Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Jan 11;16(1):319–326. doi: 10.1093/nar/16.1.319

Synthesis of DNA fragments containing 5,6-dihydrothymine, a major product of thymine gamma radiolysis.

J C Schulhof 1, D Molko 1, R Teoule 1
PMCID: PMC334629  PMID: 3340528

Abstract

5,6-Dihydrothymine is one of the most important products of base damage by gamma irradiation of DNA in anoxic conditions. This modified base is unstable in the deprotection conditions used for classical synthesis of oligonucleotides. For its incorporation in synthetic DNA fragments, a new set of amino protecting groups has been developed. The 5,6-dihydrothymidine phosphoramidite was successfully employed for the synthesis of two 14-mers and one 17-mer bearing this defect at positions corresponding to restriction enzymes sites. The presence of the modified base still intact in the oligonucleotides was evidenced by mass spectrometry in pyrolytic conditions.

Full text

PDF
319

Images in this article

323Image
on p.323

Selected References

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

  1. Efimov V. A., Reverdatto S. V., Chakhmakhcheva O. G. New effective method for the synthesis of oligonucleotides via phosphotriester intermediates. Nucleic Acids Res. 1982 Nov 11;10(21):6675–6694. doi: 10.1093/nar/10.21.6675. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Fazakerley G. V., Kraszewski A., Téoule R., Guschlbauer W. NMR and CD studies on an oligonucleotide containing N4-methylcytosine. Nucleic Acids Res. 1987 Mar 11;15(5):2191–2201. doi: 10.1093/nar/15.5.2191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ide H., Melamede R. J., Wallace S. S. Synthesis of dihydrothymidine and thymidine glycol 5'-triphosphates and their ability to serve as substrates for Escherichia coli DNA polymerase I. Biochemistry. 1987 Feb 10;26(3):964–969. doi: 10.1021/bi00377a042. [DOI] [PubMed] [Google Scholar]
  4. Li B. F., Reese C. B., Swann P. F. Synthesis and characterization of oligodeoxynucleotides containing 4-O-methylthymine. Biochemistry. 1987 Feb 24;26(4):1086–1093. doi: 10.1021/bi00378a015. [DOI] [PubMed] [Google Scholar]
  5. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  6. Molko D., Delort A. M., Guy A., Teoule R. Synthèse d'un fragment de DNA comportant la dihydro-5,6 thymine. Biochimie. 1985 Jul-Aug;67(7-8):801–809. doi: 10.1016/s0300-9084(85)80171-1. [DOI] [PubMed] [Google Scholar]
  7. Ono A., Ueda T. Synthesis of decadeoxyribonucleotides containing N6-methyladenine, N4-methylcytosine, and 5-methylcytosine: recognition and cleavage by restriction endonucleases (nucleosides and nucleotides part 74). Nucleic Acids Res. 1987 Jan 12;15(1):219–232. doi: 10.1093/nar/15.1.219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Schulhof J. C., Molko D., Teoule R. The final deprotection step in oligonucleotide synthesis is reduced to a mild and rapid ammonia treatment by using labile base-protecting groups. Nucleic Acids Res. 1987 Jan 26;15(2):397–416. doi: 10.1093/nar/15.2.397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Seela F., Kehne A. Palindromic octa- and dodecanucleotides containing 2'-deoxytubercidin: synthesis, hairpin formation, and recognition by the endodeoxyribonuclease EcoRI. Biochemistry. 1987 Apr 21;26(8):2232–2238. doi: 10.1021/bi00382a024. [DOI] [PubMed] [Google Scholar]
  10. Sinha N. D., Biernat J., McManus J., Köster H. Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucleic Acids Res. 1984 Jun 11;12(11):4539–4557. doi: 10.1093/nar/12.11.4539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Tanaka T., Letsinger R. L. Syringe method for stepwise chemical synthesis of oligonucleotides. Nucleic Acids Res. 1982 May 25;10(10):3249–3260. doi: 10.1093/nar/10.10.3249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Téoule R., Bonicel A., Bert C., Cadet J., Polverelli M., Fougué B. Hgammadrolgammases acide et enzymatique du fragment thymine modifié et lié à la chaîne polynucléotidique après irradiation y in vitro de l'ADN de E. coli. C R Acad Sci Hebd Seances Acad Sci D. 1974 Dec 2;279(23):1797–1799. [PubMed] [Google Scholar]
  13. Webb T. R., Matteucci M. D. Hybridization triggered cross-linking of deoxyoligonucleotides. Nucleic Acids Res. 1986 Oct 10;14(19):7661–7674. doi: 10.1093/nar/14.19.7661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Wiebers J. L. Detection and identification of minor nucleotides in intact deoxyribonucleic acids by mass spectrometry. Nucleic Acids Res. 1976 Nov;3(11):2959–2970. doi: 10.1093/nar/3.11.2959. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES