursor 1-[N-[-3-(tert-butyloxycarbonyiamino) propyl]hexanamide]-2,3,3-trimethyll-5-sulfo-3H-indoGum, inner salt (Sl).
To a 100 mL round bottom flask with a ;>tir bar is added 1-[N-[5-carboxypentylJ-2,3,3-trimethyl-5-sulfo-3H-indolium, inner salt (50) (1.70 mmol) and 40 mL of N,N-dimethyIformamide. The mixture is heated at 50°C until a homogeneous solution is obtained. To this solution is added 1,3-dicyclohexylcarbodiimide (2.30 mmol), N-hydroxysuccinimide (2.34 mmol) and t-butyl N-(3-aminopropyi)carbamate (2.29 mmol). Th.e reaction mixture is heated at 50°C for 30 min and then mom temperature I6 hours. The reaction mixture is filtered, the solvents are removed under reduced pressure and the solid is azeotroped two times with methanol. The solid is purified by Reversed Phase Chromatography to give 1-[N-[-3-(tert-butyloxycarbonylamino)propylJ
hexanarnideJ-2,3,3-trimethyl-5-sulfo-3H-indolium, inner salt (51) as a solid.
Example 26 - Cyanine-3 dyes derived from (51).
A solution of (51) (0.291 mmol) and (14) (0.281 mmol) is heated to reflux in pyridine (30 mL) and triethyl orthoformate (2.4 mmol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflux for an additional 4 hours and cooled to room temperature. 'The solvents are removed under reduced pressure and the solid is azeotroped two times with methanol.
The purple solid is purified by Reversed Phase Chromatography and the isolated products are passed over an AGSOW-X4, 200-400 mesh K+ form, column to give 1-jN-[3-(tert-butyloxycarbonylamino)-propyl]hexanannideJ-2-[3-[1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylideneJ-1-propenylJ-3,3-dimethyl-S-suifo-3H-indolium; potassium salt (S2), 1-[N-[3-(teat-butyloxycarbonyl-amino) propyl]hexanamide]-2-[3-[ 1-[N-[3-(tert-butyloxycarbonylamino)-propyl]hexanamide]-1,3-dihydro-3,3-dimethyl-S-suifo-2H-indol-2-ylidene)-1-propenyl]-3,3-dimethyl-S-sulfo-3H-indolium, potassium salt (S3) and the related S diethyl salt as solids.
Example 27 - Cyanine-5 dyes derived from (51).
A solution of (S1) (0.291 mmol) and (14) (0.292 mmol) and potassium acetate (78 mg, 0.79 mmoi) in methanol (1S mL) is heated to reflex and 1,3,3-trimethoxypmpene (O.S mL, 3.64 mrnol) is added via syringe over 1 hour in four equal portions. The suspension is then heated to reflex for an additional 3 hours and cooled to room temperature. The methanol is removed under reduced pressure and the solid is purified by Reversed Phase t:hromatography to give 1-[N-[3-(tert-butyloxycarbonylamino)propyl]-hexanamide]-2-[S-[1-ethyl-1,3-dihydro-3,3-dimethyl-S-sulfo-2H-indol-2-ylidene]-1,3-pentadienyl]-3,3-dimethyl-1S S-sulfo-3H-indolium, potassium salt (S4), 1-[N-j[3-{tert-butyloxycarbonyl-amino)propyl]hexanamide]-2-[S-[ 1-[N-[3-(tent-butyloxycarbonylamino)propyl]-hexanamide]-1,3-dihydro-3,3-dimethyl-S-sulfo-2H-indol-2-ylidene]-1,3-pentadienyl]-3,3-dimethyl-S-sulfo-3H-indolium, potassium salt (SS) and the related diethyl salt as solids.
Example 28 - Bonding of dye (44) to a target nucleotide derivative.
To a 2 mL vial with a stir bar is added (44) ( 17 ~nol) and 1 M potassium phosphate (4.0 mL) and methanol (2 mL) and the resulting solution is stirred at room temperature for 1 hour to give 1-[3-thiopropyl] ~-[S-[1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadlienyl]-3,3-dimethyl-3H-indolium, inner salt (56). To this solution is added (36) (34 ~nol) and the reaction mixture is stirred for 1 hour and then purified to give 5-[3-[3-[3-[1-[3-thiopmpyl]-2-[5-[1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-uidol-2-ylidene]-1,3-5 pentadienyl]-3,3-dimethyl-3H-indolium]-2,5-pyrrolidindione]prapanamido]-1-propynyl]-2'-deoxycytidine triphosphate (46).
Example 29 - Bonding dye (15) with streptavidin.
