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Original Articles

Quantum Chemical Studies of Structures and Binding in Noncanonical RNA Base pairs: The Trans Watson-Crick:Watson-Crick Family

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Pages 709-732 | Received 27 Nov 2007, Published online: 15 May 2012

References and Footnotes

  • Gesteland , R. F. , Cech , T. R. and Atkins , J. F. 2006 . The RNA World, 3 Ed. NY : Cold Spring Harbor Laboratory Press .
  • Leontis , N. B. and Westhof , E. 2001 . RNA , 7 : 499 – 512 .
  • Westhof , E. and Fritsch , V. 2000 . Structure , 8 : R55 – R65 .
  • Noller , H. F. 2005 . Science , 309 : 1508 – 1514 . (a). (b) T. Hermann and E. Westhof. Chemistry & Biology 6, R335–R343 (2002)
  • Leontis , N. B. , Stombaugh , J. and Westhof , E. 2002 . Nucleic Acids Res , 30 : 3497 – 3531 .
  • Šponer , J. E. , Špačková , N. , Kulhánek , P. , Leszczynski , J. and Šponer , J. 2005 . J Phys Chem A , 109 : 2292 – 2301 .
  • Šponer , J. E. , Špačková , N. , Leszczynski , J. and Šponer , J. 2005 . J Phys Chem B , 109 : 11399 – 11410 .
  • Šponer , J. and Hobza , P. 2003 . Collect Czech Chem Commun , 68 : 2231 – 2282 .
  • Nissen , P. , Ippolito , J. A. , Ban , N. , Moore , P. B. and Steitz , T. A. 2001 . Proc Natl Acad Sci , 98 : 4899 – 4903 .
  • Razgá , F. , Koca , J. , Šponer , J. and Leontis , N. B. 2005 . Biophys J , 88 : 3466 – 3485 .
  • Ramakrishnan , V. and Moore , P. B. 2001 . Curr Opin Struct Biol , 11 : 144 – 154 .
  • Šponer , J. E. , Leszczynski , J. , Sychrovský , V. and Šponer , J. 2005 . J Phys Chem B , 109 : 18680 – 18689 . (a). (b) J. E. Šponer, K. Reblova, A. Mokdad, V. Sychrovský, J. Leszczynski, and J. Šponer. J Phys Chem B 111, 9153–9164 (2005)
  • Oliva , R. , Cavallo , L. and Tramontano , A. 2006 . Nucleic Acids Res , 34 : 865 – 879 . (a) (b) T. Christian, R. S. Lipman, C. Evilia, and Y. M. Hou. J Mol Biol 303, 503–514 (2000). (c) R. Oliva, L. Cavallo, and A. Tramontano. RNA 13, 1–10 (2007)
  • Bhattacharyya , D. , Koripella , S. C. , Mitra , A. , Rajendran , V. B. and Sinha , B. 2007 . J Biosci , 32 : 809 – 825 . (a). (b) A. Roy, M. Bhattacharyya, and D. Bhattacharyya. J Phys Chem B DOI: 10.1021/jp076921e(c) P. Sharma, A. Mitra, S. Sharma, H. Singh, and D. Bhattacharyya (Communicated)
  • Sharma , P. , Mitra , A. , Sharma , S. and Singh , H. 2007 . J Chem Sci , 119 : 525 – 531 .
  • Gould , B. L. and Kollman , P. A. 1994 . J Am Chem Soc , 116 : 2493 – 2499 .
  • Danilov , V. I. and Anisimov , V. M. 2005 . J Biomol Struct Dyn , 22 : 471 – 482 .
  • Hesselmann , A. , Jansewn , G. and Schutz , M. 2006 . J Am Chem Soc , 128 : 11730 – 11731 .
  • Mukherjee , S. , Majumdar , S. and Bhattacharya , D. 2005 . J Phys Chem B , 109 : 10484 – 10492 .
  • Šponer , J. , Jurecka , P. and Hobza , P. 2004 . J Am Chem Soc , 126 : 10142 – 10151 . (a). (b) J. Šponer. Personal communication (2007)
  • Das , J. , Mukherjee , S. , Mitra , A. and Bhattacharyya , D. 2006 . J Biomol Struct Dyn , 24 : 149 – 162 .
  • Sayle , R. and Milner-White , E. J. 1995 . Trends in Biochem Sci , 20 : 374 – 376 . (a). (b) H. J. Bernstein. Trends in Biochem Sci 9, 453–455 (2000)
  • Schaftenaar , G. and Noordik , J. H. 2000 . J Comput Aided Mol Design , 14 : 123 – 134 .
  • Frisch , M. J. and et al . 2003 . Gaussian03 revision B.05 Pittsburgh , PA : Gaussian, Inc. .
