Free terminal amines in DNA-binding peptides alter the product distribution from guanine radicals produced by single electron oxidation

References

• Angelov D, Spassky A, Berger M, Cadet J. 1997. High-intensity UV laser photolysis of DNA and purine 2′-deoxyribonucleosides: Formation of 8-oxopurine damage and oligonucleotide strand cleavage as revealed by HPLC and gel electrophoresis studies. Journal of the American Chemical Society 119:11373–11380.
   Web of Science ®Google Scholar
• Angelov D, Beylot B, Spassky A. 2005. Origin of the heterogenous distribution of the yield of guanyl radical in UV laser photolyzed DNA. Biophysical Journal 88:2766–2778.
   PubMed Web of Science ®Google Scholar
• Ayene IS, Koch CJ, Krisch RE. 1996. SV40 Simulation of the cellular oxygen effect with an SV40 DNA model system using DNA strand breaks as an end point. Radiation Research 146:501–509.
   PubMed Web of Science ®Google Scholar
• Ayene IS, Koch CJ, Krisch RE. 2007. DNA strand breakage by bivalent metal ions and ionizing radiation. International Journal of Radiation Biology 83:195–210.
   PubMed Web of Science ®Google Scholar
• Becker D, Adikhary A, Sevilla M. 2010. In: Wishart JF, Rao BSM, editors. Chapter: Mechanisms of radiation induced DNA damage: direct effects. Recent trends in radiation chemistry. Singapore: World Scientific Publishing. 509.
   Google Scholar
• Bloomfield VA. 1996. DNA condensation. Current Opinion in Structural Biology 6:334–341.
   PubMed Web of Science ®Google Scholar
• Box HC, Budzinski E. 1971. Oxidation and reduction of amino acids by ionizing radiation. Journal of Chemical Physics 55:2446–2449.
   Web of Science ®Google Scholar
• Cadet J, Douki T, Ravanat J-L. 2008. Oxidatively generated damage to the guanine moiety of DNA: Mechanistic aspects and formation in cells. Accounts of Chemical Research 41:1075–1083.
   PubMed Web of Science ®Google Scholar
• Cadet J, Douki T, Ravanat JL. 2010. Oxidatively generated base damage to cellular DNA. Free Radicals in Biology and Medicine 49:9–21.
   PubMed Web of Science ®Google Scholar
• Candeias LP, Steenken S. 2003. Reaction of HO• with guanine derivatives in aqueous solution: Formation of two different redox-active OH-adduct radicals and their unimolecular transformation reactions. Properties of G(-H)•. Chemistry 4:475–484.
   Google Scholar
• Chan W, Chen B, Wang L, Taghizadeh K, Demott MS, Dedon PC. 2010. Quantification of the 2-deoxyribonolactone and nucleoside 5′-aldehyde products of 2-deoxyribose oxidation in DNA and cells by isotope-dilution gas chromatography mass spectrometry: Differential effects of γ-radiation and Fe2+ -EDTA. Journal of the American Chemical Society 132:6145–6153.
   PubMed Web of Science ®Google Scholar
• Chapman JD, Reuvers AP, Borsa J, Greenstock CL. 1973. Chemical radioprotection and radiosensitization of mammalian cells growing in vitro. Radiation Research 56:291–306.
   PubMed Web of Science ®Google Scholar
• Colson AO, Sevilla MD. 1995. Elucidation of primary radiation damage in DNA through application of ab initio molecular orbital theory. International Journal of Radiation Biology 67:627–645.
   PubMed Web of Science ®Google Scholar
• Costa D, Miguel MG, Lindman B. 2007. Effect of additives on swelling of covalent DNA gels. Journal of Physical Chemistry B 111:8444–8452.
   PubMed Web of Science ®Google Scholar
• Cullis PM, Malone ME, Merson-Davies LA. 1996. Guanine radical cations are precursors of 7,8-dihydro-8-oxo-2′-deoxyguanosine but are not precursors of immediate strand breaks in DNA. Journal of the American Chemical Society 118:2775–2781.
   Web of Science ®Google Scholar
• Dedon PC. 2008. The chemical toxicology of 2-deoxyribose oxidation in DNA. Chemical Research in Toxicology 21:206–219.
   PubMed Web of Science ®Google Scholar
• Do TT, Tang VJ, Aguilera JA, Perry CC, Milligan JR. 2011. Characterization of a lipophilic plasmid DNA condensate formed with a cationic peptide fatty acid conjugate. Biomacromolecules 12:1731–1737.
   PubMed Web of Science ®Google Scholar
• Douki T, Cadet J. 1999. Modification of DNA bases by photosensitized one-electron oxidation. International Journal of Radiation Biology 75:571–581.
   PubMed Web of Science ®Google Scholar
• Douki T, Ravanat JL, Pouget JP, Testard I, Cadet J. 2006. Minor contribution of direct ionization to DNA base damage induced by heavy ions. International Journal of Radiation Biology 82:119–127.
