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For: Wellenzohn B, Flader W, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions. Biochemistry 2002;41:4088-95. [PMID: 11900552 DOI: 10.1021/bi015642t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Xiao S, Zhu H, Wang L, Liang H. DNA conformational flexibility study using phosphate backbone neutralization model. SOFT MATTER 2014;10:1045-1055. [PMID: 24983118 DOI: 10.1039/c3sm52345d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
2
Zhitnikova MY, Boryskina OP, Shestopalova AV. Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. J Biomol Struct Dyn 2013;32:1670-85. [PMID: 23998351 DOI: 10.1080/07391102.2013.830579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
3
Khesbak H, Savchuk O, Tsushima S, Fahmy K. The Role of Water H-Bond Imbalances in B-DNA Substate Transitions and Peptide Recognition Revealed by Time-Resolved FTIR Spectroscopy. J Am Chem Soc 2011;133:5834-42. [DOI: 10.1021/ja108863v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
4
Boryskina OP, Tkachenko MY, Shestopalova AV. Protein-DNA complexes: specificity and DNA readout mechanisms. ACTA ACUST UNITED AC 2011. [DOI: 10.7124/bc.00007c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
5
Oguey C, Foloppe N, Hartmann B. Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions. PLoS One 2010;5:e15931. [PMID: 21209967 PMCID: PMC3012109 DOI: 10.1371/journal.pone.0015931] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 11/30/2010] [Indexed: 01/05/2023]  Open
6
Boryskina OP, Tkachenko MY, Shestopalova AV. Variability of DNA structure and protein-nucleic acid reconginition. ACTA ACUST UNITED AC 2010. [DOI: 10.7124/bc.00016a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
7
Sequence-Dependent DNA Flexibility Mediates DNase I Cleavage. J Mol Biol 2010;395:123-33. [DOI: 10.1016/j.jmb.2009.10.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 10/09/2009] [Accepted: 10/12/2009] [Indexed: 11/17/2022]
8
Hart K, Nilsson L. Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: a molecular dynamics study. Proteins 2009;73:325-37. [PMID: 18433057 DOI: 10.1002/prot.22062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
9
Heddi B, Foloppe N, Bouchemal N, Hantz E, Hartmann B. Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition. J Am Chem Soc 2007;128:9170-7. [PMID: 16834390 DOI: 10.1021/ja061686j] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
10
René B, Masliah G, Antri SE, Fermandjian S, Mauffret O. Conformations and Dynamics of the Phosphodiester Backbone of a DNA Fragment That Bears a Strong Topoisomerase II Cleavage Site. J Phys Chem B 2007;111:4235-43. [PMID: 17391020 DOI: 10.1021/jp0683115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
11
Heddi B, Foloppe N, Hantz E, Hartmann B. The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J Mol Biol 2007;368:1403-11. [PMID: 17395202 DOI: 10.1016/j.jmb.2007.03.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 03/01/2007] [Accepted: 03/06/2007] [Indexed: 11/17/2022]
12
Wibowo FR, Rauch C, Trieb M, Liedl KR. M.TaqI facilitates the base flipping via an unusual DNA backbone conformation. Biopolymers 2005;79:128-38. [PMID: 16047360 DOI: 10.1002/bip.20341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
13
Madhumalar A, Bansal M. Sequence preference for BI/BII conformations in DNA: MD and crystal structure data analysis. J Biomol Struct Dyn 2005;23:13-27. [PMID: 15918673 DOI: 10.1080/07391102.2005.10507043] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
14
Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1574-1400(05)01006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
15
Wibowo FR, Trieb M, Rauch C, Wellenzohn B, Liedl KR. The N6-Methyl Group of Adenine Further Increases the BI Stability of DNA Compared to C5-Methyl Groups. J Phys Chem B 2004;109:557-64. [PMID: 16851047 DOI: 10.1021/jp048519v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
16
Cheatham TE. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr Opin Struct Biol 2004;14:360-7. [PMID: 15193317 DOI: 10.1016/j.sbi.2004.05.001] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
17
Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Mayer E, Liedl KR. Daunomycin Intercalation Stabilizes Distinct Backbone Conformations of DNA. J Biomol Struct Dyn 2004;21:713-24. [PMID: 14769064 DOI: 10.1080/07391102.2004.10506961] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
18
Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Liedl KR. Dynamics of DNA:  BI and BII Phosphate Backbone Transitions. J Phys Chem B 2004. [DOI: 10.1021/jp037079p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
19
Djuranovic D, Hartmann B. DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations. Biopolymers 2004;73:356-68. [PMID: 14755572 DOI: 10.1002/bip.10528] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
20
Wibowo FR, Rauch C, Trieb M, Wellenzohn B, Liedl KR. Water-mediated contacts in thetrp-repressor operator complex recognition process. Biopolymers 2004;73:668-81. [PMID: 15048770 DOI: 10.1002/bip.20023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
21
Obika S, Reddy SY, Bruice TC. Sequence specific DNA binding of Ets-1 transcription factor: molecular dynamics study on the Ets domain--DNA complexes. J Mol Biol 2003;331:345-59. [PMID: 12888343 DOI: 10.1016/s0022-2836(03)00726-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
22
Djuranovic D, Hartmann B. Conformational characteristics and correlations in crystal structures of nucleic acid oligonucleotides: evidence for sub-states. J Biomol Struct Dyn 2003;20:771-88. [PMID: 12744707 DOI: 10.1080/07391102.2003.10506894] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
23
Chirakul P, Sigurdsson ST. Stereospecific syntheses of 3'-deuterated pyrimidine nucleosides and their site-specific incorporation into DNA. Org Lett 2003;5:917-9. [PMID: 12633105 DOI: 10.1021/ol034102g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
24
Rauch C, Trieb M, Flader W, Wellenzohn B, Winger RH, Mayer E, Hallbrucker A, Liedl KR. PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA. J Mol Biol 2002;324:491-500. [PMID: 12445784 DOI: 10.1016/s0022-2836(02)01089-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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