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. 1995 Nov 11;23(21):4495–4501. doi: 10.1093/nar/23.21.4495

Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies.

H Li 1, K Porter 1, F Huang 1, B R Shaw 1
PMCID: PMC307409  PMID: 7501475

Abstract

A set of three 14mer oligodeoxyribonucleotides of sequence d(5'-CTATGGCCTCAG*CT-3'/3'-GATACCGGAGTCGA-5') containing G* variants either as 2'-deoxyguanosine phosphate (unmodified), N7-cyanoborane 2'-deoxyguanosine phosphate (base-modified) or 2'-deoxyguanosine boranophosphate (backbone-modified) were synthesized by template-directed primer extension. Both the N7-cyanoborane 2'-deoxyguanosine triphosphate and 2'-deoxyguanosine alpha-boranotriphosphate nucleotides are good substrates for Sequenase. We infer that a single Sp boranophosphate linkage (which has a stereochemistry equivalent to the corresponding Rp thiophosphate analog) is formed in the backbone-modified 14mer. Thermally induced helix-coil transitions were monitored for the hybridized duplexes using UV and circular dichroism (CD) spectroscopy. The CD spectra of the two types of boron-modified hybrids closely resemble the unmodified parent duplex, forming B-type helices in 150 mM NaCl, 1 mM EDTA, 10 mM phosphate, pH 7.4, buffer. UV melting results indicate that both hybrids have stabilities comparable with the parent duplex as measured by Tm or delta G degree 25. These studies indicate that singly modified base- or backbone-boronated DNA are good analogs of normal DNA.