   PubMed Web of Science ®Google Scholar
• Gasparutto D, Ravanat J-L, Gérot O, Cadet J. 1998. Characterization and chemical stability of photooxidized oligonucleotides that contain 2,2-diamino-4-[(2-deoxy-β-d-erythro-pentofuranosyl)amino]-5(2H)-oxazolone. Journal of the American Chemical Society 120:10283–10286.
   Web of Science ®Google Scholar
• Haraguchi K, Delaney MO, Wiederholt CJ, Sambandam A, Hantosi Z, Greenberg MM. 2002. Synthesis and characterization of oligodeoxynucleotides containing formamidopyrimidine lesions and nonhydrolyzable analogues. Journal of the American Chemical Society 124:3263–3269.
   PubMed Web of Science ®Google Scholar
• He S, Arscott PG, Bloomfield VA. 2000. Condensation of DNA by multivalent cations: Experimental studies of condensation kinetics. Biopolymers 53:329–341.
   PubMed Web of Science ®Google Scholar
• Held KD, Awad S. 1991. Effects of polyamines and thiols on the radiation sensitivity of bacterial transforming DNA. International Journal of Radiation Biology 59:699–710.
   PubMed Web of Science ®Google Scholar
• Hosford ME, Muller JG, Burrows CJ. 2004. Spermine participates in oxidative damage of guanosine and 8-oxoguanosine leading to deoxyribosylurea formation. Journal of the American Chemical Society 126:9540–9541.
   PubMed Web of Science ®Google Scholar
• Johansen ME, Muller JG, Xu X, Burrows CJ. 2005. Oxidatively induced DNA protein cross linking between single stranded binding protein and oligodeoxynucleotides containing 8-oxo-7,8-dihydro-2′-deoxyguanosine. Biochemistry 44:5660–5671.
   PubMed Web of Science ®Google Scholar
• Kino K, Saito I, Sugiyama H. 1998. Product analysis of GG-specific photooxidation of DNA via electron transfer: 2-aminoimidazolone as a major guanine oxidation product. Journal of the American Chemical Society 120:7373–7374.
   Web of Science ®Google Scholar
• Ly A, Bullick S, Won JH, Milligan JR. 2006. Cationic peptides containing tyrosine protect against radiation induced oxidative damage. International Journal of Radiation Biology 82:421–433.
   PubMed Web of Science ®Google Scholar
• Mascotti DP, Lohman TM. 1997. Thermodynamics of oligoarginines binding to RNA and DNA. Biochemistry 36:7272–7279.
   PubMed Web of Science ®Google Scholar
• Milligan JR, Aguilera JA, Nguyen TT, Paglinawan RA, Ward JF. 2000a. DNA strand-break yields after post-irradiation incubation with base excision repair endonucleases implicate hydroxyl radical pairs in double-strand break formation. International Journal of Radiation Biology 76:1475–1483.
   PubMed Web of Science ®Google Scholar
• Milligan JR, Aguilera JA, Paglinawan RA, Ward JF. 2000b. Mechanism of DNA damage by thiocyanate radicals. International Journal of Radiation Biology 76:1305–1314.
   PubMed Web of Science ®Google Scholar
• Morpurgo M, Radu A, Bayer EA, Wilchek M. 2004. DNA condensation by high-affinity interaction with avidin. Journal of Molecular Recognition 17:558–566.
   PubMed Web of Science ®Google Scholar
• Neta P, Huie RE, Ross AB. 1988. Rate constants for reactions of inorganic radicals in aqueous solution. Journal of Physical and Chemical Reference Data 17:1027–1285.
   Web of Science ®Google Scholar
• Newton GL, Aguilera JA, Ward JF, Fahey RC. 1997. Effect of polyamine-induced compaction and aggregation of DNA on the formation of radiation-induced strand breaks: Quantitative models for cellular radiation damage. Radiation Research 148:272–284.
   PubMed Web of Science ®Google Scholar
• Newton GL, Ly A, Tran NQ, Ward JF, Milligan JR. 2004. Radioprotection of plasmid DNA by oligolysines. International Journal of Radiation Biology 80:643–651.
   PubMed Web of Science ®Google Scholar
• Nowicka AM, Zabost E, Gilant E, Stojek Z. 2011. Influence of percentage of guanine molecules, OH radicals, UV irradiation and temperature on electrooxidation of short synthetic oligonucleotides. Physical Chemistry Chemical Physics 13:7500–7507.
   PubMed Web of Science ®Google Scholar
• O'Neill P, Wardman P. 2009. Radiation chemistry comes before radiation biology. International Journal of Radiation Biology 85:9–25.
   PubMed Web of Science ®Google Scholar
• Pal C, Hüttermann J. 2006. Post-irradiation electron transfer vs. differential radical decay in X-irradiated DNA and its mixtures with additives. Electron spin resonance spectroscopy in LiBr glass at low temperatures. Journal of Physical Chemistry B 110:14976–1487.
   PubMed Web of Science ®Google Scholar
• Perrier S, Hau J, Gasparutto D, Cadet J, Favier A, Ravanat JL. 2006. Characterization of lysine-guanine cross-links upon one-electron oxidation of a guanine-containing oligonucleotide in the presence of a trilysine peptide. Journal of the American Chemical Society 128:5703–5710.
