A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs Dedicated to the memory of Professor Ivano Bertini.

Journal of Inorganic Biochemistry

Volumn 127, Issue , 2013, Pages 203-210

  Kumbhar, Sadhana ^a   Johannsen, Silke ^b   Sigel, Roland K O ^b   Waller, Mark P ^a   Müller, Jens ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

DNA; Metal mediated base pairs; Nucleobases; QM MM

Indexed keywords

DOUBLE STRANDED DNA; SILVER;

ARTICLE; BASE PAIRING; CONFORMATION; DENSITY FUNCTIONAL THEORY; DNA STRUCTURE; FEASIBILITY STUDY; MOLECULAR MECHANICS; NUCLEAR MAGNETIC RESONANCE IMAGING; PROTEIN DATA BANK; QUANTUM MECHANICS; RELIABILITY;

DNA; METAL-MEDIATED BASE PAIRS; NUCLEOBASES; QM/MM;

BASE PAIRING; DNA; HYDROGEN BONDING; IMIDAZOLES; MODELS, MOLECULAR; QUANTUM THEORY; SILVER;

EID: 84884354289     PISSN: 01620134     EISSN: 18733344     Source Type: Journal    
DOI: 10.1016/j.jinorgbio.2013.03.009     Document Type: Article

References (63)

