Molecular electrostatic potentials of DNA base-base pairing and mispairing

Journal of Molecular Modeling

Volumn 18, Issue 1, 2012, Pages 91-101

  Otero Navas, Ivonne ^a   Seminario, Jorge M ^a  

^a Department of Electrical and Computer Engineering   (United States)

Author keywords

Base mispairing; Base pairing; DNA energetics; Molecular electrostatic potential; Pair dissociation energy; Potential tunnel; Watson Crick pair

Indexed keywords

ADENINE; CYTOSINE; GUANINE; THYMINE;

ARTICLE; BASE MISPAIRING; BASE PAIRING; BINDING AFFINITY; DISSOCIATION; ELECTRIC POTENTIAL; ENERGY; GEOMETRY; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; STATIC ELECTRICITY;

ADENINE; BASE PAIR MISMATCH; BASE PAIRING; CYTOSINE; DNA; GUANINE; HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; STATIC ELECTRICITY; THERMODYNAMICS; THYMINE;

EID: 84856285418     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1028-1     Document Type: Article

References (75)

1. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids-a structure for deoxyribose nucleic acid. Nature 171:737-738
2. Kornberg A (1980) DNA replication. Freeman, San Francisco
3. Nir E, Plützer C, Kleinermanns K, de Vries M (2002) Properties of isolated DNA bases, base pairs and nucleosides examined by laser spectroscopy. Eur Phys J D 20:317-329 (Pubitemid 36185330)
4. Showalter AK, Tsai MD (2001) A DNA polymerase with specificity for five base pairs. J Am Chem Soc 123:1776-1777. doi:10.1021/ja005758x (Pubitemid 32179435)
5. Friedberg EC, Walker GC, Siebe W (1995) DNA repair and mutagenesis. ASM, Washington, DC
6. Loft S, Poulsen HE (1996) Cancer risk and oxidative DNA damage in man. J Mol Spectrosc Med 74:297-312 (Pubitemid 26195901)
7. Nir E, Kleinermanns K, de Vries MS (2000) Pairing of isolated nucleic-acid bases in the absence of the DNA backbone. Nature 408:949-951 (Pubitemid 32101635)
8. Krueger AT, Kool ET (2007) Model systems for understanding DNA base pairing. Curr Opin Chem Biol 11:588-594 (Pubitemid 350180575)
9. Edirisinghe N, Apalkov V, Berashevich J, Chakraborty T (2010) Electrical current through DNA containing mismatched base pairs. Nanotechnology 21:245101
10. Apalkov V, Berashevich J, Chakraborty T (2010) Unique magnetic signatures of mismatched base pairs in DNA. J Chem Phys 132:085102
11. Aboul-ela F, Koh D, Tinoco IJ (1985) Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G+dCT3YT3G (X, Y=A, C, G, T). Nucleic Acids Res 13:4811-4824
12. Schofield MJ, Hsieh P (2003) DNA MISMATCH REPAIR: Molecular mechanisms and biological function. Annu Rev Microbiol 57:579-608. doi: 10.1146/annurev.micro.57.030502.090847 (Pubitemid 37406637)
13. Modrich P (1987) DNA Mismatch correction. Annu Rev Biochem 56:435-466. doi: 10.1146/annurev.bi.56.070187.002251
14. Werntges H, Steger G, Riesner D, Fritz HJ (1986) Mismatches in DNA double strands: thermodynamic parameters and their correlation to repair efficiencies. Nucleic Acids Res 14:3773-3790. doi: 10.1093/nar/14.9.3773 (Pubitemid 16120509)
15. Marra G, Schär P (1999) Recognition of DNA alterations by the mismatch repair system. Biochem J 338:1-13 (Pubitemid 29097278)
16. Patel DJ, Ikuta S, Kozlowski S, Itakura K (1983) Sequence dependence of hydrogen exchange kinetics in DNA duplexes at the individual base pair level in solution. Proc Natl Acad Sci USA 80:2184-2188
17. Goodman MF (1997) Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity. Proc Natl Acad Sci USA 94:10493-10495 (Pubitemid 27430760)
18. Jauregui LA, Seminario JM (2008) A DNA sensor for sequencing and mismatches based on electron transport through Watson-Crick and Non-Watson-Crick base pairs. IEEE Sensors J 8:803-814
19. Moore CL, Zivkovic A, Engels JW, Kuchta RD (2004) Human DNA primase uses Watson-Crick hydrogen bonds to distinguish between correct and incorrect nucleoside triphosphates. Biochemistry 43:12367-12374. doi: 10.1021/bi0490791 (Pubitemid 39280581)
20. Wolfle WT, Washington MT, Kool ET, Spratt TE, Helquist SA, Prakash L, Prakash S (2005) Evidence for a Watson-Crick hydrogen bonding requirement in DNA synthesis by human DNA polymerase {kappa}. Mol Cell Biol 25:7137-7143. doi: 10.1128/mcb.25.16.7137-7143.2005 (Pubitemid 41105910)
21. Mizukami S, Kim TW, Helquist SA, Kool ET (2006) Varying DNA base-pair size in subangstrom increments: evidence for a loose, not large, active site in low-fidelity Dpo4 polymerase. Biochemistry 45:2772-2778. doi: 10.1021/bi051961z (Pubitemid 43334526)