   PubMed Web of Science ®Google Scholar
• Perry CC, Tang VJ, Konigsfeld KM, Aguilera JA, Milligan JR. 2011. Use of a coumarin-labeled hexa-arginine Peptide as a fluorescent hydroxyl radical probe in a nanoparticulate plasmid DNA condensate. Journal of Physical Chemistry B 115:9889–9897.
   PubMed Web of Science ®Google Scholar
• Pimblott SM, LaVerne JA. 1998. Effect of electron energy on the radiation chemistry of liquid water. Radiation Research 150:159–169.
   PubMed Web of Science ®Google Scholar
• Sage E, Harrison L. 2010. Clustered DNA lesion repair in eukaryotes: Relevance to mutagenesis and cell survival. Mutation Research 711:123–133.
   PubMed Web of Science ®Google Scholar
• Schleif RF, Wensink PC. 1981. Practical methods in molecular biology. New York: Springer.
   Google Scholar
• Sevilla MD, Bernhard WA. 2008. In: Spotheim-Maurizot M, Mostafavi M, Douki T, Belloni J, editors. Mechanisms of direct damage to DNA. Radiation chemistry from basics to application in material and life sciences. Les Ulis, France: EDP Sciences. 191.
   Google Scholar
• Sharma KK, Tyagi R, Purkayastha S, Bernhard WA. 2010. One-electron oxidation of DNA by ionizing radiation: Competition between base-to-base hole-transfer and hole-trapping. Journal of Physical Chemistry B 114:7672–7680.
   PubMed Web of Science ®Google Scholar
• Shinde SS, Maroz A, Hay MP, Anderson RF. 2009. One-electron reduction potential of the neutral guanyl radical in the GC base pair of duplex DNA. Journal of the American Chemical Society 131: 5203–5207.
   PubMed Web of Science ®Google Scholar
• Spinks JWT, Woods RJ. 1990. An introduction to radiation chemistry. 3rd ed. New York: Wiley.
   Google Scholar
• Spotheim-Maurizot M, Davidkova M. 2011. Radiation damage to DNA in DNA-protein complexes. Mutation Research 711:41–48.
   PubMed Web of Science ®Google Scholar
• Stivers JT, Jiang YL. 2003. A mechanistic perspective on the chemistry of DNA repair glycosylases. Chemical Reviews 103:2729–2759.
   PubMed Web of Science ®Google Scholar
• Swarts SG, Gilbert DC, Sharma KK, Razskazovskiy Y, Purkayastha S, Naumenko KA, Bernhard WA. 2007. Mechanisms of direct radiation damage in DNA, based on a study of the yields of base damage, deoxyribose damage, and trapped radicals in d(GCACGCGTGC)2. Radiation Research 168:367–381.
   PubMed Web of Science ®Google Scholar
• Teif VB, Bohinc K. 2011. Condensed DNA: Condensing the concepts. Progress in Biophysics and Molecular Biology 105:208–222.
   PubMed Web of Science ®Google Scholar
• Tsoi M, Do TT, Tang V, Aguilera JA, Perry CC, Milligan JR. 2010. Characterization of condensed plasmid DNA models for studying the direct effect of ionizing radiation. Biophysical Chemistry 147:104–110.
   PubMed Web of Science ®Google Scholar
• Udovicić L, Mark F, Bothe E. 1996. Single-strand breaks in double-stranded DNA irradiated in anoxic solution: Contribution of tert-butanol radicals. Radiation Research 146:198–205.
   PubMed Web of Science ®Google Scholar
• van Holde KE. 1989. Chromatin. New York: Springer.
   Google Scholar
• Vilfan ID, Conwell CC, Sarkar T, Hud NV. 2006. Time study of DNA condensate morphology: Implications regarding the nucleation, growth, and equilibrium populations of toroids and rods. Biochemistry 45:8174–8183.
   PubMed Web of Science ®Google Scholar
• von Sonntag C. 1987. The chemical basis of radiation biology. Taylor and Francis: Philadelphia.
   Google Scholar
• von Sonntag C. 2006. Free radical induced DNA damage and its repair, a chemical perspective. Springer: New York.
   Google Scholar
• von Sonntag C. 2010. In: Wishart JF, Rao BSM, editors. Radiation induced DNA damage: indirect effects. Recent trends in radiation chemistry. Singapore: World Scientific Publishing. 543.
   Google Scholar
• Wardman P. 1989. Reduction potentials of one electron couples involving free radicals in aqueous solution. Journal of Physical and Chemical Reference Data 18:1637–1755.
   Web of Science ®Google Scholar
• Webb CF, Jones GD, Ward JF, Moyer DJ, Aguilera JA, Ling LL. 1993. Mechanisms of radiosensitization in bromodeoxyuridine-substituted cells. International Journal of Radiation Biology 64:695–705.
   PubMed Web of Science ®Google Scholar
• Zhang W, Bond JP, Anderson CF, Lohman TM, Record MT Jr. 1996. Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA. Proceedings of the National Academy of Sciences of the USA 93:2511–2516.
   PubMed Web of Science ®Google Scholar