Streptavidin (15 mg) is dissolved in 1 rnL O.1M sodium phosphate buffer, pH 7Ø Sulfosuccinimidyl4-[N-maleimidomethyl] cyclohexane-1-carboxylate (9 10 mg) in 0.2 mL dimethylsulfoxide is added to the streptavidin solution at room temperature, mixed for 1 hour and purified by gel filtration chromatography to give maleimide derivatized streptavidin. To a 1.5 mL solution of maleimide derivatized streptavidin (3.5 mg) in 0.1 M sodium phosphate, 5 mM EDTA buffer, pH 6.0, 1 mg of Cyanine 3 Dye (15) is added followed by 0.15 mL of 1M
15 hydroxylamine pH 7Ø The solution is mixed at room temperature for 1 hour and then 20 p,L of O.1M N-ethyhnaleimide is added and the mixture is stored at 4°C
for 16 hours. The mixture is purified by geI filtration chromatography to give streptavidin modified with Cyanine 3 Dye (15).
Example 30 - Banding dye 16 with streptavidin.
20 Streptavidin (15 mg) is dissolved in 1 mL O.1M sodium phosphate buffer, pH 7Ø Sulfosuccinimidyl 4-jN-maleimidomethyl] cyclohexane-1-carboxylate (9 mg) in 0.2 mL dimethylsulfoxide is added to the streptavidin solution at room temperature, mixed for 1 hour and purified by gel filtration chromatography to give maleimide derivatized streptavidin. To a 1.5 ;mL solution of maleimide derivatized streptavidin (3.5 mg) in O.1 M sodium phosphate, 5 mM EDTA bu#~er, pH 6.0, 1 mg of Cyanine 3 Dye (16) is added folllowed by 0.15 mI, of 1M
hydroxylamine pH 7Ø The solution is mixed at room temperature for 1 hour and S then 20 u.L of O.1M N-ethylmaleimide is added and the mixture is stored at 4°C
for 16 hours. The mixture is purified by gel filtration chromatography to give streptavidin modified with Cyanine 3 Dye (16).
Example 31 - Bonding of dye (15) with neurotensin on resin.
Fmoc-Neurotensin on Resin (Wang polymer) 100 mg (substitution 0.6 mmol/g) is swelled in dimethy formamide {DMF} for :30 minutes where Fmoc has the structure:
(57) Fmoc is removed by reaction with 25% Piperidine/D:~ (about 20 ml x 3 min, wash with DMF, and 20 ml x 20 min). Resin is washed with DMF 7 x 20 ml (1 rnin each washing step). 25 mg of (N-[gamma-malemadobutryioxy]succinimide IS ester (Sulfo-GMBS) in DMF (15 ml) is added and mixed with resin 24 hours.
After reaction the resin is washed 7 x 20 ml of DMF. Cyanine (15) {10 mg) solution in DMF/methanol (15 ml) is added along v~rith 5 ml 1 M solution of hydroxylamine in water. Reaction is performed overnight. After washing with DMF (7 x 20 mI) and methanol (3 x 30 ml) resin is .dried. Labeled peptide is cleaved from resin with Reagent K (92.5% TFA/2.5% EDT/2.5% water/2.5% TIS) ml for 2 hours. Crude peptide is precipitated with cold diethyl ether and centrifuged. Precipitate is dissolved in 50% Acetonitrilelwater and lyophilized.
Example 32 - Bonding of dye (15) with galanin on resin.
5 Fmoc-Galinin on Resin is swelled as in Example 31. Orthogonal protection on Lys 25 ((4,4-dimethyl-2,6 dioxocycIohex-1-ylidene)ethyl-Dde) is removed by reaction with 2% hydrazine hydrate (2 :K 20 ml, 2 min). Resin is washed 6 times with DMF (20 ml}. 25 mg of Sulfo-GMBS in DMF (15 ml) is added and mixed with resin for 24 hours. After reaction the resin was washed 7 x 10 20 ml of DMF, { 1 S) ( 10 mg) solution in DMF/MeOH ( 15 ml} is added along with 5 rnl 1 M solution of hydroxylamine in water. Reaction is performed overnight.
Labeled galanin is purified and isolated as per Example 32.
Example 33 - Bonding of dye (29) with a native peptide - bradykinin.
Bradykinin {3 mg) dissolved in 1 ml of 50 mM sodium dihydrogen phosphate pH 7.5, and added sulfoGMBS (3.4 mg), rnixed for 2 hours in room temperature. To the reaction mixture is added 1 ml of solution {5.8 mg) of (29) in sodium dihydrogen phosphate pH 7.5 and 0.5 ml 1 M hiydroxylamine (pH 7), and mixed overnight. Labeled peptide is lyophilized.
E%ample 34 - Bonding of dye (29} with liposomes.
ZO The procedure of Example 33 is repeated with the substitution of liposomes as per Example 1 of U.S. Patent 4,089,801 for bradykinin, where the Iiposome includes lecithin and amyloglucoside therein. A labeled liposome is purified therefrom.

