Effects of molecular motion on charge transfer/transport through DNA duplexes with and without base pair mismatch

References

• Endres , R.G. , Cox , D.L. and Singh , R.R.P. 2004 . The quest for high-conductance DNA . Rev. Mod. Phys. , 76 : 195
   Web of Science ®Google Scholar
• Porath , D. , Cuniberti , G. and Di Felice , R. 2004 . Charge transport in DNA-based devices . Top. Curr. Chem. , 237 : 183
   Google Scholar
• Hihath , J. , Xu , B.Q. , Zhang , P.M. and Tao , N.J. 2005 . Study of single-nucleotide polymorphisms by means of electrical conductance measurements . Proc. Natl. Acad. Sci. USA , 102 : 16979
   Google Scholar
• Delaney , S. , Yoo , J. , Stemp , E.D.A. and Barton , J.K. 2004 . Charge equilibration between two distinct sites in double helical DNA . Proc. Natl. Acad. Sci. USA , 101 : 10511
   Google Scholar
• Zheng , L. , Burke , P.J. and Brody , J.P. 2004 . Nanobiophotonics and Biomedical Applications , Edited by: Cartwright , A.N. Vol. 5331 , 126 Bellingham, WA, USA : SPIE . Proc. of SPIE
   Google Scholar
• Troisi , A. and Orlandi , G. 2002 . Hole migration in DNA: a theoretical analysis of the role of structural fluctuations . J. Phys. Chem. , B106 : 2093
   Google Scholar
• Tanaka , S. and Sengoku , Y. 2003 . Nuclear quantum effects on electron transfer reactions in DNA hairpins . Phys. Rev. , E68 : 031905
   Google Scholar
• Lewis , J.P. , Cheatham , Th.E. III , Stairkov , E.B. , Wang , H. and Sankey , O.F. 2003 . Dynamically amorphous character of electronic states in Poly(dA)-Poly(dT) DNA . J. Phys. Chem. , B107 : 2581
   Google Scholar
• Voityuk , A.A. , Siriwong , K. and Rösch , N. 2004 . Environmental fluctuations facilitate electron-hole transfer from guanine to adenine in DNA pi-Stacks . Angew. Chem. Int. Ed. , 43 : 624
   Google Scholar
• Starikov , E.B. , Tanaka , S. , Kurita , N. , Sengoku , Y. , Natsume , T. and Wenzel , W. 2005 . Investigation of a Kubo-formula-based approach to estimate DNA conductance in an atomistic model . Eur. Phys. J , E18 : 437
   Google Scholar
• Kelley , S.O. , Boon , E.M. , Barton , J.K. , Jackson , N.M. and Hill , M.G. 1999 . Single-base mismatch detection based on charge transduction through DNA . Nucleic Acids Res. , 27 : 4830
   PubMed Web of Science ®Google Scholar
• HyperChem 6.03, Hypercube, Inc. Florida, USA (2000)
   Google Scholar
• J.W. Ponder TINKER 3.9 (2003) http://dasher.wustl.edu/tinker/
   Google Scholar
• Cornell , W.D. , Cieplak , P. , Bayly , C.I. , Gould , I.R. , Merz , K.M. Jr. , Ferguson , D.M. , Spellmeyer , D.C. , Fox , T. , Caldwell , J.W. and Kollman , P.A. 1995 . A second generation force field for the simulation of proteins, nucleic acids, and organic molecules . J. Am. Chem. Soc. , 117 : 5179
   Web of Science ®Google Scholar
• Jorgensen , W.L. , Chandrasekhar , J. , Madura , J. , Impey , R.W. and Klein , M.L. 1983 . Comparison of simple potential functions for simulating liquid water . J. Chem. Phys. , 79 : 926
   Web of Science ®Google Scholar
• Griffith , D. and Amrhein , C. 1997 . Multivariate Statistical Analysis for Geographers , 202 – 208 . Englewood Cliffs, NJ : Prentice Hall .
   Google Scholar
• Datta , S. 1995 . Electronic Transport in Mesoscopic Systems , Cambridge, U. K. : Cambridge University Press .
   Google Scholar
• Verges , J.A. 1999 . Computational implementation of the Kubo formula for the static conductance: Application to two-dimensional quantum dots . Comput. Phys. Comm. , 118 : 71
   Google Scholar
• Verges , J.A. 2000 . A brief comparison between two programs that compute the static conductance of a disordered two-dimensional tight-binding system . Comput. Phys. Comm. , 127 : 268
   Google Scholar
• Cuevas , J.C. , Heurich , J. , Pauly , F. , Wenzel , W. and Schön , G. 2004 . Towards a theory of electrical transport through atomic and molecular junctions . Phase Transitions , 77 : 175
   Web of Science ®Google Scholar
• Anderson , P.A. 1959 . Work function of gold . Phys. Rev. , 115 : 553
   Google Scholar
• Mitchinson , J.C. and Pringle , R.D. 1970 . Work function of a gold film measured during the nucleation of a silver overlayer . Appl. Phys. Lett. , 17 : 326
   Google Scholar
• Zhu , Q. and LeBreton , P.R. 2000 . DNA photoionization and alkylation patterns in the interior of guanine runs . J. Am. Chem. Soc. , 122 : 12824
   Web of Science ®Google Scholar
• Starikov , E.B. 2003 . Role of electron correlations in deoxyribonucleic acid duplexes: is an extended Hubbard Hamiltonian a good model in this case? . Philos. Mag. Lett. , 83 : 699
   Web of Science ®Google Scholar
• Berlin , Yu.A. , Burin , A.I. and Ratner , M.A. 2000 . DNA as a molecular wire . Superlatt. Microstruct. , 28 : 241
   Web of Science ®Google Scholar
• Majumdar , D. , Dai , D. and Balasubramanian , K. 2000 . Theoretical study of electronic states of platinum pentamer (Pt5) . J. Chem. Phys. , 113 : 7928
   Google Scholar
• Li , J. , Li , X. , Zhai , H.-J. and Wang , L.S. 2003 . Au20: a tetrahedral cluster . Science , 299 : 864
   PubMed Web of Science ®Google Scholar
• Hübsch , A. , Endres , R.G. , Cox , D.L. and Singh , R.R.P. 2005 . Optical conductivity of wet DNA . Phys. Rev. Lett. , 94 : 178102
   Google Scholar