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Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation.

Hoehn ST, Turner CJ, Stubbe J
Nucleic Acids Res 29 3413-23 (2001)
Related entries: 1g5d, 1g5e, 1gj0

Cited: 19 times
EuropePMC logo PMID: 11504879

Abstract

The antitumor antibiotic bleomycin causes two major lesions in the deoxyribose backbone of DNA: formation of 4'-keto abasic sites and formation of strand breaks with 3'-phosphoglycolate and 5'-phosphate ends. As a model for the 4'-keto abasic site, we have characterized an abasic site (X) in d(CCAAAGXACTGGG).d(CCCAGTACTTTGG) by two-dimensional NMR spectroscopy. A total of 475 NOEs and 101 dihedral angles provided the restraints for molecular modeling. Four unusual NOEs were observed between each anomer of the abasic site and the neighboring bases. In addition, four coupling constants for adjacent protons of the deoxyribose of both the alpha and beta anomers of the abasic site were observed. The modeling suggests that for both anomers the abasic site is extrahelical, without significant distortion of the backbone opposite the lesion. The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic site in our structural model for each anomer is discussed in terms of repair of such lesions in vivo.

Articles - 1giz mentioned but not cited (1)

  1. Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation. Hoehn ST, Turner CJ, Stubbe J. Nucleic Acids Res 29 3413-3423 (2001)


Reviews citing this publication (1)

  1. Recognition of damaged DNA: structure and dynamic markers. Germann MW, Johnson CN, Spring AM. Med Res Rev 32 659-683 (2012)

Articles citing this publication (17)

  1. On the formation and properties of interstrand DNA-DNA cross-links forged by reaction of an abasic site with the opposing guanine residue of 5'-CAp sequences in duplex DNA. Johnson KM, Price NE, Wang J, Fekry MI, Dutta S, Seiner DR, Wang Y, Gates KS. J Am Chem Soc 135 1015-1025 (2013)
  2. DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J. Nucleic Acids Res 36 253-262 (2008)
  3. Pre-steady-state kinetics shows differences in processing of various DNA lesions by Escherichia coli formamidopyrimidine-DNA glycosylase. Koval VV, Kuznetsov NA, Zharkov DO, Ishchenko AA, Douglas KT, Nevinsky GA, Fedorova OS. Nucleic Acids Res 32 926-935 (2004)
  4. Conformational transitions in human AP endonuclease 1 and its active site mutant during abasic site repair. Kanazhevskaya LY, Koval VV, Zharkov DO, Strauss PR, Fedorova OS. Biochemistry 49 6451-6461 (2010)
  5. Remarkable stabilization of duplex DNA containing an abasic site by non-nucleosidic phenanthroline and pyrene building blocks. Langenegger SM, Häner R. Chembiochem 6 848-851 (2005)
  6. Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling. Sicoli G, Mathis G, Aci-Sèche S, Saint-Pierre C, Boulard Y, Gasparutto D, Gambarelli S. Nucleic Acids Res 37 3165-3176 (2009)
  7. NMR solution structures of bistranded abasic site lesions in DNA. Hazel RD, Tian K, de Los Santos C. Biochemistry 47 11909-11919 (2008)
  8. Structure and dynamics of DNA duplexes containing a cluster of mutagenic 8-oxoguanine and abasic site lesions. Zálešák J, Lourdin M, Krejčί L, Constant JF, Jourdan M. J Mol Biol 426 1524-1538 (2014)
  9. The effect of DNA damage on the formation of protein/DNA complexes. Parsian AJ, Funk MC, Tao TY, Hunt CR. Mutat Res 501 105-113 (2002)
  10. Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis. Barbado C, Córdoba-Cañero D, Ariza RR, Roldán-Arjona T. Proc Natl Acad Sci U S A 115 E916-E924 (2018)
  11. DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling. Krumkacheva OA, Shevelev GY, Lomzov AA, Dyrkheeva NS, Kuzhelev AA, Koval VV, Tormyshev VM, Polienko YF, Fedin MV, Pyshnyi DV, Lavrik OI, Bagryanskaya EG. Nucleic Acids Res 47 7767-7780 (2019)
  12. Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII. Kladova OA, Kuznetsova AA, Fedorova OS, Kuznetsov NA. Genes (Basel) 8 E140 (2017)
  13. Structure of a Stable Interstrand DNA Cross-Link Involving a β-N-Glycosyl Linkage Between an N6-dA Amino Group and an Abasic Site. Kellum AH, Qiu DY, Voehler MW, Martin W, Gates KS, Stone MP. Biochemistry 60 41-52 (2021)
  14. Sequence dependence in base flipping: experimental and computational studies. O'Neil LL, Wiest O. Org Biomol Chem 6 485-492 (2008)
  15. How abasic sites impact hole transfer dynamics in GC-rich DNA sequences. Corbella M, Voityuk AA, Curutchet C. Phys Chem Chem Phys 20 23123-23131 (2018)
  16. Kinetic mechanism of the interaction of Saccharomyces cerevisiae AP-endonuclease 1 with DNA substrates. Dyakonova ES, Koval VV, Ishchenko AA, Saparbaev MK, Kaptein R, Fedorova OS. Biochemistry (Mosc) 77 1162-1171 (2012)
  17. Analysis of structural flexibility of damaged DNA using thiol-tethered oligonucleotide duplexes. Fujita M, Watanabe S, Yoshizawa M, Yamamoto J, Iwai S. PLoS One 10 e0117798 (2015)


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