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. 1979 Sep 25;7(2):453–464. doi: 10.1093/nar/7.2.453

The synthesis of oligodeoxyribonucleotides using RNA ligase.

D M Hinton, R I Gumport
PMCID: PMC328028  PMID: 386284

Abstract

T4 RNA ligase catalyzes the addition of a single deoxyribonucleoside 3',5'-bisphosphate to the 3'-hydroxyl of oligodeoxyribonucleotides (Hinton et al. (1978) Biochemistry 17, 5091). We have determined improved conditions for this reaction which give yields equal to or greater than 85% when any of five common deoxyribonucleoside bisphosphate (pdAp, pdCp, pdGp, pdTp, or pdUp) are added to dA(PDA)4. A low ATP concentration, which is constantly maintained by a regeneration system composed of phosphocreatine, creatine kinase, and myokinase, contributes to the attainment of high yields. The addition of RNase A and spermine also enhances the rates and yields of the reactions. These conditions facilitate the use of RNA ligase as a reagent for the stepwise synthesis of DNA of defined sequence.

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Selected References

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

  1. Aune K. C., Tanford C. Thermodynamics of the denaturation of lysozyme by guanidine hydrochloride. I. Depdendence on pH at 25 degrees. Biochemistry. 1969 Nov;8(11):4579–4585. doi: 10.1021/bi00839a052. [DOI] [PubMed] [Google Scholar]
  2. 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]
  3. Bruce A. G., Uhlenbeck O. C. Reactions at the termini of tRNA with T4 RNA ligase. Nucleic Acids Res. 1978 Oct;5(10):3665–3677. doi: 10.1093/nar/5.10.3665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cameron V., Soltis D., Uhlenbeck O. C. Polynucleotide kinase from a T4 mutant which lacks the 3' phosphatase activity. Nucleic Acids Res. 1978 Mar;5(3):825–833. doi: 10.1093/nar/5.3.825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cranston J. W., Silber R., Malathi V. G., Hurwitz J. Studies on ribonucleic acid ligase. Characterization of an adenosine triphosphate-inorganic pyrophosphate exchange reaction and demonstration of an enzyme-adenylate complex with T4 bacteriophage-induced enzyme. J Biol Chem. 1974 Dec 10;249(23):7447–7456. [PubMed] [Google Scholar]
  6. 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]
  7. FELSENFELD G., HUANG S. L. Some effects of charge and structure upon ionic interactions of nucleic acids. Biochim Biophys Acta. 1961 Jul 22;51:19–32. doi: 10.1016/0006-3002(61)91012-5. [DOI] [PubMed] [Google Scholar]
  8. Glynn I. M., Chappell J. B. A simple method for the preparation of 32-P-labelled adenosine triphosphate of high specific activity. Biochem J. 1964 Jan;90(1):147–149. doi: 10.1042/bj0900147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Henner D., Further J. J. Primed and unprimed synthesis of poly (dA-dT) by calf thymus DNA polymerase alpha. J Biol Chem. 1977 Mar 25;252(6):1932–1937. [PubMed] [Google Scholar]
  10. 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]
  11. LOWRY O. H., ROSEBROUGH N. J., FARR A. L., RANDALL R. J. Protein measurement with the Folin phenol reagent. J Biol Chem. 1951 Nov;193(1):265–275. [PubMed] [Google Scholar]
  12. McCoy M. I., Lubben T. H., Gumport R. I. The purification of nuclease-free T4-RNA ligase. Biochim Biophys Acta. 1979 Mar 28;562(1):149–161. doi: 10.1016/0005-2787(79)90134-5. [DOI] [PubMed] [Google Scholar]
  13. Ohtsuka E., Nishikawa S., Sugiura M., Ikehara M. Joining of ribooligonucleotides with T4 RNA ligase and identification of the oligonucleotide-adenylate intermediate. Nucleic Acids Res. 1976 Jun;3(6):1613–1623. doi: 10.1093/nar/3.6.1613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Silber R., Malathi V. G., Hurwitz J. Purification and properties of bacteriophage T4-induced RNA ligase. Proc Natl Acad Sci U S A. 1972 Oct;69(10):3009–3013. doi: 10.1073/pnas.69.10.3009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Sninsky J. J., Last J. A., Gilham P. T. The use of terminal blocking groups for the specific joining of oligonucleotides in RNA ligase reactions containing equimolar concentrations of acceptor and donor molecules. Nucleic Acids Res. 1976 Nov;3(11):3157–3166. doi: 10.1093/nar/3.11.3157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Walker G. C., Uhlenbeck O. C., Bedows E., Gumport R. I. T4-induced RNA ligase joins single-stranded oligoribonucleotides. Proc Natl Acad Sci U S A. 1975 Jan;72(1):122–126. doi: 10.1073/pnas.72.1.122. [DOI] [PMC free article] [PubMed] [Google Scholar]

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