WO1990009786A1 - Heterologous block oligomers - Google Patents
Heterologous block oligomers Download PDFInfo
- Publication number
- WO1990009786A1 WO1990009786A1 PCT/US1990/000884 US9000884W WO9009786A1 WO 1990009786 A1 WO1990009786 A1 WO 1990009786A1 US 9000884 W US9000884 W US 9000884W WO 9009786 A1 WO9009786 A1 WO 9009786A1
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- WO
- WIPO (PCT)
- Prior art keywords
- block
- blocks
- heterologous
- oligomer
- dna
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
Definitions
- This invention relates to synthetic oligomers of unique three-dimensional structure that combine the principles of polymer, peptide and synthetic DNA chemistry to provide rationally designed drugs, drug delivery systems, research tools and other products.
- oligomer component consisting of at least three blocks.
- Oligomer A molecule having from about 12 to about 150 monomers, e.g., carbon atoms, amino acid residues or nucleotides and comprising at least one unit.
- Self-Association The capability shared by two or more blocks to form a mutual linkage, e.g., the capability of homologous nucleic acid sequences to hybridize and of certain peptides to interact.
- Homologous Bloc One of a series of blocks whose members exhibit common properties, for example, one of a series of nucleic acid, peptide or organic polymer blocks.
- Organic polymer blocks may generally comprise straight or branched chain polyolefins such as polyethylene, polypropylene or polystyrene and other kinds of polymers which are not cross-linked.
- Heterologous Block One of a series of blocks whose members do not exhibit common properties.
- Heterologous Block Oligomer (HBO)—An oligomer comprising at least one unit of the schematic formula A1-B-A2 in which the block B is heterologous with respect to at least one of the blocks Ai and A2 and is constrained into a generally looped configuration by the self-association energy of the blocks A ⁇ and A2 or in which the blocks Ai and A2 are heterologous and are constrained into a spatially juxtaposed position by the internal self-association of the block B.
- SUMMARY OF THE INVENTION HBO's provide a broad spectrum of novel molecules. The new molecules may be predesigned to achieve objectives which have been realized, with some difficulty, if at all.
- HBO detergents can be formed with self-associated DNA blocks joined by simple linker blocks. The properties of these detergent molecules can be exploited in several ways. Micelles formed primarily of the self-associated DNA blocks may permit the passage of any short, double-stranded DNA through the bloodstream. Antisense molecules and short duplex DNA's more intrinsically resistant to DNase could be delivered in this fashion. "Suicide" substrates of duplex DNAs can be constructed to target tissues and neoplastic or virus infected cells. The inclusion of a hydrophobic linker block in these HBOs facilitates diffusion or transport across cell membranes at the requisite site.
- FIGURES Figure 1 is a two-dimensional generalized schematic depiction of an HBO in which the A ⁇ and A2 blocks are self-associated.
- the Ai and A2 blocks may be self-associating oligonucleotides, peptides or the like and the linker block B provides a preselected property, e.g., hydrophobicity.
- linker block B may be nucleic acid sequences when the Ai and A2 blocks are self-associating peptides.
- Formula I schematically represents one form of an HBO of the kind depicted by Figure 1:
- R is an alkyl or aryl group of from about l to about 10 carbon atoms and x may be from about 3 to about 12. When x is greater than about 10, these HBO's are surfactive.
- n The number, n, of B block moieties depends upon the properties desired in the HBO. For many purposes n is from about 5 to about 20.
- Figure 2 depicts an HBO in which the linker block B is internally self-associating, e.g., a homologous DNA sequence, flanked by ⁇ and A2 blocks such as peptides or organic polymers which do not self-associate and which are constrained in juxtaposition by the self-association energy of the linker block.
- Suitable DNA sequences for the B blocks of such HBOs include a stretch of hydrized nucleotides, generally a sequence of about 15 to 50 bases to provide the self-association energy appropriate to maintain the desired juxtaposition of the Ai and A2 blocks.
- Suitable peptides for use as A blocks contain from about 5 to about 30 residues.
- Suitable A block polymers include RNA, DNA, peptides or mixed RNA-DNA polymers having 12 to 150 nucleotides.
- Appropriate selection of the Ai, B and A2 blocks yields bioengineered catalysts in which catalysis is carried out by an appropriately constrained peptide, protein or RNA block.
- hydrophobic B blocks e.g., amino-alkyl phosphonates, amino-aryl phosphonates, yield HBOs which are surfactants, particularly when the self-associating blocks are DNA.
- Figure 3 is a copy of an autoradiograph illustrating the utility of an HBO as a human methyl transferase substrate.