Example 35 - Bonding of 1-(3-N-acetylaminopropyl]-2-[5-1-[ethyl-1,3 dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene]-1,3-pentadienyl]-3,3-dimethyl-5-sulfo-3H-indolium, potassium salt (58) to a target nucleotide derivative.
The dye (58) is prepared as per Examples I and I 1 using the amine analog to the dye precursor (5). The dye (58) is combined with (36) as per Example 28 to yield the amine analog to (46).
Those skilled in the art will appreciate from the foregoing description and examples that the broad teaching ofthe present invention can be irnpiernented in a variety of forms. Therefore, while this invention has been described in connection with particular examples thereof, the true scope of the invention should not be so limited since other modifications will become apparent to one skilled in the art upon review of the specification and the following claims.
All patents and other publications cited herein sire expressly incorporated by reference to the same extent as if each individual publication were specifically and individually indicated to be incorporated by reference.

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Claims

1. A compound of the formula:
wherein Y1 is selected from a group consisting of:
wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, a C0-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonyl, carboxyl, hydroxyl, substituted amines and quaternary amines;
wherein R9, R9', R10 and R10' are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S; and wherein R11 is selected from a group consisting of:

wherein R13, R'13, R"13 and R'''13 are each independently C1-C30 alkyl, Q is sulfur, nitrogen-hydrogen or oxygen, X is a halogen and Y is a halogen.

2. The compound of claim 1 wherein R11 reacts with a deprotecting agent to form a reactive group selected from a group consisting of: thiol, amine and hydroxyl.

3. The compound of claim 1 wherein R13 comprises more than two carbon atoms.

4. The compound of claim 1 wherein at least two adjacent R groups of R1-R4, R9, R9', R10 and R10' are fused to form a ring structure.

5. The compound of claim 1 wherein at least one of R1-R4, R9, R9', R10 and R10' is the C0-C4 alkyl group having the hydrophilic substituent.

6. A compound of the formula:
wherein Y1 is selected from a group consisting of:

wherein R1, R2, R3, and R4 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, a C0-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate;
carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein R9 and R10 are each independently selected from a group consisting of C1-C30 alkyl, and a heteroatom substituted C1-C30 alkyl wherein the heteroatom is O, N or S;
wherein R11 is selected from a group consisting of R14SH, R14NH2 and R14OH; and wherein R14 is selected from a group consisting of C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonyl, or halogen atom or a heteroatom substituted phenyl.

7. The compound of claim 6 wherein at least one of R1-R4, R9, R9', R10 and R10' is the C0-C4 alkyl group having the hydrophilic substituent.

8. The compound of claim 6 wherein at least two adjacent R groups of R1-R4, R9, R9', R10 and R10' are fused to form a ring structure.