1. J. Müller Metallomics 2 2010 318 327
2. T.J. Bandy, A. Brewer, J.R. Burns, G. Marth, T. Nguyen, and E. Stulz Chem. Soc. Rev. 40 2011 138 148
3. J. Müller Eur. J. Inorg. Chem. 2008 3749 3763
4. P. Scharf, and J. Müller ChemPlusChem 78 2013 20 34
5. D.A. Megger, N. Megger, and J. Müller Met. Ions Life Sci. 10 2012 295 317
6. Y. Takezawa, and M. Shionoya Acc. Chem. Res. 45 2012 2066 2076
7. A. Ono, H. Torigoe, Y. Tanaka, and I. Okamoto Chem. Soc. Rev. 40 2011 5855 5866
8. G.H. Clever, C. Kaul, and T. Carell Angew. Chem. Int. Ed. 46 2007 6226 6236
9. S. Johannsen, S. Paulus, N. Düpre, J. Müller, and R.K.O. Sigel J. Inorg. Biochem. 102 2008 1141 1151
10. D.A. Megger, C. Fonseca Guerra, F.M. Bickelhaupt, and J. Müller J. Inorg. Biochem. 105 2011 1398 1404
11. S. Katz Nature 194 1962 569
12. R.H. Jensen, and N. Davidson Biopolymers 4 1966 17 32
13. G.L. Eichhorn, J.J. Butzow, P. Clark, and E. Tarien Biopolymers 5 1967 283 296
14. K. Tanaka, A. Tengeiji, T. Kato, N. Toyama, and M. Shionoya Science 299 2003 1212 1213
15. C. Kaul, M. Müller, M. Wagner, S. Schneider, and T. Carell Nat. Chem. 3 2011 794 800
16. K. Seubert, C. Fonseca Guerra, F.M. Bickelhaupt, and J. Müller Chem. Commun. 47 2011 11041 11043
17. N. Megger, L. Welte, F. Zamora, and J. Müller Dalton Trans. 40 2011 1802 1807
18. S. Johannsen, N. Megger, D. Böhme, R.K.O. Sigel, and J. Müller Nat. Chem. 2 2010 229 234
19. D. Böhme, N. Düpre, D.A. Megger, and J. Müller Inorg. Chem. 46 2007 10114 10119
20. W. He, R.M. Franzini, and C. Achim Prog. Inorg. Chem. 55 2007 545 611
21. S. Liu, G.H. Clever, Y. Takezawa, M. Kaneko, K. Tanaka, X. Guo, and M. Shionoya Angew. Chem. Int. Ed. 50 2011 8886 8890
22. S. Taherpour, H. Lönnberg, and T. Lönnberg Org. Biomol. Chem. 11 2013 991 1000
23. J. Müller, D. Böhme, P. Lax, M. Morell Cerdà, and M. Roitzsch Chem. Eur. J. 11 2005 6246 6253
24. K. Petrovec, B.J. Ravoo, and J. Müller Chem. Commun. 48 2012 11844 11846
25. K. Spiegel, U. Rothlisberger, and P. Carloni J. Phys. Chem. B 108 2004 2699 2707
26. K. Spiegel, and A. Magistrato Org. Biomol. Chem. 4 2006 2507 2517
27. A. Magistrato, P. Ruggerone, K. Spiegel, P. Carloni, and J. Reedijk J. Phys. Chem. B 110 2006 3604 3613
28. S. Kumbhar, F.D. Fischer, and M.P. Waller J. Chem. Inf. Model. 51 2012 93 98
29. S. Dapprich, I. Komáromi, K.S. Byun, K. Morokuma, and M.J. Frisch J. Mol. Struct. (THEOCHEM) 461-462 1999 1 21
30. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. Montgomery, J.A., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, and D.J. Fox 2009 Gaussian, Inc. Wallingford CT
31. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman J. Am. Chem. Soc. 117 1995 5179 5197
32. A.K. Rappé, and W.A. Goddard III J. Phys. Chem. 95 1991 3358 3363
33. S. Grimme J. Comput. Chem. 27 2006 1787 1799
34. P.A.M. Dirac Proc. R. Soc. Lond. A123 1929 714 733
35. J.C. Slater Phys. Rev. 81 1951 385 390
36. S.H. Vosko, L. Wilk, and M. Nusair Can. J. Chem. 58 1980 1200 1211
37. A.D. Becke Phys. Rev. A 38 1988 3098 3100
38. J.P. Perdew Phys. Rev. B 33 1986 8822 8824
39. A.D. Becke J. Chem. Phys. 98 1993 5648 5652
40. C. Lee, W. Yang, and R.G. Parr Phys. Rev. B 37 1988 785 789
41. S. Grimme J. Comput. Chem. 25 2004 1463 1473
42. S. Huzinaga, and B. Miguel Chem. Phys. Lett. 175 1990 289 291
43. S. Huzinaga, and M. Klobukowski Chem. Phys. Lett. 212 1993 260 264
44. http://www.theochem.uni-stuttgart.de/pseudopotentials 2003
45. L.E. Roy, P.J. Hay, and R.L. Martin J. Chem. Theory Comput. 4 2008 1029 1031
46. P.J. Hay, and W.R. Wadt J. Chem. Phys. 82 1985 270 283
47. W.R. Wadt, and P.J. Hay J. Chem. Phys. 82 1985 284 298
48. P.J. Hay, and W.R. Wadt J. Chem. Phys. 82 1985 299 310
49. HyperChem 7.52 release for Windows; HyperCube, Inc., Gainesville, Florida, USA http://www.hyper.com 2005
50. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein J. Chem. Phys. 79 1983 926 935
51. B. Assadollahzadeh, and P. Schwerdtfeger Chem. Phys. Lett. 462 2008 222 228
52. M.P. Waller, H. Braun, N. Hojdis, and M. Bühl J. Chem. Theory Comput. 3 2007 2234 2242
53. S. Grimme, and J.-P. Djukic Inorg. Chem. 50 2011 2619 2628
54. C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clore J. Magn. Reson. 160 2003 65 73
55. R. Koradi, M. Billeter, and K. Wüthrich J. Mol. Graphics 14 1996 51 55
56. X.-J. Lu, and W.K. Olson Nucleic Acids Res. 31 2003 5108 5121
57. P.K. Samanta, A.K. Manna, and S.K. Pati Chem. Asian J. 7 2012 2718 2728
58. A. Bondi J. Phys. Chem. 68 1964 441 451
59. R.F.W. Bader Chem. Rev. 91 1991 893 928
60. S. Atwell, E. Meggers, G. Spraggon, and P.G. Schultz J. Am. Chem. Soc. 123 2001 12364 12367
61. R. Chandrasekaran, and S. Arnott J. Biomol. Struct. Dyn. 13 1996 1015 1027
62. J. Müller, A.A. Lugovskoy, G. Wagner, and S.J. Lippard Biochemistry 41 2002 42 51
63. L. Rulíšek, and U. Ryde Coord. Chem. Rev. 257 2013 445 458