22. Kim TW, Delaney JC, Essigmann JM, Kool ET (2005) Probing the active site tightness of DNA polymerase in subangstrom increments. Proc Natl Acad Sci USA 102:15803-15808. doi: 10.1073/pnas.0505113102 (Pubitemid 41552823)
23. Kim TW, Brieba LG, Ellenberger T, Kool ET (2006) Functional evidence for a small and rigid active site in a high fidelity DNA polymerase. J Biol Chem 281:2289-2295. doi: 10.1074/jbc.M510744200 (Pubitemid 43845820)
24. Mitsui T, Kimoto M, Harada Y, Yokoyama S, Hirao I (2005) An efficient unnatural base pair for a base-pair-expanded transcription system. J Am Chem Soc 127:8652-8658. doi: 10.1021/ja0425280 (Pubitemid 40868247)
25. Yang Z, Sismour AM, Sheng P, Puskar NL, Benner SA (2007) Enzymatic incorporation of a third nucleobase pair. Nucleic Acids Res 35:4238-4249. doi: 10.1093/nar/gkm395 (Pubitemid 47244580)
26. Sismour AM, Benner SA (2005) The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system. Nucleic Acids Res 33:5640-5646. doi: 10.1093/nar/gki873 (Pubitemid 41548830)
27. Danilov VI, Anisimov VM (2005) Post Hartree-Fock studies of the canonical Watson-Crick DNA base pairs: molecular structure and the nature of stability. J Biomol Struct Dyn 22:471-482 (Pubitemid 40105183)
28. Hobza P, Sponer J (1999) Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem Rev 99:3247-3276 (Pubitemid 129583053)
29. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (2000) Hydrogen bonding in DNA base pairs: reconciliation of theory and experiment. J Am Chem Soc 122:4117-4128 (Pubitemid 30304846)
30. Das J, Mukherjee S, Mitra A, Bhattacharyya D (2006) Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. J Biomol Struct Dyn 24:149-161 (Pubitemid 44570211)
31. Bhattacharyya D, Koripella SC, Mitra A, Rajendran VB, Sinha B (2007) Theoretical analysis of noncanonical base pairing interactions in RNA molecules. J Biosci 32:809-825 (Pubitemid 47435514)
32. 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 C.02. Gaussian Inc, Wallingford CT
33. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, Revision A.02. Gaussian Inc, Wallingford CT
34. Lescoute A, Westhof E (2006) The interaction networks of structured RNAs. Nucleic Acids Res 34:6587-6604 (Pubitemid 46017953)
35. Leontis NB, Westhof E (1998) Conserved geometrical base-pairing patterns in RNA. Q Rev Biophys 31:399-455. doi: 10.1017/S0033583599003479
36. Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499-512 (Pubitemid 32416808)
37. Becke AD (1993) A new mixing of Hartree-Fock and local density-functional theories. J Chem Phys 98:1372-1377
38. Perdew JP (1991) Unified theory of exchange and correlation beyond the local density approximation. In: Ziesche P, Eschrig H (eds) Electronic structure of solids. Akademie, Berlin, pp 11-20
39. Petersson GA, Bennett A, Tensfeldt TG, Al-Laham MA, Shirley WA, Mantzaris J (1988) A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements. J Chem Phys 89:2193-2218
40. Petersson GA, Al-Laham MA (1991) A complete basis set model chemistry. II. Open-shell systems and the total energies of the first-row atoms. J Chem Phys 94:6081-6090
41. Habibollahzadeh D, Grodzicki M, Seminario JM, Politzer P (1991) Computational study of the concerted gas-phase triple dissociations of 1,3,5-triazacyclohexane and its 1,3,5-trinitro derivative (RDX). J Phys Chem 95:7699-7702
42. 2 and the energetics of some possible decomposition steps. Chem Phys Lett 216:348-352
43. Seminario JM, Concha MC, Politzer P (1995) A density functional/molecular dynamics of the structure of liquid nitromethane. J Chem Phys 102:8281-8282
44. Politzer P, Seminario JM (1993) Energy changes associated with some decomposition steps of 1,3,3-trinitroazetidine-a nonlocal density-functional study. Chem Phys Lett 207:27-30
45. Politzer P, Seminario JM, Bolduc PR (1989) A proposed interpretation of the destabilizing effect of hydroxyl-groups on nitroaromatic molecules. Chem Phys Lett 158:463-469
46. Seminario JM, Concha MC, Politzer P (1992) Calculated sructures and relative tabilities of furoxan, some 1,2 dinitrosoethylenes and other isomers. J Comput Chem 13:177-182
47. Murray JS, Redfern PC, Seminario JM, Politzer P (1990) Anomalous energy effects in some aliphatic and alicyclic aza systems and their nitro-derivatives. J Phys Chem A 94:2320-2323
48. Seminario JM, Araujo RA, Yan L (2004) Negative differential resistance in metallic and semiconducting clusters. J Phys Chem B 108:6915-6918
