How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking interactions in adenine-cytosine complex?

Journal of Molecular Modeling

Volumn 15, Issue 6, 2009, Pages 615-622

  Czyznikowska, Zaneta ^a  

^a NICOLAUS COPERNICUS UNIVERSITY   (Poland)

Author keywords

Intermolecular interactions; Nucleic acid base complexes; Stacking interactions

Indexed keywords

ADENINE; CYTOSINE; DNA B; HYDROXYL RADICAL;

AB INITIO CALCULATION; CHEMICAL MODIFICATION; COMPLEX FORMATION; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENERGY; INTERMOLECULAR INTERACTION ENERGY; MOLECULAR INTERACTION; MOLECULAR STABILITY; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL;

ADENINE; ALGORITHMS; CYTOSINE; DNA; HYDROXYL RADICAL; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 67349211791     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-008-0447-0     Document Type: Conference Paper

References (48)

1. Sentürker S, Karahalil B, Inal M, Yilmaz H, Müslümanoglu H, Gedikoglu G, Dizdaroglu M (1997) Oxidative DNA base damage and antioxidant enzyme levels in childhood acute lymphoblastic leukemia. FEBS Lett 416:286-290
2. Alam ZI, Jenner A, Daniel SE, Lees AJ, Cairns N, Marsden CD, Jenner P, Halliwell B (1997) Oxidative DNA damage in the parkinsonian brain: An apparent selective increase in 8-hydroxyguanine levels in substantia nigra. J Neurochem 69:1196-1203
3. Schwarz KB, Kew M, Klein A, Abrams RA, Sitzmann J, Jones L, Sharma S, Britton RS, Bisceglie AMD, Groopman J (2001) Increased hepatic oxidative DNA damage in patients with hepatocellular carcinoma. Dig Dis Sci 46:2173-2178
4. Wagner JR, Hu CC, Ames BN (1992) Endogenous oxidative damage of deoxycytidine in DNA. Proc Natl Acad Sci 89:3380-3384
5. Imlay JA, Linn S (1988) DNA damage and oxygen radical toxicity. Science 240:1302-1309
6. Henle ES, Linn S (1997) Formation, prevention, and repair of DNA damage by iron/hydrogen peroxide. J Biol Chem 272:19,095-19,098
7. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709-715
8. Seeberg E, Eide L, Bjoras M (1995) The base excision repair pathway. Trends Biochem Sci 20:391-397
9. Wallace S (2002) Biological consequences of free radical-damaged. Free Radic Biol Med 33:1-14
10. Cooke MS, Evans MD, Dizdaroglu M, Lunec J (2003) Oxidative DNA damage: mechanisms, mutation, and disease. FASEB J 17:1195-1214
11. Reynisson J, Steenken S (2005) The calculated base pairing energy of 8-oxoguanine in the syn-anti conformation with cytosine, thymine, adenine and guanine. J Mol Struct (THEOCHEM) 723:29-36
12. Barone F, Lankas F, Spackova N, Šponer J, Karran P, Bignami M, Mazzei F (2005) Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence. Biophys Chemis 118:31-41
13. Ishida H (2002) Molecular dynamics simulation of 7,8-dihydro-8-Oxoguanine DNA. J Biomol Struc Dyn 19:839-851
14. Fujimoto H, Pinak M, Nemoto T, Bunta JK (2003) Structural analysis of base mispairing in DNA containing oxidative guanine lesion. J Mol Biol 325:433-442
15. Cysewski P, Czeleń P (2007) Theoretical analysis of the effects of guanine oxidative damage on the properties of B-DNA telomere fragments. J Mol Model 13:739-750
16. Czyznikowska Z, Zaleśny R, Cysewski P (2008) Quantum chemical study of the nature of stacking interactions of 2-oxo-adenine with native B-DNA purines. Pol J Chem 82:2269-2279
17. Da̧bkowska I, Jurečka P, Hobza P (2005) On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level. J Chem Phys 122:204,322
18. Da̧bkowska I, Gonzales HV, Jurečka P, Hobza P (2005) Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5′- d(GCGAAGC)-3′ hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels. J Phys Chem A 109:1131-1136
19. Toczyłowski RR, Cybulski S (2003) An analysis of the interactions between nucleic acid bases: Hydrogen-bonded base pairs. J Phys Chem A 107:418-426
20. Czyznikowska Z. (2008) On the importance of electrostatics in stabilization of stacked guanine-adenine complexes appaearing in B-DNA crystals. J Mol Struct (THEOCHEM) 895:161-167
21. Czyznikowska Z., Zaleśny R (2008) Theoretical insights into the nature of intermolecular interactions in cytosine dimer. Biophys Chem 139:137-143
22. Hobza P, Šponer J (2002) Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations. J Am Chem Soc 124:11,802-11,808
23. McConnell TL, Wetmore SD (2007) How do size-expanded DNA nucleobases enhance duplex stability? Computational analysis of the hydrogen-bonding and stacking ability of xDNA bases. J Phys Chem B 111:2999-3009
24. Řezáč J, Hobza P (2007) On the nature of DNA-duplex stability. Chem Eur J 13:2983-2989
25. Cysewski P, Czyznikowska-Balcerak Z, Szefler B (2003) An ab initio post SCF study on stacking interactions of 8-oxo-9-methylguanine with four canonical DNA bases. Pol J Chem 77:1287-1300
26. Cysewski P, Czyznikowska-Balcerak Z. (2005) The MP2 quantum chemistry study on the local minima of guanine stacked with all four nucleic acid bases in conformations corresponding to mean B-DNA. J Mol Struct (Theochem) 757:29-36
27. Cysewski P, Czyznikowska-Balcerak Z. (2007) A post-SCF quantum chemistry study on local minima of 8-oxo-guanine stacked with all four nucleic acid bases in B-DNA conformarions. J Heterocyclic Chem 44:765-773
28. Rutledge LR, Wheaton CA, Wetmore SD (2007) A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine. Phys Chem Chem Phys 9:497-509
29. Šponer J, Riley KE, Hobza P (2008) Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 10:2595-2610
30. Langner KM, Sokalski WA, Leszczynski J (2007) Intriguing relations of interaction energy components in stacked nucleic acids. J Chem Phys 127:111,102
31. Cysewski P, Czyznikowska Z, Zaleśny R, Czeleń P (2008) The post-SCF quantum chemistry characteristics of guanine-guanine stacking in B-DNA. Phys Chem Chem Phys 10:2665-2672
32. Czyznikowska Z, Zaleśny R, Ziółkowski M, Gora RW, Cysewski P (2007) The nature of interactions in uracil dimer: An ab initio study. Chem Phys Lett 450:132-137
33. Toczyłowski RR, Cybulski S (2005) An analysis of the electrostatic interaction between nucleic acid bases. J Chem Phys 123:154,312
34. Cybulski H, Sadlej J (2008) Symmetry-adapted perturbation-theory interaction-energy decomposition for hydrogen-bonded and stacking structures. J Chem Theory Comput 4:892-897
35. Fiethen A, Jansen G, Hesselmann A, Schütz M (2008) Stacking energies for average B-DNA structures from the combined density functional theory and symmetry- adapted perturbation theory approach. J Am Chem Soc 130:1802-1803
36. Hesselmann A, Jansen G, Schütz M (2006) Interaction energy contributions of H- bonded and stacked structures of the AT and GC DNA base pairs from the combined density functional theory and intermolecular perturbation theory approach. J Am Chem Soc 128:11,730-11,731
37. Sedlák R, Jurečka P, Hobza P (2007) Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry. J Chem Phys 127:075,104
38. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, revision D.01. Gaussian, Inc., Wallingford, CT
39. Lu XJ, Olson WK (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108-5121
40. Werner HJ, Knowles PJ, Lindh R, Manby FR, Schütz M, Celani P, Korona T, Rauhut G, Amos RD, Bernhardsson A, Berning A, Cooper DL, Deegan MJO, Dobbyn AJ, Eckert F, Hampel C, Hetzer G, Lloyd AW, McNicholas SJ, Meyer W, Mura ME, Nicklass A, Palmieri P, Pitzer R, Schumann U, Stoll H, Stone AJ, Tarroni R, Thorsteinsson T Molpro, version 2006.1
41. Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553-566
42. Kamiya H (2003) Mutagenic potentials of damaged nucleic acids produced by reactive oxygen/nitrogen species: Approaches using synthetic oligonucleotides and nucleotides. Nucleic Acids Res 2:517-531
43. Gutowski M, van Duijneveldt FB, Chałasiński G, Piela L (1987) Proper correction for the basis set superposition error in SCF calculations of intermolecular interactions. Mol Phys 61:233-247
44. Sokalski WA, Roszak S, Pecul K (1988) An efficient procedure for decomposition of the SCF interaction energy into components with reduced basis set dependence. Chem Phys Lett 153:153-159
45. Cybulski SM, Chałasiński G, Moszyński R (1990) On decomposition of second-order Møller-Plesset supermolecular interaction energy and basis set effects. J Chem Phys 92:4357-4363
46. Gora RW, Bartkowiak W, Roszak S, Leszczynski J (2002) A new theoretical insight into the nature of intermolecular interactions in the molecular crystal of urea. J Chem Phys 117:1031-1039
47. Gora RW, Bartkowiak W, Roszak S, Leszczynski J (2004) Intermolecular interactions in solution: Elucidating the influence of the solvent. J Chem Phys 120:2802-2813
48. Gora RW, Grabowski SJ, Leszczynski J (2005) Dimers of formic acid, acetic acid, formamide and Pyrrole-2-carboxylic acid: An ab initio study. J Phys Chem A 109:6397-6405