Probing the nature of hydrogen bonds in DNA base pairs

Journal of Molecular Modeling

Volumn 12, Issue 2, 2006, Pages 221-228

  Mo, Yirong ^a  

^a WESTERN MICHIGAN UNIVERSITY   (United States)

Author keywords

Charge transfer; DNA base pair; Electrostatic interaction; Hydrogen bond; Resonance assisted hydrogen bonding (RAHB)

Indexed keywords

ADENINE; CARBONYL DERIVATIVE; CYTOSINE; DNA; GUANINE; THYMINE;

ARTICLE; BASE PAIRING; CHEMICAL ANALYSIS; DIPOLE; ELECTRICITY; ELECTRON TRANSPORT; HYDROGEN BOND; NUCLEIC ACID BASE SUBSTITUTION; POLARIZATION; PRIORITY JOURNAL;

EID: 30644456810     PISSN: 16102940     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. U Burkert NL Allinger 1982 Molecular mechanics American Chemical Society Washington DC
2. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comp Chem 4:187-217 10.1002/jcc.540040211
3. Reindl B, Clark T, Schleyer PvR (1996) J Comp Chem 17:1406-1430 10.1002/ (SICI)1096-987X(199609)17:12<1406::AID-JCC3>3.3.CO;2-P
4. Kitaura K, Morokuma K (1976) Int J Quantum Chem 10:325-340 10.1002/ qua.560100211
5. Stevens WJ, Fink WH (1987) Chem Phys Lett 139:15-22 10.1016/ 0009-2614(87)80143-4
6. Gutowski M, Piela L (1988) Mol Phys 64:337-355
7. Cybulski SM, Scheiner S (1990) Chem Phys Lett 166:57-64 10.1016/ 0009-2614(90)87050-2
8. Moszynski R, Heijmen TGA, Jeziorski B (1994) Mol Phys 88:741-758 10.1080/ 00268979650026262
9. Glendening ED, Streitwieser A (1994) J Chem Phys 100:2900-2909 10.1063/ 1.466432
10. van der Vaart A, Merz KM Jr (1999) J Phys Chem A 103:3321-3329 10.1021/ jp9844967
11. Mo Y, Gao J, Peyerimhoff SD (2000) J Chem Phys 112:5530-5538 10.1063/ 1.481185
12. Gentle IR, Ritchie GLD (1989) J Phys Chem 93:7740-7744 10.1021/ j100359a041
13. Craven IE, Hesling MR, Laver DR, Lukins PB, Ritchie GLD, Vrbancich J (1989) J Phys Chem 93:627-631 10.1021/j100339a026
14. Dougherty DA (1996) Science 271:163-168 8539615
15. Mecozzi S, West AP, Dougherty DA (1996) J Am Chem Soc 118:2307-2308 10.1021/ja9539608
16. Cubero E, Luque FJ, Orozco M (1998) Proc Natl Acad Sci USA 95:5976-5980 10.1073/pnas.95.11.5976
17. Caldwell JW, Kollman PA (1995) J Am Soc Chem 117:4177-4178 10.1021/ ja00119a037
18. Mo Y, Subramanian G, Ferguson DM, Gao J (2002) J Am Chem Soc 124:4832-4837 10.1021/ja0174433
19. Morokuma K (1977) Acc Chem Res 10:294-300 10.1021/ar50116a004
20. GA Jeffrey 1997 An introduction to hydrogen bonding Oxford University Press New York
21. Šponer J, Jurecka P, Hobza P (2004) J Am Chem Soc 126:10142-10151 10.1021/ja048436s
22. Cheatham III TE, Kollman PA, (2000) Ann Rev Phys Chem 51:435-71
23. Kratochvíl M, Šponer J, Hobza P (2000) J Am Chem Soc 122:3495-3499 10.1021/ja9936060
24. Guerra CF, Bickelhaupt FM (1999) Angew Chem Int Ed 38:2942-2945 10.1002/ (SICI)1521-3773(19991004)38:19<2942::AID-ANIE2942>3.0.CO;2-V
25. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (1999) Chem Eur J 5:3581-3594 10.1002/ (SICI)1521-3765(19991203)5:12<3581::AID-CHEM3581>3.0.CO;2-Y
26. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (2000) J Am Chem Soc 122:4117-4128 10.1021/ja993262d
27. Mo Y, Peyerimhoff SD (1998) J Chem Phys 109:1687-1697 10.1063/1.476742
28. Cubero E, Luque FJ, Orozco M (2001) J Am Chem Soc 123:12018-12025 10.1021/ja011200t
29. Boys SF, Bernardi F (1970) Mol Phys 19:553-566
30. Mo Y, Gao J (2001) J Phys Chem A 105:6530-6536 10.1021/jp010348w
31. Mo Y, Song L, Wu W, Zhang Q (2004) J Am Chem Soc 126:3974-3982 10.1021/ ja039778l
32. Gianinetti E, Raimondi, Tornaghi E (1996) Int J Quantum Chem 60:157-166 10.1002/(SICI)1097-461X(1996)60:1<157::AID-QUA17>3.0.CO;2-C
33. Gianinetti E, Vandoni I, Famulari A, Raimondi M (1998) Adv Quantum Chem 31:251-266
34. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JJ, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA (1993) J Comput Chem 14:1347-1363 10.1002/jcc.540141112
35. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JAJ, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98, Ed. A.9. Gaussian Inc, Pittsburgh PA
36. Bertran J, Oliva A, Rodríguez-Santiago L, Sodupe M (1998) J Am Chem Soc 120:8159-8167 10.1021/ja9804417
37. Brameld K, Dasgupta S, Goddard WA III (1997) J Phys Chem B 101:4851-4859 10.1021/jp970199a
38. Gilli G, Bellucci F, Ferretti V, Bertolasi V (1989) J Am Chem Soc 111:1023-1028 10.1021/ja00185a035
39. Bertolasi V, Gilli P, Ferretti V, Gilli G (1991) J Am Chem Soc 113:4917-4925 10.1021/ja00013a030
40. Steiner T (1998) Chem Commun 411-]412
41. Gilli P, Bertolasi V, Ferretti V, Gilli G (2000) J Am Chem Soc 122:10405-10417 10.1021/ja000921+
42. Munn RW, Eckhardt CJ (2001) J Phys Chem A 105:6938-6942 10.1021/jp011038g
43. Gilli P, Bertolasi V, Pretto L, Ferretti V, Gilli G (2004) J Am Chem Soc 126:3845-3855 10.1021/ja030213z
44. Fiacco DL, Mo Y, Hunt SW, Ott ME, Roberts A, Leopold KR (2000) J Phys Chem A 105:484-493 10.1021/jp0031810
45. Sutor DJ (1962) Nature 195:68-69
46. GR Desiraju T Steiner 2001 The weak hydrogen bond in structural chemistry and biology Oxford University Press New York
47. Meadows ES, De Wall SL, Barbour LJ, Fronczek FR, Kim M-S, Gokel GW (2000) J Am Chem Soc 122:3325-3335 10.1021/ja9940672
48. Senes A, Ubarretxena-Belandia I, Engelman DM (2001) Proc Natl Acad Sci USA 98:9056-9061 10.1073/pnas.161280798
49. Aravinda S, Shamala N, Bandyopadhyay A, Balaram P (2003) J Am Chem Soc 125:15065-15075 10.1021/ja0372762
50. Manikandan K, Ramakumar S (2004) Proteins 56:768-781 10.1002/prot.20152
51. Petrella RJ, Karplus M (2004). Proteins 54:716-726 10.1002/prot.10577
52. Guo H, Beahm RF, Guo H (2004) J Phys Chem B 108:18065-18072 10.1021/ jp0480192
53. Śponer J, Leszczynski J, Hobza P (1996) J Phys Chem 100:1965-1974 10.1021/jp952760f
54. J Śponer, P Hobza, 1998 In: PvR Schleyer (ed) Encyclopedia of computational chemistry Wiley New York 777-789
55. W Saenger 1984 Principles of nucleic acid structure (and references therein) Springer Berlin Heidelberg New York 123-124