- Figure 4 illustrates a three nucleotide rule DNA methylation with DNA methyl transferase.
- This example demonstrates the scope and significance of the invention. To do so, it identifies a specific question which has arisen in scientific research, describes the design of an HBO for use in answering the question, exemplifies the synthesis of the postulated HBO and shows that the synthesized HBO functions as intended.
- the question addressed concerns the substrate specificity of the human DNA methyltransferase, i.e., whether the enzyme is capable of methyla ing across a gap in duplex DNA.
- a 30 mer and a 13 er were selected to provide a gapped duplex DNA as depicted by Formula II:
- linker block raised two questions: (1) what moiety should be used to construct it, and (2) how long should it be? Hydrophobic moieties were rejected to preclude any test of the capability of the enzyme to interact with a detergent.
- L is — HN—(CH 2 ) 3 —O—P- li 0
- Oliqodeoxynucleotide Preparation and Characterization Single strand oligodeoxynucleotides were synthesized using the phosphoramidite method (Sinha, N.D., et al.. Nucleic Acids Res. 12:4539-4557 (1984)). The single stranded products were purified by polyacrylamide gel electrophoresis and high performance liquid chromatography as described by Tan, et al., Cold Spring Harbor Symp. on Quantitative Biology XLVII 383-391 (1982) . The sequence of each of the oligodeoxynucleotides was verified using the method of Maxam and Gilbert.
- Duplex Oligodeoxynucleotides Oligodeoxynucleotide concentrations were determined from absorbance at 260 nm. Duplex oligodeoxynucleotides were annealed from equimolar amounts of each single strand, as described in Smith, S.S., et al.. Nucleic Acids Res. 15:6899-6916 (1987) . The formation of duplex molecules was confirmed by electrophoretic separation of 32 P end-labelled duplexes (Smith, supra) on non-denaturing polyacrylamide gels. See Maniatis, T., et al. Biochemistry 14:3787-3794 (1975). End-labelled duplex molecules were further characterized by restriction analysis also as previously described in Smith.
- the HBO was synthesized in a manner similar to the standard production of oligodeoxynucleotides.
- the amino group is protected by a monomethyoxyl trityl MMT or dimethoryl trityl DMT group and the phosphate group is simultaneously activated. After the MMT or DMT group was removed, the amino group was neutralized after each addition so that the next monomer could be added.
- the HBO product of this example is an excellent substrate for human DNA methyltransferase as evidenced by the following test which is dependent on the spatial conformation of the molecule.
- DNA(cytosine-5)methyltransferase was purified from human placentas as described in Smith, supra. When stored under the conditions described there, the enzyme loses less than 50% of its activity per year at -70 ⁇ C. Two sets of assay conditions were employed. The unit of enzyme activity is defined in terms of the assay conditions used during enzyme puri ication with heat-denatured Micrococcus lysodeikticus DNA substrate (Smith supra) . A unit of enzyme activity is the amount required to catalyze the incorporation of 1 pmole of methyl groups into TCA insoluble DNA in one hour at 37°C under those conditions.
- the enzyme was dialyzed for 3 hours in a Hoefer microdialyzer (Health Products Inc., Rockford, 111.) against 38 M glycine, 17% v/v glycerol, 5 mM Tris, 10 mM ⁇ -mercaptoethanol, pH 7.8 at 4*C.
- the final reaction volume of 100 ⁇ l contained: 0.4 ⁇ g total DNA, 50 mM HEPES pH 7.0, 50 mM NaCl, 2 mM DTT, 75 ⁇ Spermine, 10% v/v glycerol and 6.0 mM [ 3 H]AdoMet (Amersham, 15 Ci/mmole) .
- Reaction mixtures were pre-incubated at 37 ⁇ C for 15 minutes before the addition of 44 U of DNA methyltransferase to initiate the reaction. The reaction rate was linear under these conditions for 30 minutes. After 20 minutes of incubation, the reactions were stopped by the addition of 5 ml of cold TCA (5% w/v TCA containing 5 mM potassium pyrophosphate) . Tritium incorporated into TCA insoluble DNA was determined as previously described (Smith, S.S., supra) .
- the labelled duplexes were cleaved with restriction endonucleases Mbol and Mspl.
- the products were electrophoretically separated and 3 H labelled DNA fragments were detected by fluorescence enhanced autoradiography as previously described in Smith, et al.
- the HBO molecule is refractory to digestion by Mspl, consistent with the fact that the looped molecule cannot generate a complete duplex Mspl site.
- the same molecule is cleaved by Mbol to about 70% completion.
- the cleavage product is only slightly shorter than the uncut molecule suggesting that Mbol cleavage occurs on the cut site on the unmethylated portion of the molecule to produce a molecule that is six nucleotides shorter (on the 3' end) than the parent molecule.
