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457 related items for PubMed ID: 23891726

  • 1. RNA structure and dynamics: a base pairing perspective.
    Halder S, Bhattacharyya D.
    Prog Biophys Mol Biol; 2013 Nov; 113(2):264-83. PubMed ID: 23891726
    [Abstract] [Full Text] [Related]

  • 2. Stacking geometry for non-canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion-corrected DFT-D study.
    Mondal M, Mukherjee S, Halder S, Bhattacharyya D.
    Biopolymers; 2015 Jun; 103(6):328-38. PubMed ID: 25652776
    [Abstract] [Full Text] [Related]

  • 3. Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis.
    Das J, Mukherjee S, Mitra A, Bhattacharyya D.
    J Biomol Struct Dyn; 2006 Oct; 24(2):149-61. PubMed ID: 16928138
    [Abstract] [Full Text] [Related]

  • 4. Quantum chemical studies of structures and binding in noncanonical RNA base pairs: the trans Watson-Crick:Watson-Crick family.
    Sharma P, Mitra A, Sharma S, Singh H, Bhattacharyya D.
    J Biomol Struct Dyn; 2008 Jun; 25(6):709-32. PubMed ID: 18399704
    [Abstract] [Full Text] [Related]

  • 5. Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.
    Sponer JE, Spacková N, Kulhanek P, Leszczynski J, Sponer J.
    J Phys Chem A; 2005 Mar 17; 109(10):2292-301. PubMed ID: 16838999
    [Abstract] [Full Text] [Related]

  • 6. Structures of non-canonical tandem base pairs in RNA helices: review.
    Heus HA, Hilbers CW.
    Nucleosides Nucleotides Nucleic Acids; 2003 Mar 17; 22(5-8):559-71. PubMed ID: 14565230
    [Abstract] [Full Text] [Related]

  • 7. Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies.
    Roy A, Panigrahi S, Bhattacharyya M, Bhattacharyya D.
    J Phys Chem B; 2008 Mar 27; 112(12):3786-96. PubMed ID: 18318519
    [Abstract] [Full Text] [Related]

  • 8. Isostericity and tautomerism of base pairs in nucleic acids.
    Westhof E.
    FEBS Lett; 2014 Aug 01; 588(15):2464-9. PubMed ID: 24950426
    [Abstract] [Full Text] [Related]

  • 9. Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations.
    Mládek A, Sharma P, Mitra A, Bhattacharyya D, Sponer J, Sponer JE.
    J Phys Chem B; 2009 Feb 12; 113(6):1743-55. PubMed ID: 19152254
    [Abstract] [Full Text] [Related]

  • 10. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.
    Csaszar K, Spacková N, Stefl R, Sponer J, Leontis NB.
    J Mol Biol; 2001 Nov 09; 313(5):1073-91. PubMed ID: 11700064
    [Abstract] [Full Text] [Related]

  • 11. On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology.
    Sharma P, Sponer JE, Sponer J, Sharma S, Bhattacharyya D, Mitra A.
    J Phys Chem B; 2010 Mar 11; 114(9):3307-20. PubMed ID: 20163171
    [Abstract] [Full Text] [Related]

  • 12. Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).
    Chen X, McDowell JA, Kierzek R, Krugh TR, Turner DH.
    Biochemistry; 2000 Aug 01; 39(30):8970-82. PubMed ID: 10913310
    [Abstract] [Full Text] [Related]

  • 13. Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view.
    Sponer JE, Réblova K, Mokdad A, Sychrovský V, Leszczynski J, Sponer J.
    J Phys Chem B; 2007 Aug 02; 111(30):9153-64. PubMed ID: 17602515
    [Abstract] [Full Text] [Related]

  • 14. Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study.
    Halder A, Halder S, Bhattacharyya D, Mitra A.
    Phys Chem Chem Phys; 2014 Sep 14; 16(34):18383-96. PubMed ID: 25070186
    [Abstract] [Full Text] [Related]

  • 15. RNA solvation: a molecular dynamics simulation perspective.
    Auffinger P, Westhof E.
    Biopolymers; 2014 Sep 14; 56(4):266-74. PubMed ID: 11754340
    [Abstract] [Full Text] [Related]

  • 16. DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.
    Shankar A, Jagota A, Mittal J.
    J Phys Chem B; 2012 Oct 11; 116(40):12088-94. PubMed ID: 22967176
    [Abstract] [Full Text] [Related]

  • 17. Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs.
    Lee JC, Gutell RR.
    J Mol Biol; 2004 Dec 10; 344(5):1225-49. PubMed ID: 15561141
    [Abstract] [Full Text] [Related]

  • 18. Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study.
    Zendlová L, Hobza P, Kabelác M.
    J Phys Chem B; 2007 Mar 15; 111(10):2591-609. PubMed ID: 17302446
    [Abstract] [Full Text] [Related]

  • 19. A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis.
    Réblová K, Šponer JE, Špačková N, Beššeová I, Šponer J.
    J Phys Chem B; 2011 Dec 01; 115(47):13897-910. PubMed ID: 21999672
    [Abstract] [Full Text] [Related]

  • 20. Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
    Dutheil JY, Jossinet F, Westhof E.
    Mol Biol Evol; 2010 Aug 01; 27(8):1868-76. PubMed ID: 20211929
    [Abstract] [Full Text] [Related]

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