Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1991 Jun 11;19(11):3073–3080. doi: 10.1093/nar/19.11.3073

Structural and kinetic aspects of chemical reactions in DNA duplexes. Information on DNA local structure obtained from chemical ligation data.

N G Dolinnaya 1, A V Tsytovich 1, V N Sergeev 1, T S Oretskaya 1, Z A Shabarova 1
PMCID: PMC328273  PMID: 2057363

Abstract

Chemical ligation of oligonucleotides in double-stranded helices has been considered in its structural-kinetic aspect. A study was made of (i) two series of DNA duplexes with various arrangements of reacting groups in the ligation junction induced by mispairing or by alteration of furanose structure (the replacement of dT unit with rU, aU, IU, xU, dxT ones) and of (ii) eight synthetic water-soluble carbodiimides with different substituents at N1 and N3 atoms. We assumed that some information on the local structure of modified sites in the duplex can be obtained from kinetic parameters of oligonucleotide coupling reaction. The ratio of kinetic constants k3/(k2 + k3) for productive and nonproductive decomposition of the activated phosphomonoester derivative apparently reflects the reaction site structure: for a given duplex this parameter is virtually independent of the condensing agent composition. Based on the analysis of the chemical ligation kinetics a suggestion has been made about the conformation of some modified units in the double helix.

Full text

PDF
3073

Images in this article

3076Image
on p.3076
3077Image
on p.3077
3077Image
on p.3077
3078Image
on p.3078

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Dolinnaya N. G., Sokolova N. I., Gryaznova O. I., Shabarova Z. A. Site-directed modification of DNA duplexes by chemical ligation. Nucleic Acids Res. 1988 May 11;16(9):3721–3738. doi: 10.1093/nar/16.9.3721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Doornbos J., Barascut J. L., Lazrek H., Imbach J. L., van Westrenen J., Visser G. M., van Boom J. H., Altona C. Conformational analysis of oligoarabinonucleotides. An NMR and CD study. Nucleic Acids Res. 1983 Jul 11;11(13):4583–4600. doi: 10.1093/nar/11.13.4583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Jacobson B. S., Fairman K. R. A colorimetric assay for carbodiimides commonly used in peptide synthesis and carboxyl group modification. Anal Biochem. 1980 Jul 15;106(1):114–117. doi: 10.1016/0003-2697(80)90125-6. [DOI] [PubMed] [Google Scholar]
  4. Kalnik M. W., Norman D. G., Li B. F., Swann P. F., Patel D. J. Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. Role of flanking sequence and temperature in modulating the equilibrium between looped out and stacked thymidine bulge states. J Biol Chem. 1990 Jan 15;265(2):636–647. [PubMed] [Google Scholar]
  5. Mellema J. R., Haasnoot C. A., van der Marel G. A., Wille G., van Boeckel C. A., van Boom J. H., Altona C. Proton NMR studies on the covalently linked RNA-DNA hybrid r(GCG)d(TATACGC). Assignment of proton resonances by application of the nuclear Overhauser effect. Nucleic Acids Res. 1983 Aug 25;11(16):5717–5738. doi: 10.1093/nar/11.16.5717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. OHTSUKA E., MOON M. W., KHORANA H. G. STUDIES ON POLYNUCLEOTIDES. 43. THE SYNTHESIS OF DEOXRIBOPOLYNUCLEOTIDES CONTAINING REPEATING DINUCLEOTIDE SEQUENCES. J Am Chem Soc. 1965 Jul 5;87:2956–2970. doi: 10.1021/ja01091a028. [DOI] [PubMed] [Google Scholar]
  7. Ohtsuka E., Ishino Y., Ibaraki K., Ikehara M. Recognition by restriction endonuclease EcoRI of deoxyoctanucleotides containing modified sugar moieties. Eur J Biochem. 1984 Mar 15;139(3):447–450. doi: 10.1111/j.1432-1033.1984.tb08025.x. [DOI] [PubMed] [Google Scholar]
  8. Pieters J. M., Mans R. M., van den Elst H., van der Marel G. A., van Boom J. H., Altona C. Conformational and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments. Nucleic Acids Res. 1989 Jun 26;17(12):4551–4565. doi: 10.1093/nar/17.12.4551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Roongta V. A., Jones C. R., Gorenstein D. G. Effect of distortions in the deoxyribose phosphate backbone conformation of duplex oligodeoxyribonucleotide dodecamers containing GT, GG, GA, AC, and GU base-pair mismatches on 31P NMR spectra. Biochemistry. 1990 Jun 5;29(22):5245–5258. doi: 10.1021/bi00474a005. [DOI] [PubMed] [Google Scholar]
  10. Roy S., Sklenar V., Appella E., Cohen J. S. Conformational perturbation due to an extra adenosine in a self-complementary oligodeoxynucleotide duplex. Biopolymers. 1987 Dec;26(12):2041–2052. doi: 10.1002/bip.360261206. [DOI] [PubMed] [Google Scholar]
  11. Shabarova Z. A. Chemical development in the design of oligonucleotide probes for binding to DNA and RNA. Biochimie. 1988 Oct;70(10):1323–1334. doi: 10.1016/0300-9084(88)90003-x. [DOI] [PubMed] [Google Scholar]
  12. Shabarova Z. A., Veiko V. P., Dolinnaia N. G., Drutsa V. L., Metelev V. G. Khimicheskie reaktsii v dvuspiral'nykh nukleinovykh kislotakh. III. Sintez kontsevykh invertirovannykh povtorov IS1-élementa. Bioorg Khim. 1987 May;13(5):628–642. [PubMed] [Google Scholar]
  13. Tsytovich A. V., Dolinnaia N. G., Shabarova Z. A. T4-DNK-ligaza: substratnye svoistva sinteticheskikh DNK-dupleksov so strukturnymi anomaliiami. Mol Biol (Mosk) 1988 May-Jun;22(3):690–699. [PubMed] [Google Scholar]
  14. Werntges H., Steger G., Riesner D., Fritz H. J. Mismatches in DNA double strands: thermodynamic parameters and their correlation to repair efficiencies. Nucleic Acids Res. 1986 May 12;14(9):3773–3790. doi: 10.1093/nar/14.9.3773. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES