Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases

Journal of Molecular Modeling

Volumn 19, Issue 3, 2013, Pages 1089-1098

  Song, Qi Xia ^a   Ding, Zhen Dong ^a   Liu, Jian Hua ^a   Li, Yan ^a   Wang, Hai Jun ^a  

^a JIANGNAN UNIVERSITY   (China)

Author keywords

Binding energy; DNA bases; Hydrogen bond; MP2; N6 methyladenine

Indexed keywords

6 N METHYLADENINE; ADENINE; CYTOSINE; DNA BASE; GUANINE; SOLVENT;

AQUEOUS SOLUTION; ARTICLE; BASE PAIRING; BINDING KINETICS; DNA BINDING; GAS; MOLECULAR STABILITY; PRIORITY JOURNAL; SOLVENT EFFECT; THEORETICAL STUDY; TRANS ISOMER;

EID: 84962343554     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1628-4     Document Type: Article

References (51)

1. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids. Nature 171(4356):737-738. doi: 10.1038/171738a0
2. Szatyłowicz H, Sadlej-Sosnowska N (2010) Characterizing the strength of individual hydrogen bonds in DNA base pairs. J Chem Inf Model 50(12):2151-2161. doi: 10.1021/ci100288h
3. Czyznikowska Z, Gora RW, Zalesny R, Lipkowski P, Jarzembska KN, Dominiak PM, Leszczynski J (2010) Structural variability and the nature of intermolecular interactions in watson-crick B-DNA base pairs. J Phys Chem B 114. doi: 10.1021/jp101258q
4. Paragi G, Szajli E, Bogar F, Kovacs L, Guerra CF, Bickelhaupt FM (2008) Hydrogen bonding of 3- and 5-methyl-6-aminouracil with natural DNA bases. New J Chem 32(11):1981-1987. doi: 10.1039/b803593h
5. Xue C, Popelier PLA (2008) Computational study of substituent effects on the interaction energies of hydrogen-bonded watson-crick cytosine:guanine base pairs. J Phys Chem B 112(16):5257-5264. doi: 10.1021/jp7108913
6. Xue C, Popelier PLA (2009) Prediction of interaction energies of substituted hydrogen-bonded watson-crick cytosine:Guanine8X base pairs. J Phys Chem B 113(10):3245-3250. doi: 10.1021/jp8071926
7. Vanyushin BF, Tkacheva SG, Belozersky AN (1970) Rare bases in animal DNA. Nature 225(5236):948-949. doi: 10.1038/225948a0
8. Ratel D, Ravanat JL, Berger F, Wion D (2006) N6-Methyladenine: the other methylated base of DNA. Bioessays 28(3):309-315. doi: 10.1002/bies.20342
9. Wion D, Casadesús J (2006) N6-Methyl-adenine: an epigenetic signal for DNA-protein interactions. Nat Rev Microbiol 4(3):183-192. doi: 10.1038/nrmicro1350
10. Barbeyron T, Kean K, Forterre P (1984) DNA adenine methylation of GATC sequences appeared recently in the Escherichia coli lineage. Journal of bacteriology 160 (2):586. doi: http://jb.asm.org/content/160/2/586.
11. Banerjee A, Rao DN (2011) Functional analysis of an acid adaptive DNA adenine methyltransferase from helicobacter pylori 26695. PLoS One 6(2):e16810. doi: 10.1371/journal.pone.0016810
12. Robertson KD, Jones PA (2000) DNA methylation: past, present and future directions. Carcinogenesis 21(3):461-467. doi: 10.1093/carcin/21.3.461
13. Chen RZ, Pettersson U, Beard C, Jackson-Grusby L, Jaenisch R (1998) DNA hypomethylation leads to elevated mutation rates. Nature 395(6697):89-93. doi: 10.1038/25779
14. Vanyushin BF (2005) Enzymatic DNA methylation is an epigenetic control for genetic functions of the cell. Biochem Mosc 70(5):488-499. doi: 10.1007/s10541-005-0143-y
15. Vanyushin BF (2006) DNA methylation and epigenetics. Russ J Genet 42(9):985-997. doi: 10.1134/s1022795406090055
16. Cheng X (1995) Structure and function of DNA methyltransferases. Annu Rev Biophys Biomol Struct 24(1):293-318. doi: 10.1146/annurev.bb.24.060195.00 1453
17. Forde GK, Kedzierski P, Sokalski WA, Forde AE, Hill GA, Leszczynski J (2006) Physical nature of interactions within the active site of cytosine-5-methyltransferase. J Phys Chem A 110(6):2308-2313. doi: 10.1021/jp056415u
18. Vanyushin BF, Belozersky AN, Kokurina NA, Kadirova DX (1968) 5-Methylcytosine and 6-methylaminopurine in bacterial DNA. Nature 218(5146):1066-1067. doi: 10.1038/2181066a0
19. Collier J (2009) Epigenetic regulation of the bacterial cell cycle. Curr Opin Microbiol 12(6):722-729. doi: 10.1016/j.mib.2009.08.005
20. Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM (2011) Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc 133:2080-2083. doi: org/10.1021/ja110157u
21. Low DA, Weyand NJ, Mahan MJ (2001) Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect Immun 69(12):7197-7204. doi: 10.1128/IAI.69.12.7197-7204.2001
22. Vanyushin BF, Alexandrushkina NI, Kirnos MD (1988) N6-Methyladenine in mitochondrial DNA of higher plants. FEBS Lett 233(2):397-399. doi: 10.1016/0014-5793(88)80469-1
23. Fedoreyeva LI, Vanyushin BF (2002) N6-Adenine DNA-methyltransferase in wheat seedlings. FEBS Lett 514(2-3):305-308. doi: 10.1016/S0014-5793(02)02384-0
24. Li D, Delaney JC, Page CM, Yang X, Chen AS, Wong C, Drennan CL, Essigmann JM (2012) Exocyclic carbons adjacent to the N6 of adenine are targets for oxidation by the escherichia coli adaptive response protein AlkB. J Am Chem Soc. doi: 10.1021/ja3010094