9. A process for preparing a compound (1) as claimed in claim 1 which comprises:
reacting a nitrogen containing heterocyclic compound with XR13Q moiety of a bifunctional hydrocarbon wherein X is chlorine, bromine or iodine, R13 is C1-C30 alkyl and Q is sulfur, nitrogen or oxygen.

10. The process of claim 9 wherein Q is sulfur.

11. The process of claim 9 wherein said bifunctional hydrocarbon is a thiol.

12. The process of claim 9 wherein said bifunctional hydrocarbon is an amine.

13. The process of claim 9 wherein said bifunctional hydrocarbon is an alcohol.

14. The process of claim 9 wherein said bifunctional hydrocarbon comprises a protected substituent of Q.

15. A dye compound comprising the formula:

wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, a C0-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines;
wherein Y1 and Y2 are each independently selected from a group consisting of:
wherein R9, R'9, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11 and R12 are each independently selected from a group consisting of C1-C30 alkyl, phenyl substituted C1-C30, C1-C30 having a protected substituent selected from a group consisting of:

wherein R13, R'13, R"13 and R"13 are each independently C1-C30 alkyl; Q is sulfur, nitrogen or oxygen, X is a halogen and Y is a halogen and at least one of R11 and R12 is the C1-C30 having the protected substituent; and L is selected from a group consisting of methine, a methine group having a substituent C1-C30 alkyl group and a substituted C1-C30 alkyl group having a phenyl, hydroxyl, sulfanyl, a halogen atom, a heteroatom substituted phenyl and a C1-C4 alkoxyl where n is 1, 2, 3 or greater.

16. The dye compound of claim 15 wherein at least one of R1-R12, R9' and R10' is the C0-C4 alkyl group having the hydrophilic substituent.

17. The dye compound of claim 15 wherein at least two adjacent R
groups of R1-R8, R9, R9', R10 and R10' are fused to form a ring structure.

18. The dye compound of claim 15 wherein both R11 and R12 are the C1-C30 having the protected substituent.

19. The dye compound of claim 15 wherein only one of R11 and R12 are the C1-C30 having the protected substituent.

20. The dye compound of claim 15 wherein the protected substituent reacts with a deprotecting agent to form a reactive group selected from a group consisting of: thiol, amine and hydroxyl.

21. A dye compound comprising the formula:

wherein R1, R2, R3, R4, R5, R6, R7, and R8 are each independently selected from a group consisting of hydrogen, C1-C6 alkyl group, a C0-C4 alkyl group having a hydrophilic substituent selected from a group consisting of sulfonate, carboxylate, hydroxyl, substituted amines and quaternary amines, such that at least one of R1-R12, R9' and R10' is the C0-C4 alkyl group having the hydrophilic substituent;

wherein Y1 and Y2 are each independently selected from a group consisting of:

wherein R9, R'9, R10, and R'10 are each independently selected from a group consisting of C1-C6 alkyl, and a heteroatom substituted C1-C6 alkyl wherein the heteroatom is O, N or S;
wherein R11, and R12 are each independently selected from a group consisting of R14H, and nucleophilic substituent: R14SH, R14NH2 and R14OH;
wherein R14 is selected from a group consisting of C3-C30 alkyl and C3-C30 alkyl having a phenyl, hydroxyl, sulfonyl, or halogen atom or a heteroatom substituted phenyl; and L is selected from a group consisting of methine, a methine group having a substituent C1-C30 alkyl group and a substituted C1-C30 alkyl group having a phenyl, hydroxyl, sulfonyl, a halogen atom, a heteroatom substituted phenyl and a C1-C4 alkoxyl where n is 1, 2, 3 or greater.

22. The dye compound of claim 21 wherein at least two adjacent R
groups of R1-R8, R9, R9', R10 and R10' are fused to form a ring structure.

23. The dye compound of claim 21 wherein R11 and R12 are both the nucleophilic substituents.

24. The dye compound of claim 21 wherein only one of R11 and R12 is the nucleophilic substituent.

25. A process for preparing a compound (2) as claimed in claim 15 which comprises reacting a compound (1) with a molecule selected from the group consisting of: trialkyl orthoformate, dialkyl amide, trialkoxy alkene and C3-bisaldehyde wherein the alkyl and alkoxy groups are independently C1-C6 and the alkene is C3 or C5 in the presence of a base and the C3-C12 bisaldehyde in the presence of an alcohol.