- This partial cleavage pattern could be produced by the presence of the linkers in the loop, or it could mean that the fold-back structure does not form in a way that provides the enzyme with a completely recognizable cleavage site.
- the DNA methyltransferase recognizes the structure and actively methylates it.
- Table I shows that the presence of a methyl group at the end of the short arm of the loop stimulates the reaction more than 100 fold (48L-1) , while the presence of the methyl group at position 17 (bases numbered from the 5' end of the molecule) (48L-2) does not stimulate the reaction rate.
- Enzymatic methylation of the HBO 48L-2 is demonstrated by the strong tritium signal in lanes 2 and 3 of the Figure 3 autoradiograph.
- HBO 48L-2 was exposed to human DNA methyltransferase in the presence of S adenosyl methionine as the methyl group donor.
- the reaction product was separated by polyacrylamide gel electrophoresis and the presence of enzymatically tritiated DNA was demonstrated by fluorescence enhanced autoradiography.
- lanes 1 and 7 include markers corresponding to 18, 24 and 30 bases.
- Mbol and Mspl identify restriction enzymes.
- HBO's of all types may be synthesized by techniques known to the skilled man.
- Linker blocks B may be added to pre-self associated A and A2 blocks as typified by the example. Alternatively, all of the blocks may be separately synthesized and the desired HBO constructed from these prefabricated blocks. Such a procedure is preferred for the production of HBO's which involve the linkage of peptide and DNA blocks.
- Example II illustrates one method for producing an HBO of schematic formula (DNA-2)-peptide-(DNA-1) .
- MMT-Cl monomethoxytrityl chloride
- the MMT-amino alkanol product is purified by chromatography and then reacted with an appropriate phosphitylating agent forming a cyanoethyl- diisopropylamino phosphite or a hydrogen phosphonate reagent or any other phosphite reagent known to the skilled worker.
- the product of this reaction is an activated phosphite reagent useful in any standard DNA synthesis machine.
- This activated phosphate reagent is coupled to the 5'OH of a growing DNA molecule synthesized in known manner on a solid support such as controlled pore glass (CPG) .
- CPG controlled pore glass
- the MMT group is then removed with dichloroacetic acid or trichloroacetic acid and the amino group is neutralized to permit coupling to the next incoming phosphite reagent.
- Neutralization is accomplished by treating the growing DNA molecule with a dilute basic solution such as 1% triethyl amine in acetonitrile for a few seconds to convert the protonated amino group into a free amino group.
- a DNA fragment with a free carboxylic acid on the 3' end is synthesized on a solid support, for example, by connecting a DMT protected hydroxy carboxylic acid such as the DMT protected 6-hydroxyhexanoic acid to an amino-propyl CPG using a carbodiimide. After the coupling, the DMT group is removed in known manner using dichloroacetic acid in dichloromethane. A second reaction with a DMT protected hydroxy carboxylic acid is completed. The DMT group is again removed and again coupled with the DMT-protected 6-hydroxyhexanoic acid using a carbodiimide and dimethylaminopyridine to provide controlled pore glass as a support for the synthesis of DNA-2 in known manner.
Abstract
Description
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Applications Claiming Priority (4)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US31493589A | 1989-02-24 | 1989-02-24 | |
US314,935 | 1989-02-24 | ||
US31767089A | 1989-03-01 | 1989-03-01 | |
US317,670 | 1989-03-01 |
Publications (1)
Publication Number | Publication Date |
---|---|
WO1990009786A1 true WO1990009786A1 (en) | 1990-09-07 |
Family
ID=26979635
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US1990/000884 WO1990009786A1 (en) | 1989-02-24 | 1990-02-23 | Heterologous block oligomers |
Country Status (5)
Country | Link |
---|---|
EP (1) | EP0428635A4 (en) |
JP (1) | JPH04501804A (en) |
AU (1) | AU5192190A (en) |
CA (1) | CA2028153A1 (en) |
WO (1) | WO1990009786A1 (en) |
Cited By (7)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO1992002534A2 (en) * | 1990-08-03 | 1992-02-20 | Sterling Drug, Inc. | Compounds and methods for inhibiting gene expression |
