1,587
Views
10
CrossRef citations to date
0
Altmetric
Original Article

Radical-induced purine lesion formation is dependent on DNA helical topology

, , , , , , , & show all
Pages S91-S101 | Received 01 Jun 2016, Accepted 02 Oct 2016, Published online: 28 Nov 2016

References

  • Geacintov NE, Shafirovich V. Reaction of small reactive species with DNA. In: Chatgilialoglu C, Studer A, eds. Encyclopedia of radicals in chemistry, biology and materials. Chichester: Wiley; 2012:1283–1317.
  • Cadet J, Douki T, Gasparutto D, Ravanat J-L, Wagner JR. Oxidatively generated nucleobase modifications in isolated and cellular DNA. In: Chatgilialoglu C, Studer A, eds. Encyclopedia of radicals in chemistry, biology and materials. Chichester: Wiley; 2012:1319–1344.
  • Gimisis T, Chatgilialoglu C. Oxidatively formed sugar radicals in nucleic acids. In: Chatgilialoglu C, Studer A, eds. Encyclopedia of radicals in chemistry, biology and materials. Chichester: Wiley; 2012:1345–1370.
  • Chatgilialoglu C, Ferreri C, Terzidis MA. Purine 5',8-cyclonucleoside lesions: chemistry and biology. Chem Soc Rev 2011;40:1368–1382.
  • Kuraoka I, Bender C, Romieu A, Cadet J, Wood RD, Lindahl T. Removal of oxygen free-radical-induced 5',8-purine cyclodeoxynucleosides from DNA by the nucleotide excision-repair pathway in human cells. Proc Natl Acad Sci U S A 2000;97:3832–3837.
  • Kropachev K, Ding S, Terzidis MA, Masi A, Liu Z, Cai Y, et al. Structural basis for the recognition of diastereomeric 5’,8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system. Nucleic Acid Res 2014;42:5020–5032.
  • Cadet J, Douki T, Ravanat J-L. Oxidatively generated damage to the guanine moiety of DNA: mechanistic aspects and formation in cells. Acc Chem Res 2008;41:1075–1083.
  • Chatgilialoglu C, Krokidis MG, Papadopoulos K, Terzidis MA. Purine 5',8-cyclo-2'-deoxynucleoside lesions in irradiated DNA. Radiat Phys Chem 2016;128:75–81.
  • Battino R, Rettich TR, Tominaga T. Solubility of oxygen and ozone in liquids. J Phys Chem Ref Data 1983;12:163–178.
  • Bergeron F, Auvré F, Radicella JP, Ravanat J-L. HO* radicals induce an unexpected high proportion of tandem base lesions refractory to repair by DNA glycosylases. Proc Natl Acad Sci U S A 2010;107:5528–5533.
  • Belmadoui N, Boussicault F, Guerra M, Ravanat J-L, Chatgilialoglu C, Cadet J. Radiation-induced formation of purine 5',8-cyclonucleosides in isolated and cellular DNA: high stereospecificity and modulating effect of oxygen. Org Biomol Chem 2010;8:3211–3219.
  • Terzidis MA, Ferreri C, Chatgilialoglu C. Radiation-induced formation of purine lesions in single and double stranded DNA: revised quantification. Front Chem 2015;3:Article 18.
  • Terzidis MA, Chatgilialoglu C. An ameliorative protocol for the quantification of purine 5′,8-cyclo-2′-deoxynucleosides in oxidized DNA. Front Chem 2015;3:Article 47.
  • Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A 1987;84:7024–7027.
  • Sinden RR. The helix turns at 60: writhing free in chromosomes. Nat Struct Mol Biol 2013;20:251–253.
  • Cai Y, Kropachev K, Terzidis MA, Masi A, Chatgilialoglu C, Shafirovich V, et al. Differences in the access of lesions to the nucleotide excision repair machinery in nucleosomes. Biochemistry 2015;54:4181–4185.
  • Lipps HJ, Rhodes D. G-quadruplex structures: in vivo evidence and function. Trends Cell Biol 2009;19:414–422.
  • Hsu SD, Varnai P, Bugaut A, Reszka AP. A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics. J Am Chem Soc 2011;131:13399–13409.