  • Schmidt , M. W. , Baldridge , K. K. , Boatz , J. A. , Elbert , S. T. , Gordan , M. S. , Jensen , J. , Koseky , S. , Matsunaga , N. , Nguyen , K. A. , Su , S. J. , Windus , T. L. , Dupuis , M. and Montgomery , J. A. 1993 . J Comput Chem , 14 : 1347 – 1363 .
  • Kitaura , K. and Morokuma , K. 1976 . Int J Qunatum Chem , 10 : 325 – 331 .
  • Dey , D. , Bose , A. , Bhattacharyya , D. , Basu , S. , Maity , S. S. and Ghosh , S. 2007 . J Phys Chem A , 111 : 10500 – 10506 .
  • Morokuma , K. and Kitaura , K. 1981 . Chemical Applications of Atomic and Molecular Electrostatic Potentials. Edited by: Politer , P. and Truhlar , D. G. New York : Plenum Press . (a). (b) W. Chen and M. S. Gordon. J Phys Chem 100, 14316–14328 (1996)
  • Reed , A. E. , Weinstock , R. B. and Weinhold , F. 1985 . J Chem Phys , 83 : 735 – 746 . (a). (b) A. E. Reed, L. A. Curtsiss, and F. Weinhold. Chem Rev 88, 899–926 (1988). (c) A. E. Reed, P. v. R. Schleyer. J Am Chem Soc 109, 7362–7373 (1987)
  • Bader , R. F. W. 1990 . A Quantum Theory. , (a), Atoms in molecules. The Clarendon Press, Oxford. (b) R. F. W. Bader. Chem Rev 91, 893–928 (1991)
  • Zhanpeisov , N. U. , Šponer , J. and Leszczynski , J. 1998 . J Phys Chem A , 102 : 10374 – 10379 .
  • Mukherjee , M. Bansal and Bhattacharyya , D. 2006 . J Comput Aided Mol Des , 20 : 629 – 646 .
  • Cammi , R. , Bonaccorsi , R. and Tomasi , J. 1985 . Theor Chim Acta , 68 : 271 – 283 .
  • Popelier , P. L. A. 1998 . J Phys Chem A , 102 : 1873 – 1878 .
  • Scheiner , S. , Grabowski , S. J. and Kar , T. 2001 . J Phys Chem , 105 : 10607 – 10612 . (a). A. (b) S. Wojtulewski and S. J. Grabowski. J Mol Struct: THEOCHEM 645, 287–294 (2003). (c) W. D. Arnold and E. Oldfield. J Am Chem Soc 122, 12835–12841 (2000). (d) S. J. Grabowski. J Mol Struct: THEOCHEM562, 137–143 (2001)
  • Bader , R. F. W. and Essen , H. 1984 . J Chem Phys , 80 : 1943 – 1960 .
  • Šponer , J. , Mokdad , A. , Šponer , J. E. , Špačková , N. , Leszczynski , J. and Leontis , N. B. 2003 . J Mol Biol , 330 : 967 – 978 .
  • Ruis , B. L. , Kivens , B. W. J. and Siliciano , P. G. 1994 . Nucleic Acids Res , 22 : 5190 – 5195 .
  • Lescoute , A. , Leontis , N. B. , Massire , C. and Westhof , E. 2005 . Nucleic Acids Res , 33 : 2395 – 2409 . (a). (b) M. Sarvar, C. I. Zirbel, J. Stombaugh, A. Mokdad, and N. B. Leontis. J Math Biol 2007 (in press)
  • Grimme , S. 2006 . J Comput Chem , 27 : 1787 – 1799 . (a). (b) S. Grimme, J. Antony, T. Schwabe, and C. M. Lichtenfeld. Org Biomol Chem 5, 741–758 (2007)
  • Leontis , N. B. and Westhof , E. 1998 . RNA , 4 : 134 – 1153 .
  • ISIS/Draw 2.5 free, MDL Informations System, 14600 Catalina Street, San-Leandro, California 94677, USA.
  • DeLano , W. L. 2002 . The PyMOL Molecular Graphics System DeLano Scientific, San Carlos, CA, USA
  • The Leontis-Westhof (LW) notation2 is followed using the following format: <Base1:Base2 (A/U/G/C)> <Edge1:Edge2 (W/H/S)> <Glycosidic bond orientation(Cis/Trans)> where A, U, G, C, W, H, S stands for adenine, uracil, guanine, cytosine, Watson-Crick edge, Hoogsteen edge, and Sugar edge, respectively
  • In case of triplets and quartets, the letters in bold indicate the W:W trans pair. The other partners and edges involved are indicated within parentheses

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