49. Seminario JM, De La Cruz C, Derosa PA, Yan L (2004) Nanometer-size conducting and insulating molecular devices. J Phys Chem B 108:17879-17885
50. Derosa PA, Guda S, Seminario JM (2003) A programmable molecular diode driven by charge-induced conformational changes. J Am Chem Soc 125:14240-14241 (Pubitemid 37452339)
51. 3. Int J Quantum Chem 61:515-523 (Pubitemid 127572075)
52. n (n=1-4) Using DFT. Int J Quantum Chem 65:749-758 (Pubitemid 127616649)
53. Derosa PA, Seminario JM, Balbuena PB (2001) Properties of small bimetallic Ni-Cu clusters. J Phys Chem A 105:7917-7925 (Pubitemid 35381701)
54. Seminario JM, Ma Y, Agapito LA, Yan L, Araujo RA, Bingi S, Vadlamani NS, Chagarlamudi K, Sudarshan TS, Myrick ML, Colavita PE, Franzon PD, Nackashi DP, Cheng L, Yao Y, Tour JM (2004) Clustering effects on discontinuous gold film nanocells. J Nanosci Nanotechnol 4:907-917
55. Seminario JM, Derosa PA, Cordova LE, Bozard BH (2004) A molecular device operating at Terahertz frequencies. IEEE Trans Nanotech 3:215-218
56. Choi D-S, Huang S, Huang M, Barnard TS, Adams RD, Seminario JM, Tour JM (1998) Revised structures of N-substituted dibrominated pyrrole derivatives and their polymeric products. Termaleimide models with low optical bandgaps. J Org Chem 63:2646-2655 (Pubitemid 128494265)
57. Murray JS, Seminario JM, Politzer P (1994) Does antiaromaticity imply net destabilization. Int J Quantum Chem 49:575-579
58. Politzer P, Seminario JM (1989) Computational analysis of the structures, bond properties, and electrostatic potentials of some nitrotetrahedranes and nitroazatetrahedranes. J Phys Chem 93:4742-4745
59. Seminario JM, Politzer P (1991) First principles theoretical methods for the calculation of electronic charge densities and electrostatic potentials. In: Jeffrey GA (ed) The application of charge-density research to chemistry and drug design. Plenum, New York
60. Politzer P, Grice ME, Murray JS, Seminario JM (1993) Anomalous stabilizing and destabilizing effects in some cyclic pi-electron systems. Can J Chem 71:1123-1127
61. 2O systems under normal and supercritical conditions. Chem Phys Lett 222:25-32
62. Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev 136:B864
63. Kohn W, Sham LJ (1965) Self-consistent equations including exchange and correlation effects. Phys Rev 140:A1133
64. Sham LJ, Kohn W (1966) One-particle properties of an inhomogeneous interacting electron gas. Phys Rev 145:561-567
65. Murray JS, Peralta-Inga Z, Politzer P, Ekanayake K, LeBreton P (2001) Computational characterization of nucleotide bases: Molecular surface electrostatic potentials and local ionization energies, and local polarization energies. Int J Quantum Chem 83:245-254 (Pubitemid 32517572)
66. Politzer P, Seminario JM (1990) Relative bond strengths in tetrahedrane, prismane, and some of their aza analogs. Struct Chem 1:29-32
67. Scrocco E, Tomasi J (1973) The electrostatic molecular potential as a tool for the interpretation of molecular properties. In: New concepts II, vol 42. Topics in current chemistry. Springer. Berlin, pp 95-170. doi: 10.1007/3-540-06399-4-6
68. Jauregui LA, Salazar-Salinas K, Seminario JM (2009) Transverse electronic transport in double-stranded DNA nucleotides. J Phys Chem B 113:6230-6239. doi: 10.1021/jp808790j
69. Sivanesan D, Subramanian V, Nair BU (2001) Solvent effect on DNA base stacked dimers: an isodensity polarizable continuum model approach. Int J Quantum Chem 84:750-758 (Pubitemid 32933588)
70. Marañon J, Fantoni A, Grigera Jr. (1999) Adenine-thymine molecular dynamics simulation. Conformation, hydration and magnetic behaviour. J Mol Liq 79:177-186 (Pubitemid 129531074)
71. 2+) metal cations: absence of the base pair stabilization by metal-induced polarization effects. J Phys Chem B 103:2528-2534. doi: 10.1021/jp983744w (Pubitemid 129702513)
72. Coutinho K, Ludwig V, Canuto S (2004) Combined Monte Carlo and quantum mechanics study of the hydration of the guanine-cytosine base pair. Phys Rev E 69:061902
73. Gilbert HF (2000) Basic concepts in biochemistry, 2nd edn. McGraw-Hill, Houston
74. Tikhomirova A, Beletskaya IV, Chalikian TV (2006) Stability of DNA duplexes containing GG, CC, AA, and TT mismatches. Biochemistry 45:10563-10571. doi: 10.1021/bi060304j (Pubitemid 44320472)
75. Hunter WN, Brown T, Anand NN, Kennard O (1986) Structure of an adenine[dot]cytosine base pair in DNA and its implications for mismatch repair. Nature 320:552-555 (Pubitemid 16045124)