  • Biffi G, Tannahill D, McCafferty J, Balasubramanian S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem 2013;5:182–186.
  • Cáceres C, Wright G, Gouyette C, Parkinson G, Subirana JA. A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na + ions. Nucleic Acids Res 2004;32:1097–1102.
  • Wang Y, Patel DJ. Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure 1993;1:263–282.
  • Parkinson GN, Lee MP, Neidle S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 2002;20:876–880.
  • Luu KN, Phan AT, Kuryavyi V, Lacroix L, Patel DJ. Structure of the human telomere in K + solution: an intramolecular (3 + 1) G-quadruplex scaffold. J Am Chem Soc 2006;2:9963–9970.
  • Núñez ME, Hall DB, Barton JK. Long-range oxidative damage to DNA: effects of distance and sequence. Chem Biol 1999;6:85–97.
  • Delaney S, Barton JK. Charge transport in DNA duplex/quadruplex conjugates. Biochemistry 2003;42:14159–14165.
  • Friedman KA, Heller A. On the non-uniform distribution of guanine in introns of human genes: possible protection of exons against oxidation by proximal intron poly-G sequences. J Phys Chem B 2001;105:11859–11865.
  • Friedman KA, Heller A. Guanosine distribution and oxidation resistance in eight eukaryotic genomes. J Am Chem Soc 2004;126:2368–2371.
  • Das RS, Samaraweera M, Morton M, Gascón JA, Basu AK. Stability of N-glycosidic bond of (5′S)-8,5′-cyclo-2′-deoxyguanosine. Chem Res Toxicol 2012;25:2451–2461.
  • Huang YC, Cheng AKH, Yu H-Z, Sen D. Charge conduction properties of a parallel-stranded DNA G-quadruplex: implications for chromosomal oxidative damage. Biochemistry 2009;48:6794–6804.
  • De Champdoré M, De Napoli L, Montesarchio D, Piccialli G, Caminal C, Mulazzani QG, et al. Excess electron transfer in G-quadruplex. Chem Commun 2004;1756–1757.
  • Cosconati S, Marinelli L, Trotta R, Virno A, Mayol L, Novellino E, et al. Tandem application of virtual screening and NMR experiments in the discovery of brand new DNA quadruplex groove binders. J Am Chem Soc 2009;131:16336–16337.
  • Lim KW, Ng VCM, Martin-Pintado N, Heddi B, Phan AT. Structure of the human telomere in Na + solution: an antiparallel (2 + 2) G-quadruplex scaffold reveals additional diversity. Nucleic Acids Res 2013;41:10556–10562.
  • Wang J, Yuan B, Guerrero C, Bahde R, Gupta SW. Quantification of oxidative DNA lesions in tissues of long-Evans cinnamon rats by capillary high-performance liquid chromatography-tandem mass spectrometry coupled with stable isotope-dilution method. Anal Chem 2011;83:2201–2209.
  • Liao Q, Chiu NHL, Shen C, Chen Y, Vouros P. Investigation of enzymatic behavior of benzonase/alkaline phosphatase in the digestion of oligonucleotides and DNA by ESI-LC/MS. Anal Chem 2007;79:1907–1917.
  • Cavallo L, Kleinjung J, Fraternali F. POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res 2003;31:3364–3366.
  • Kleinjung J, Fraternali F. POPSCOMP: an automated interaction analysis of biomolecular complexes. Nucleic Acids Res 2005;33:342–346.
  • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:27–28.
  • Hasel W, Hendrickson TF, Still WC. A rapid approximation to the solvent accessible surface areas of atoms. Tetrahedron Comput Methodol 1988;1:103–116.
  • Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 2006;34:116–118.
  • Buxton GV, Greenstock CL, Helman WP, Ross AB. Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals (*OH/*O−) in aqueous solution. J Phys Chem Ref Data 1988;17:513–886.
  • Wang J, Clauson CL, Robbins PD, Niedernhofer LJ, Wang Y. The oxidative DNA lesions 8,5'-cyclopurines accumulate with aging in a tissue-specific manner. Aging Cell 2012;11:714–716.