25. Engel J, von Hippel PH (1978) Effects of methylation on the stability of nucleic acid conformations. Studies at the polymer level. J Biol Chem 253(3):927-934. doi:http://www.jbc.org/content/253/3/927.short
26. Diekmann S (1987) DNA methylation can enhance or induce DNA curvature. The EMBO J 6(13):4213-4217. doi: http://www.ncbi.nlm.nih.gov/pmc/articles/ PMC553906/
27. Lozynski M, Rusinska-Roszak D, Mack H-G (1998) Hydrogen bonding and density functional calculations: the B3LYP approach as the shortest Way to MP2 results. J Phys Chem A 102(17):2899-2903. doi: 10.1021/jp973142x
28. Miertuš S, Scrocco E, Tomasi J (1981) Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects. Chem Phys 55(1):117-129. doi: 10.1016/0301-0104(81)85090-2
29. Miertus S, Tomasi J (1982) Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes. Chem Phys 65(2):239-245
30. Hobza P, Zahradník R (1988) Intermolecular complexes: the role of van der Waals systems in physical chemistry and in the biodisciplines. Elsevier, Amsterdam
31. van Duijneveldt FB, van Duijneveldt-van de Rijdt JGCM, van Lenthe JH (1994) State of the art in counterpoise theory. Chem Rev 94(7):1873-1885. doi: 10.1021/cr00031a007
32. Boys S, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19(4):553-566. doi: 10.1080/00268977000101561
33. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88(6):899-926. doi: 10.1021/cr00088a005
34. Bader RFW (1990) Atoms in molecules: a quantum theory. Oxford University Press, Oxford
35. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JAJ, 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, Hasegaw J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, 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 (2003) Gaussian 03. Gaussian Inc, Pittsburgh
36. Biegler-König F, Schönbohm J (2002) AIM2000, a program to analyze and visualize atoms in molecules, version 2.0, Bielefeld, Germany
37. Bae SH, Cheong HK, Cheong C, Kang S, Hwang DS, Choi BS (2003) Structure and dynamics of hemimethylated GATC sites. J Biol Chem 278(46):45987-45993. doi: 10.1074/jbc.M306038200
38. Sternglanz H, Bugg CE (1973) Conformation of N6-methyladenine, a base involved in DNA modification: restriction processes. Science 182(4114):833. doi: 10.1126/science.182.4114.833
39. Fazakerley GV, Quignard E, Teoule R, Guy A, Guschlbauer W (1987) A two-dimensional 1H-NMR study of the dam methylase site: comparison between the hemimethylated GATC sequence, its unmethylated analogue and a hemimethylated CATG sequence. Eur J Biochem 167(3):397-404. doi: 10.1111/j.1432-1033.1987. tb13351.x
40. van de Sande J, Ramsing N, Germann M, Elhorst W, Kalisch B, von Kitzing E, Pon R, Clegg R, Jovin T (1988) Parallel stranded DNA. Science 241(4865):551-557. doi: 10.1126/science. 3399890
41. Otto C, Thomas GA, Rippe K, Jovin TM, Peticolas WL (1991) The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick. Biochemistry 30(12):3062-3069. doi: 10.1021/bi00226a012
42. Rentzeperis D, Rippe K, Jovin TM, Marky LA (1992) Calorimetric characterization of parallel-stranded DNA: stability, conformational flexibility, and ion binding. J Am Chem Soc 114(15):5926-5928. doi: 10.1021/ja00041a003
43. Gorb L, Podolyan Y, Dziekonski P, Sokalski WA, Leszczynski J (2004) Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-hartree-fock ab initio study. J Am Chem Soc 126(32). doi: 10119-10129. doi:10.1021/ja049155n
44. Reynisson J, Steenken S (2002) DFT studies on the pairing abilities of the one-electron reduced or oxidized adenine-thymine base pair. Phys Chem Chem Phys 4(21):5353-5358. doi: 10.1039/B206342E
45. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (1999) The nature of the hydrogen bond in DNA base pairs: the role of charge transfer and resonance assistance. Chemistry-Eur J 5:3581. doi: 10.1002/(SICI)1521-3765(19991203)5: 12<3581::AID-CHEM3581>3.0.CO;2-Y
46. Koch U, Popelier PLA (1995) Characterization of C-H-O hydrogen bonds on the basis of the charge density. J Phys Chem 99(24):9747-9754. doi: 10.1021/j100024a016
47. Bondi A (1964) van der Waals volumes and radii. J Phys Chem 68(3):441-451. doi: 10.1021/j100785a001
48. Bader RFW (1998) A bond path: a universal indicator of bonded interactions. J Phys Chem A 102(37):7314-7323. doi: 10.1021/jp981794v
49. Popelier PLA (1998) Characterization of a dihydrogen bond on the basis of the electron density. J Phys Chem A 102(10):1873-1878. doi: 10.1021/jp9805048
50. Parr RG, Yang W (1994) Density-functional theory of atoms and molecules, vol 16. Oxford University Press, USA
51. Wiberg K (1968) Application of the pople-santry-segal CNDO method to the cyclopropylcarbinyl and cyclobutyl cation and to bicyclobutane. Tetrahedron 24(3):1083-1096. doi: 10.1016/0040-4020(68)88057-3