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Original Articles

Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis

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Pages 13-27 | Received 12 Nov 2004, Published online: 15 May 2012

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Mariia Yu. Zhitnikova, Olena P. Boryskina & Anna V. Shestopalova. (2014) Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein–DNA recognition. Journal of Biomolecular Structure and Dynamics 32:10, pages 1670-1685.
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Vigneshwar Ramakrishnan, Srivatsan Jagannathan, Abdul Rajjak Shaikh & Raj Rajagopalan. (2012) Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain. Journal of Biomolecular Structure and Dynamics 29:4, pages 743-756.
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Difei Wang, NikolaiB. Ulyanov & VictorB. Zhurkin. (2010) Sequence-dependent Kink-and-Slide Deformations of Nucleosomal DNA Facilitated by Histone Arginines Bound in the Minor Groove. Journal of Biomolecular Structure and Dynamics 27:6, pages 843-859.
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James C. Robertson & Thomas E CheathamIIIIII. (2015) DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations. The Journal of Physical Chemistry B 119:44, pages 14111-14119.
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Aleksandra Karolak & Arjan van der Vaart. (2015) BII stability and base step flexibility of N6-adenine methylated GATC motifs. Biophysical Chemistry 203-204, pages 22-27.
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Rodrigo Galindo‐Murillo, Christina Bergonzo & Thomas E. CheathamIIIIII. (2014) Molecular Modeling of Nucleic Acid Structure: Setup and Analysis. Current Protocols in Nucleic Acid Chemistry 56:1.
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Evgenia N. Nikolova, Gavin D. Bascom, Ioan Andricioaei & Hashim M. Al-Hashimi. (2012) Probing Sequence-Specific DNA Flexibility in A-Tracts and Pyrimidine-Purine Steps by Nuclear Magnetic Resonance 13 C Relaxation and Molecular Dynamics Simulations . Biochemistry 51:43, pages 8654-8664.
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Kiran R. Gore, Ganesh N. Nawale, S. Harikrishna, Vinita G. Chittoor, Sushil Kumar Pandey, Claudia Höbartner, Swati Patankar & P. I. Pradeepkumar. (2012) Synthesis, Gene Silencing, and Molecular Modeling Studies of 4′- C -Aminomethyl-2′- O -methyl Modified Small Interfering RNAs . The Journal of Organic Chemistry 77:7, pages 3233-3245.
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S. Campagne, V. Gervais & A. Milon. (2011) Nuclear magnetic resonance analysis of protein–DNA interactions. Journal of The Royal Society Interface 8:61, pages 1065-1078.
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Sukanya Halder & Dhananjay Bhattacharyya. (2010) Structural Stability of Tandemly Occurring Noncanonical Basepairs within Double Helical Fragments: Molecular Dynamics Studies of Functional RNA. The Journal of Physical Chemistry B 114:44, pages 14028-14040.
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Arvind Marathe, Deepti Karandur & Manju Bansal. (2009) Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. BMC Structural Biology 9:1.
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Alexander D. MacKerell, Jr.. (2009) Contribution of the Intrinsic Mechanical Energy of the Phosphodiester Linkage to the Relative Stability of the A, B I , and B II Forms of Duplex DNA . The Journal of Physical Chemistry B 113:10, pages 3235-3244.
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Katarina Hart & Lennart Nilsson. (2008) Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study. Proteins: Structure, Function, and Bioinformatics 73:2, pages 325-337.
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Stephen Neidle. 2008. Principles of Nucleic Acid Structure. Principles of Nucleic Acid Structure 38 80 .
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Surjit B. Dixit, Sergei Y. Ponomarev & David L. Beveridge. (2006) Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA. Journal of Chemical Information and Modeling 46:3, pages 1084-1093.
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Chia C. Shih & Solon Georghiou. (2006) Large-amplitude fast motions in double-stranded DNA driven by solvent thermal fluctuations. Biopolymers 81:6, pages 450-463.
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