EP0506944A1 (en) * | 1990-10-23 | 1992-10-07 | City Of Hope | Mechanism based inhibitors of dna methyltransferase |
WO1993019768A1 (en) * | 1992-04-03 | 1993-10-14 | The Regents Of The University Of California | Self-assembling polynucleotide delivery system |
US6376248B1 (en) | 1997-03-14 | 2002-04-23 | Life Technologies, Inc. | Peptide-enhanced transfections |
US6504019B2 (en) | 2000-03-24 | 2003-01-07 | Bayer Corporation | Nucleic acid probes having highly hydrophilic non-nucleosidic tags with multiple labels, and uses thereof |
US9358300B2 (en) | 1998-11-12 | 2016-06-07 | Life Technologies Corporation | Transfection reagents |
US10195280B2 (en) | 2014-07-15 | 2019-02-05 | Life Technologies Corporation | Compositions and methods for efficient delivery of molecules to cells |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US4415732A (en) * | 1981-03-27 | 1983-11-15 | University Patents, Inc. | Phosphoramidite compounds and processes |
US4757141A (en) * | 1985-08-26 | 1988-07-12 | Applied Biosystems, Incorporated | Amino-derivatized phosphite and phosphate linking agents, phosphoramidite precursors, and useful conjugates thereof |
US4904582A (en) * | 1987-06-11 | 1990-02-27 | Synthetic Genetics | Novel amphiphilic nucleic acid conjugates |
-
1990
- 1990-02-23 AU AU51921/90A patent/AU5192190A/en not_active Abandoned
- 1990-02-23 CA CA 2028153 patent/CA2028153A1/en not_active Abandoned
- 1990-02-23 EP EP19900904153 patent/EP0428635A4/en not_active Withdrawn
- 1990-02-23 WO PCT/US1990/000884 patent/WO1990009786A1/en not_active Application Discontinuation
- 1990-02-23 JP JP50436790A patent/JPH04501804A/en active Pending
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US4415732A (en) * | 1981-03-27 | 1983-11-15 | University Patents, Inc. | Phosphoramidite compounds and processes |
US4757141A (en) * | 1985-08-26 | 1988-07-12 | Applied Biosystems, Incorporated | Amino-derivatized phosphite and phosphate linking agents, phosphoramidite precursors, and useful conjugates thereof |
US4904582A (en) * | 1987-06-11 | 1990-02-27 | Synthetic Genetics | Novel amphiphilic nucleic acid conjugates |
Non-Patent Citations (1)
Title |
---|
See also references of EP0428635A4 * |
Cited By (14)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO1992002534A3 (en) * | 1990-08-03 | 1992-06-11 | Sterling Drug Inc | Compounds and methods for inhibiting gene expression |
WO1992002534A2 (en) * | 1990-08-03 | 1992-02-20 | Sterling Drug, Inc. | Compounds and methods for inhibiting gene expression |
EP0506944A4 (en) * | 1990-10-23 | 1994-08-17 | Hope City | Mechanism based inhibitors of dna methyltransferase |
EP0506944A1 (en) * | 1990-10-23 | 1992-10-07 | City Of Hope | Mechanism based inhibitors of dna methyltransferase |
US6300317B1 (en) * | 1992-04-03 | 2001-10-09 | The Regents Of The University Of California | Self-assembling polynucleotide delivery system |
AU682308B2 (en) * | 1992-04-03 | 1997-10-02 | Regents Of The University Of California, The | Self-assembling polynucleotide delivery system |
WO1993019768A1 (en) * | 1992-04-03 | 1993-10-14 | The Regents Of The University Of California | Self-assembling polynucleotide delivery system |
AU682308C (en) * | 1992-04-03 | 2006-08-17 | Regents Of The University Of California, The | Self-assembling polynucleotide delivery system |
US6376248B1 (en) | 1997-03-14 | 2002-04-23 | Life Technologies, Inc. | Peptide-enhanced transfections |
US9358300B2 (en) | 1998-11-12 | 2016-06-07 | Life Technologies Corporation | Transfection reagents |
US6504019B2 (en) | 2000-03-24 | 2003-01-07 | Bayer Corporation | Nucleic acid probes having highly hydrophilic non-nucleosidic tags with multiple labels, and uses thereof |
US10195280B2 (en) | 2014-07-15 | 2019-02-05 | Life Technologies Corporation | Compositions and methods for efficient delivery of molecules to cells |
US10792362B2 (en) | 2014-07-15 | 2020-10-06 | Life Technologies Corporation | Compositions and methods for efficient delivery of molecules to cells |
US11872285B2 (en) | 2014-07-15 | 2024-01-16 | Life Technologies Corporation | Compositions and methods for efficient delivery of molecules to cells |
Also Published As
Publication number | Publication date |
---|---|
EP0428635A4 (en) | 1993-03-10 |
JPH04501804A (en) | 1992-04-02 |
CA2028153A1 (en) | 1990-08-25 |
AU5192190A (en) | 1990-09-26 |
EP0428635A1 (en) | 1991-05-29 |
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