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. 1991 Feb 11;19(3):585–590. doi: 10.1093/nar/19.3.585

Ligation with T4 RNA ligase of an oligodeoxyribonucleotide to covalently-linked cross-sectional base-pair analogues of short, normal, and long dimensions.

A Petric 1, B Bhat 1, N J Leonard 1, R I Gumport 1
PMCID: PMC333652  PMID: 2011530

Abstract

Compounds that are covalent analogues of nucleic acid base pairs of normal, long, and short C1' to C1' dimensions [B. Devadas and N.J. Leonard (1990) J. Am. Chem. Soc., 112, 3125-3135.] have been added to the oligodeoxyribonucleotide d(A)6 with bacteriophage T4 RNA ligase as a prelude to placing them at defined loci within nucleic acid duplexes. Analogue cross sections that represent a normal Watson-Crick base pair as well as a pyrimidine-pyrimidine and a purine-purine apposition were ligated in modest yields (approximately 20%) to the oligonucleotide. Ligation conditions were optimized for each analogue, and the cross section was joined to only a single oligonucleotide in each case. The structures of the ligated products were proved by HPLC, enzymatic degradation, and spectroscopic analyses.

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Selected References

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

  1. Barrio J. R., Barrio M. C., Leonard N. J., England T. E., Uhlenbeck O. C. Synthesis of modified nucleoside 3',5'-bisphosphates and their incorporation into oligoribonucleotides with T4 RNA ligase. Biochemistry. 1978 May 30;17(11):2077–2081. doi: 10.1021/bi00604a009. [DOI] [PubMed] [Google Scholar]
  2. Brennan C. A., Manthey A. E., Gumport R. I. Using T4 RNA ligase with DNA substrates. Methods Enzymol. 1983;100:38–52. doi: 10.1016/0076-6879(83)00044-0. [DOI] [PubMed] [Google Scholar]
  3. England T. E., Uhlenbeck O. C. Enzymatic oligoribonucleotide synthesis with T4 RNA ligase. Biochemistry. 1978 May 30;17(11):2069–2076. doi: 10.1021/bi00604a008. [DOI] [PubMed] [Google Scholar]
  4. Fareed G. C., Wilt E. M., Richardson C. C. Enzymatic breakage and joining of deoxyribonucleic acid. 8. Hybrids of ribo- and deoxyribonucleotide homopolymers as substrates for polynucleotide ligase of bacteriophage T4. J Biol Chem. 1971 Feb 25;246(4):925–932. [PubMed] [Google Scholar]
  5. Gumport R. I., Hinton D. M., Pyle V. S., Richardson R. W. T4 RNA ligase as a nucleic acid synthesis and modification reagent. Nucleic Acids Symp Ser. 1980;(7):167–171. [PubMed] [Google Scholar]
  6. Hayashi K., Nakazawa M., Ishizaki Y., Obayashi A. Influence of monovalent cations on the activity of T4 DNA ligase in the presence of polyethylene glycol. Nucleic Acids Res. 1985 May 10;13(9):3261–3271. doi: 10.1093/nar/13.9.3261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hinton D. M., Baez J. A., Gumport R. I. T4 RNA Ligase joins 2'-deoxyribonucleoside 3',5'-bisphosphates to oligodeoxyribonucleotides. Biochemistry. 1978 Nov 28;17(24):5091–5097. doi: 10.1021/bi00617a004. [DOI] [PubMed] [Google Scholar]
  8. Hinton D. M., Brennan C. A., Gumport R. I. The preparative synthesis of oligodeoxyribonucleotides using RNA ligase. Nucleic Acids Res. 1982 Mar 25;10(6):1877–1894. doi: 10.1093/nar/10.6.1877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hinton D. M., Gumport R. I. The synthesis of oligodeoxyribonucleotides using RNA ligase. Nucleic Acids Res. 1979 Sep 25;7(2):453–464. doi: 10.1093/nar/7.2.453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Jay E., Bambara R., Padmanabhan R., Wu R. DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping. Nucleic Acids Res. 1974 Mar;1(3):331–353. doi: 10.1093/nar/1.3.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. McCoy M. I., Gumport R. I. T4 ribonucleic acid ligase joins single-strand oligo(deoxyribonucleotides). Biochemistry. 1980 Feb 19;19(4):635–642. doi: 10.1021/bi00545a005. [DOI] [PubMed] [Google Scholar]
  12. Pheiffer B. H., Zimmerman S. B. Polymer-stimulated ligation: enhanced blunt- or cohesive-end ligation of DNA or deoxyribooligonucleotides by T4 DNA ligase in polymer solutions. Nucleic Acids Res. 1983 Nov 25;11(22):7853–7871. doi: 10.1093/nar/11.22.7853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Rusche J. R., Howard-Flanders P. Hexamine cobalt chloride promotes intermolecular ligation of blunt end DNA fragments by T4 DNA ligase. Nucleic Acids Res. 1985 Mar 25;13(6):1997–2008. doi: 10.1093/nar/13.6.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Sgaramella V. Enzymatic oligomerization of bacteriophage P22 DNA and of linear Simian virus 40 DNA. Proc Natl Acad Sci U S A. 1972 Nov;69(11):3389–3393. doi: 10.1073/pnas.69.11.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Shabarova Z. A., Dolinnaya N. G., Drutsa V. L., Melnikova N. P., Purmal A. A. DNA-like duplexes with repetitions. III. Efficient template-guided chemical polymerization of d(TGGCCAAGCTp). Nucleic Acids Res. 1981 Nov 11;9(21):5747–5761. doi: 10.1093/nar/9.21.5747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Sokolova N. I., Ashirbekova D. T., Dolinnaya N. G., Shabarova Z. A. Chemical reactions within DNA duplexes. Cyanogen bromide as an effective oligodeoxyribonucleotide coupling agent. FEBS Lett. 1988 May 9;232(1):153–155. doi: 10.1016/0014-5793(88)80406-x. [DOI] [PubMed] [Google Scholar]
  17. Sugino A., Snoper T. J., Cozzarelli N. R. Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates. J Biol Chem. 1977 Mar 10;252(5):1732–1738. [PubMed] [Google Scholar]
  18. Uhlenbeck O. C., Cameron V. Equimolar addition of oligoribonucleotides with T4 RNA ligase. Nucleic Acids Res. 1977 Jan;4(1):85–98. doi: 10.1093/nar/4.1.85. [DOI] [PMC free article] [PubMed] [Google Scholar]

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