26. A process for preparing a compound (2) as claimed in claim 21 which comprises reacting a compound (1) with a molecule selected from the group consisting of: trialkyl orthoformate, dialkyl amide, trialkoxy alkene and C3-bisaldehyde wherein the alkyl and alkoxy groups are independently C1-C6 and the alkene is C3 or C5 in the presence of a base and the C3-C12 bisaldehyde in the presence of an alcohol.

27. The process of claim 25 wherein the base is selected from a group consisting of: pyridine, C1-C4 alkoxide and C1-C4 morpholine, piperidine, t-butyl amine, triethylamine, and an amine.

28. A process for coupling said compound of claim 15 to a target molecule which comprises:
reacting said compound (2) wherein R11, or R12 comprises a heteroatom containing protected substituent, with a deprotecting agent wherein the heteroatom is selected from a group consisting of sulfur, nitrogen and oxygen; and introducing said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).

29. A process for coupling a compound of claim 21 to a target molecule which comprises:
reacting said compound (2) wherein R11 or R12 comprises amine or hydroxyl with said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).

30. A process for coupling a compound of claim 21 to a target molecule which comprises:
reacting said compound (2) wherein R11 ar R12 comprises a thiol with said target molecule containing a moiety susceptible to nucleophilic addition of said compound (2).

31. The process of claim 28 wherein said target molecule selected from a group consisting of organic molecules, polymers, siliceous materials, natural and synthetic: lipid vesicles, peptides, nucleic acids, nucleotides, nucleosides, DNA, RNA, proteins, carbohydrates, oligosaccharides, polysaccharides, antibodies, cellular receptors, antigens, haptens, lectins, avidins, streptavidins, lymphokines, hormones, metabolites, toxins, virions, bacteria, fungal components, esinophils, eukaryotic cells, and derivatives thereof.

32. A compound (2) as claimed in claim 15 for use as a fluorescent dye.

33. Use of a compound (2) for labeling a target molecule.

34. A commercial package comprising a compound (2) according to claim 15 as an active ingredient together with instruction for the use thereof as a dye or hapten.

35. A commercial package comprising a compound (2) according to claim 21 as an active ingredient together with instruction for the use thereof as a dye or hapten:

36. A compound according to claim 15 substantially as described herein in any of the examples.

37. A compound according to claim 21 substantially as described herein in any of the examples.

38. The process of claim 29 wherein said target molecule selected from a group consisting of: organic molecules, polymers, siliceous materials, natural and synthetic: lipid vesicles, peptides, nucleic acids, nucleotides, nucleosides, DNA, RNA, proteins, carbohydrates, oligosaccharides, polysaccharides, antibodies, cellular receptors, antigens, haptens, lectins, avidins, streptavidins, lymphokines, hormones, metabolites, toxins, virions, bacteria, fungal components, esinophils, eukaryotic cells, and derivatives thereof.

39. The dye compound of claim 19 wherein the C1-C30 having the protected substituent is a sulfur containing moiety.

40. The dye compound of claim 19 wherein the R11, or R12 group lacking the protected C1-C30 protected substituent is the C1-C30 alkyl.

41. The dye compound of claim 21 wherein one of R11 or R12 is R14SH
and the other of R11 or R12 is R14H.

42. A compound comprising an indole nucleus having substituents wherein the substituents at indole positions 1-7 are each independently selected from a group consisting of hydrogen and C1-C30 alkyl, wherein at least one of the

43 substituents at positions 1-7 is C1-C30 alkyl and at least one of the substituents at positions 1-7 is C1-C30 alkyl having a phenyl, hydroxyl, carboxyl, sulfonyl, amine, thiol or halogen atom or a heteroatom substituted phenyl.

43. The compound of claim 42 wherein the indole position 2 substituent is methyl and the indole position 1 substituent is selected from alkyl and C1-C30 alkyl, having a phenyl, hydroxyl, carboxyl, sulfonyl, amine, thiol or halogen atom or a heteroatom substituted phenyl, and at least one of the substituents at positions 3-7 is C0-C30 alkyl.