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Selected References

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  1. Albergo D. D., Marky L. A., Breslauer K. J., Turner D. H. Thermodynamics of (dG--dC)3 double-helix formation in water and deuterium oxide. Biochemistry. 1981 Mar 17;20(6):1409–1413. doi: 10.1021/bi00509a001. [DOI] [PubMed] [Google Scholar]
  2. Aurup H., Tuschl T., Benseler F., Ludwig J., Eckstein F. Oligonucleotide duplexes containing 2'-amino-2'-deoxycytidines: thermal stability and chemical reactivity. Nucleic Acids Res. 1994 Jan 11;22(1):20–24. doi: 10.1093/nar/22.1.20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bower M., Summers M. F., Powell C., Shinozuka K., Regan J. B., Zon G., Wilson W. D. Oligodeoxyribonucleoside methylphosphonates. NMR and UV spectroscopic studies of Rp-Rp and Sp-Sp methylphosphonate (Me) modified duplexes of (d[GGAATTCC])2. Nucleic Acids Res. 1987 Jun 25;15(12):4915–4930. doi: 10.1093/nar/15.12.4915. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Burgers P. M., Eckstein F., Hunneman D. H. Stereochemistry of hydrolysis by snake venom phosphodiesterase. J Biol Chem. 1979 Aug 25;254(16):7476–7478. [PubMed] [Google Scholar]
  5. Cech C. L., Tinoco I., Jr Circular dichroism calculations for double-stranded polynucleotides of repeating sequence. Biopolymers. 1977 Jan;16(1):43–65. doi: 10.1002/bip.1977.360160105. [DOI] [PubMed] [Google Scholar]
  6. Eckstein F. Nucleoside phosphorothioates. Annu Rev Biochem. 1985;54:367–402. doi: 10.1146/annurev.bi.54.070185.002055. [DOI] [PubMed] [Google Scholar]
  7. Freier S. M., Albergo D. D., Turner D. H. Solvent effects on the dynamics of (dG-dC)3. Biopolymers. 1983 Apr;22(4):1107–1131. doi: 10.1002/bip.360220408. [DOI] [PubMed] [Google Scholar]
  8. Heinemann U., Rudolph L. N., Alings C., Morr M., Heikens W., Frank R., Blöcker H. Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix. Nucleic Acids Res. 1991 Feb 11;19(3):427–433. doi: 10.1093/nar/19.3.427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ivanov V. I., Minchenkova L. E., Schyolkina A. K., Poletayev A. I. Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers. 1973;12(1):89–110. doi: 10.1002/bip.1973.360120109. [DOI] [PubMed] [Google Scholar]
  10. Johnson B. B., Dahl K. S., Tinoco I., Jr, Ivanov V. I., Zhurkin V. B. Correlations between deoxyribonucleic acid structural parameters and calculated circular dichroism spectra. Biochemistry. 1981 Jan 6;20(1):73–78. doi: 10.1021/bi00504a013. [DOI] [PubMed] [Google Scholar]
  11. Jäger A., Levy M. J., Hecht S. M. Oligonucleotide N-alkylphosphoramidates: synthesis and binding to polynucleotides. Biochemistry. 1988 Sep 20;27(19):7237–7246. doi: 10.1021/bi00419a010. [DOI] [PubMed] [Google Scholar]
  12. Kibler-Herzog L., Zon G., Uznanski B., Whittier G., Wilson W. D. Duplex stabilities of phosphorothioate, methylphosphonate, and RNA analogs of two DNA 14-mers. Nucleic Acids Res. 1991 Jun 11;19(11):2979–2986. doi: 10.1093/nar/19.11.2979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kim M. S., Guengerich F. P. Interactions of N7-guanyl methyl- and thioether-substituted d(CATGCCT) derivatives with d(AGGNATG). Chem Res Toxicol. 1993 Nov-Dec;6(6):900–905. doi: 10.1021/tx00036a022. [DOI] [PubMed] [Google Scholar]
  14. Liaw Y. C., Gao Y. G., Marquez V. E., Wang A. H. Molecular structures of two new anti-HIV nucleoside analogs: 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine and 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)hypoxanthine. Nucleic Acids Res. 1992 Feb 11;20(3):459–465. doi: 10.1093/nar/20.3.459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Longfellow C. E., Kierzek R., Turner D. H. Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry. 1990 Jan 9;29(1):278–285. doi: 10.1021/bi00453a038. [DOI] [PubMed] [Google Scholar]
  16. Maher L. J., 3rd, Dolnick B. J. Comparative hybrid arrest by tandem antisense oligodeoxyribonucleotides or oligodeoxyribonucleoside methylphosphonates in a cell-free system. Nucleic Acids Res. 1988 Apr 25;16(8):3341–3358. doi: 10.1093/nar/16.8.3341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Marky L. A., Canuel L., Jones R. A., Breslauer K. J. Calorimetric and spectroscopic investigation of the helix-to-coil transition of the self-complementary deoxyribonucleotide ATGCAT. Biophys Chem. 1981 Apr;13(2):141–149. doi: 10.1016/0301-4622(81)80013-0. [DOI] [PubMed] [Google Scholar]
  18. Matsukura M., Shinozuka K., Zon G., Mitsuya H., Reitz M., Cohen J. S., Broder S. Phosphorothioate analogs of oligodeoxynucleotides: inhibitors of replication and cytopathic effects of human immunodeficiency virus. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7706–7710. doi: 10.1073/pnas.84.21.7706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Miller P. S., McParland K. B., Jayaraman K., Ts'o P. O. Biochemical and biological effects of nonionic nucleic acid methylphosphonates. Biochemistry. 1981 Mar 31;20(7):1874–1880. doi: 10.1021/bi00510a024. [DOI] [PubMed] [Google Scholar]
  20. Petersheim M., Turner D. H. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 1983 Jan 18;22(2):256–263. doi: 10.1021/bi00271a004. [DOI] [PubMed] [Google Scholar]
  21. Reich N. O., Sweetnam K. R. Sequence-dependent effects on DNA stability resulting from guanosine replacements by inosine. Nucleic Acids Res. 1994 Jun 11;22(11):2089–2093. doi: 10.1093/nar/22.11.2089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Rizzo V., Schellman J. A. Matrix-method calculation of linear and circular dichroism spectra of nucleic acids and polynucleotides. Biopolymers. 1984 Mar;23(3):435–470. doi: 10.1002/bip.360230305. [DOI] [PubMed] [Google Scholar]
  23. Romaniuk P. J., Eckstein F. A study of the mechanism of T4 DNA polymerase with diastereomeric phosphorothioate analogues of deoxyadenosine triphosphate. J Biol Chem. 1982 Jul 10;257(13):7684–7688. [PubMed] [Google Scholar]
  24. Seela F., Grein T. 7-Deaza-2'-deoxyadenosine and 3-deaza-2'-deoxyadenosine replacing dA within d(A6)-tracts: differential bending at 3'- and 5'-junctions of d(A6).d(T6) and B-DNA. Nucleic Acids Res. 1992 Jul 11;20(13):2297–2306. doi: 10.1093/nar/20.9.2297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Shaw B. R., Madison J., Sood A., Spielvogel B. F. Oligonucleoside boranophosphate (borane phosphonate). Methods Mol Biol. 1993;20:225–243. doi: 10.1385/0-89603-281-7:225. [DOI] [PubMed] [Google Scholar]
  26. Sheardy R. D., Levine N., Marotta S., Suh D., Chaires J. B. A thermodynamic investigation of the melting of B-Z junction forming DNA oligomers. Biochemistry. 1994 Feb 15;33(6):1385–1391. doi: 10.1021/bi00172a014. [DOI] [PubMed] [Google Scholar]
  27. Stein C. A., Subasinghe C., Shinozuka K., Cohen J. S. Physicochemical properties of phosphorothioate oligodeoxynucleotides. Nucleic Acids Res. 1988 Apr 25;16(8):3209–3221. doi: 10.1093/nar/16.8.3209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Vyazovkina E. V., Savchenko E. V., Lokhov S. G., Engels J. W., Wickstrom E., Lebedev A. V. Synthesis of specific diastereomers of a DNA methylphosphonate heptamer, d(CpCpApApApCpA), and stability of base pairing with the normal DNA octamer d(TPGPTPTPTPGPGPC). Nucleic Acids Res. 1994 Jun 25;22(12):2404–2409. doi: 10.1093/nar/22.12.2404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Williams A. P., Longfellow C. E., Freier S. M., Kierzek R., Turner D. H. Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry. 1989 May 16;28(10):4283–4291. doi: 10.1021/bi00436a025. [DOI] [PubMed] [Google Scholar]

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