Analysis of DNA-Recognizing Enzyme Interaction using Deaminated Lesions
Authors: Seung Pil Pack
Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.
Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1331205Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1002
 Doi, A., Pack, S.P., Kodaki, T., and Makino, K. (2009) Reinvestigation of the molecular influence of hypoxanthine on the DNA cleavage efficiency of restriction endonucleases BglII, EcoRI and BamHI. J. Biochem. 146, 201-208
 Suzuki, T., Yamaoka, R., Nishi, M., Ide, H., and Makino, K. (1996) Isolation and characterization of a novel product, 2 -deoxyoxanosine, from 2 -deoxyguanosine, oligodeoxynucleotide, and calf thymus DNA treated by nitrous acid and nitric oxide. J. Am. Chem. Soc. 118, 2515-2516
 Wuenschell, G.E., O’Connor, T.R., and Termini, J. (2003) Stability, miscoding potential and repair of 2 -deoxyxanthosine in DNA: implications for nitric oxide-induced mutagenesis. Biochemistry 42, 3608-3616
 Suzuki, T., Yoshida, M., Yamada, M., Ide, H., Kobayashi, M., Kanaori, K., Tajima, K., and Makino, K. (1998) Misincorporation of 2 -deoxyoxanosine 5 -triphosphate by DNA polymerases and its implication for mutagenesis. Biochemistry 37, 11592-11598
 Kamiya, H., Miura, H., Kato, H., Nishimura, S., and Ohtsuka, E. (1992) Induction of mutation of a synthetic c-Ha-ras gene containing hypoxanthine. Cancer Res. 52, 1836-1839
 Nakano, T., Asagoshi, K., Terato, H., Suzuki, T., and Ide, H. (2005) Assessment of genotoxic potential of nitric oxide-induced guanine lesions by in vitro reactions with Escherichia coli DNA polymerase I. Mutagenesis 20, 209-216
 Kamiya, H., Shimizu, M., Suzuki, M., Inoue, H., and Ohtsuka, E. (1992) Mutation induced by deoxyxanthossine in codon 12 of a synthetic c-Ha-ras gene. Nucleosides Nucleotides 11, 247-260
 Eritja, R ., Horowitz, D.M.,Walker, P.A., Ziehler-Martin, J.P., Boosalis, M.S., Goodman, M.F., Itakura, K., and Kaplan, B.E. (1986) Synthesis and properties of oligonucleotides containing 2 -deoxynebularine and 2 -deoxyxanthosine. Nucleic Acids Res. 14., 8135-8153
 Nakano, T., Terato, H., Asagoshi, K., Masaoka, A., Mukuta, M., Ohyama, Y.,Suzuki, T., Makino, K., and Ide, H. (2003) DNA-protein cross-link formation mediated by oxanine -a novel genotoxic mechanism of nitric oxide-induced DNA damage-. J. Biol. Chem. 278, 25264-25272
 Pack, S. P., Kamisetty, N.K., Nonogawa, M., Devarayapalli, K.C., Ohtani, K., Yamada, K., Yoshida, Y., Kodaki, T. and Makino, K. (2007) Direct immobilization of DNA oligomersonto the amine-functionalized glass surface for DNA microarray fabrication through the activation-free reaction of oxanine. Nucleic Acids Res. 35, e110.
 Kamisetty, N.K., Pack, S. P., Nonogawa, M., Devarayapalli, K.C., Yamada, K., Yoshida, Y., Kodaki, T. and Makino, K. (2009) Stabilization of the immobilized linkers and DNA probes for DNA microarray fabrication by end-capping of the remaining unreacted silanol on the glass. J. Biotechnol. 140, 242-245.
 Pack, S.P., Nonogawa, M., Kodaki, T., and Makino, K. (2005) Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides. Nucleic Acids Res. 33, 5771-5780
 Pack, S.P., Doi, A., Nonogawa, M., Kamisetty, N.K., Devarayapalli, K.C., Kodaki, T., and Makino, K. (2007) Biophysical stability and enzymatic recognition of oxanine in DNA. Nucleos. Nucleot. Nucl. 26, 1589-1593
 Pack, S. P., Doi, A., Choi, Y. S., Kodaki, T., and Makino, K. (2010) Biomolecular response of oxanine in DNA strands to T4 polynucleotide kinase, T4 DNA ligase and restriction enzymes. Biochem. Biophys. Res. Commun. 391, 118-122.
 Doi, A., Pack, S. P., and Makino, K. (2010) Comparison of the molecular response of NO-induced lesions in DNA strands on the reactivity of polynucleotide kinase, DNA ligase and DNA polymerase. J. Biochem. 147, 689-696.
 Rutledge, L.R., Wheaton, C.A., and Wetmore, S.D. (2007) A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine. Biophys. Chem. Chem. Phys. 9, 497-509
 Yasui, M., Suzuki, N., Miller, H., Matsuda, T., Matsui, S., and Shibutani, S. (2004) Translesion synthesis past 2 -deoxyxanthosine, a nitric oxide-derived DNA adduct, by mammalian DNA polymerases. J. Mol. Biol. 344, 665-674
 Ono, A., and Ueda, T. (1987) Minor-groove-modified oligonucleotides: synthesis of decadeoxynucleotides containing hypoxanthine, N2-methylguanine and 3-deazaadenine, and their interactions with restriction endonucleases BglII, Sau 3AI, and MboI. Nucleic Acids Res. 15, 3059-3072
 Brennan, C.A., van Cleve, M.D., and Gumport, R.I., (1986). The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J. Biol. Chem. 261, 7270-7278
 Dickson, K.S., Burns, C.M., and Richardson, J.P. (2000) Determination of the free-energy change for repair of a DNA phosphordiester bond. J. Biol. Chem. 275, 15828-15831
 Arora, K., Beard, W.A., Wilson, S.H., and Schlick, T. (2005) Mismatch-induced conformational distortions in polymerase support an induced-fit mechanism for fidelity. Biochemistry 44, 13328-13341
 Lin, P., Pedersen, L.C., Batra, V.K., Beard, W.A., Wilson, S.H., and Pedersen, L.G. (2006) Energy analysis of chemistry for correct insertion by DNA polymerase. Proc. Natl. Acad. Sci. USA 103, 13294-13299.
 Washington, M.T., Johnson, R.E., Prakash, L., and Prakash, S. (2003) The mechanism of Nucleotide incorporation by human DNA polymerase differs from that of the yeast enzymes Mol. Cell. Biol. 23, 8316-8322.
 Kunkel, T.A., and Alexander, P.S. (1986) The base substitution fidelity of eukaryotic DNA polymerases -mispairing frequencies, site preferences, insertion preferences, and base substitution by dislocation-. J. Biol. Chem. 261, 160-166
 Mizrahi, V., Benkovic, P., and Benkovic, S.J. (1986) Mechanism of DNA polymerase I: exonuclease/polymerase activity switch and DNA sequence dependence of pyrophosphorolysis and misincorporation reactions (idling-turnover/misinsertion). Proc. Natl. Acad. Sci. USA 83, 5769-5773
 Kunkel, T.A. (1985) The mutational specificity of DNA polymerase-during in vitro DNA synthesis. J. Biol. Chem. 260, 5787-5796
 Hopfield, J.J. (1980) The energy relay: a proofreading scheme based on dynamic cooperativity and lacking all characteristic symptoms of kinetic proofreading in DNA replication and protein synthesis. Proc. Natl. Acad. Sci. USA 77, 5248-5252
 Pascal, J.M., O’Brien, P.J., Tomkinson, A.E., and Ellenberger, T. (2004) Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432, 473-478