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Original Articles

Crystal Packing Effects on A-DNA Helix Parameters: A Comparative Study of the Isoforms of the Tetragonal & Hexagonal Family of Octamers with Differing Base Sequences

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Pages 11-26 | Received 22 Jun 1993, Published online: 21 May 2012

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Justin P. Peters, Ewa A. Kowal, Pradeep S. Pallan, Martin Egli & L. James Maher$suffix/text()$suffix/text(). (2018) Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography. Journal of Biomolecular Structure and Dynamics 36:11, pages 2753-2772.
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ThomasE. Cheatham$suffix/text()$suffix/text(), Piotr Cieplak & PeterA. Kollman. (1999) A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat. Journal of Biomolecular Structure and Dynamics 16:4, pages 845-862.
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LuzimarG. Fernandez, JuanA. Subirana, Nuria Verdaguer, Dmitrii Pyshnyi, Lourdes Campos & Lucy Malinina. (1997) Structural Variability of A-DNA in Crystals of the Octamer d(pCpCpCpGpCpGpGpG). Journal of Biomolecular Structure and Dynamics 15:1, pages 151-163.
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Jiří Šponer, Jan Florián, Pavel Hobza & Jerzy Leszczynski. (1996) Nonplanar DNA Base Pairs. Journal of Biomolecular Structure and Dynamics 13:5, pages 827-833.
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Articles from other publishers (19)

Weiwei He, Anja Henning-Knechtel & Serdal Kirmizialtin. (2022) Visualizing RNA Structures by SAXS-Driven MD Simulations. Frontiers in Bioinformatics 2.
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Weiwei He, Yen-Lin Chen, Lois Pollack & Serdal Kirmizialtin. (2021) The structural plasticity of nucleic acid duplexes revealed by WAXS and MD. Science Advances 7:17.
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Justin A. Lemkul & Alexander D. MacKerellJr.Jr.. (2017) Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA. Journal of Chemical Theory and Computation 13:5, pages 2072-2085.
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Monica Purushothaman, Anna Varghese, Pradeep Kumar Mandal & Namasivayam Gautham. (2014) Structure of d(CCCCGGTACCGGGG) 2 at 1.65 Å resolution . Acta Crystallographica Section F Structural Biology Communications 70:7, pages 860-865.
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Núria Escaja, Irene Gómez-Pinto, Enrique Pedroso & Carlos González. (2007) Four-Stranded DNA Structures Can Be Stabilized by Two Different Types of Minor Groove G:C:G:C Tetrads. Journal of the American Chemical Society 129:7, pages 2004-2014.
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Franklin A. Hays, Amy Teegarden, Zebulon J. R. Jones, Michael Harms, Dustin Raup, Jeffrey Watson, Emily Cavaliere & P. Shing Ho. (2005) How sequence defines structure: A crystallographic map of DNA structure and conformation. Proceedings of the National Academy of Sciences 102:20, pages 7157-7162.
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Thereza A. Soares, Philippe H. Hünenberger, Mika A. Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto D. Lins, Chris Oostenbrink & Wilfred F. van Gunsteren. (2005) An improved nucleic acid parameter set for the GROMOS force field. Journal of Computational Chemistry 26:7, pages 725-737.
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Thomas E. Cheatham IIIPeter A. Kollman. (2000) Molecular Dynamics Simulation of Nucleic Acids. Annual Review of Physical Chemistry 51:1, pages 435-471.
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David R. Bevan, Leping Li, Lee G. Pedersen & Thomas A. Darden. (2000) Molecular Dynamics Simulations of the d(CCAACGTTGG)2 Decamer: Influence of the Crystal Environment. Biophysical Journal 78:2, pages 668-682.
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Yong Xiong & Muttaiya Sundaralingam. (1998) Crystal structure and conformation of a DNA–RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)–r(GAAGAAGAA). Structure 6:12, pages 1493-1501.
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Uwe Mueller, Gottfried Maier, Alberto Mochi Onori, Luciano Cellai, Hermann Heumann & Udo Heinemann. (1998) Crystal Structure of an Eight-Base Pair Duplex Containing the 3‘-DNA−RNA-5‘ Junction Formed during Initiation of Minus-Strand Synthesis of HIV Replication. Biochemistry 37:35, pages 12005-12011.
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Valentina Tereshko, Sergei Gryaznov & Martin Egli. (1998) Consequences of Replacing the DNA 3‘-Oxygen by an Amino Group:  High-Resolution Crystal Structure of a Fully Modified N3‘ → P5‘ Phosphoramidate DNA Dodecamer Duplex. Journal of the American Chemical Society 120:2, pages 269-283.
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Thomas E. CheathamIIIIII, Michael F. Crowley, Thomas Fox & Peter A. Kollman. (1997) A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions. Proceedings of the National Academy of Sciences 94:18, pages 9626-9630.
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Thomas E. Cheatham & Peter A. Kollman. (1997) Molecular Dynamics Simulations Highlight the Structural Differences among DNA:DNA, RNA:RNA, and DNA:RNA Hybrid Duplexes. Journal of the American Chemical Society 119:21, pages 4805-4825.
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E.B Starikov. (1997) Chemical physics of solid-state nucleic acids: new intriguing horizons. Physics Reports 284:1-2, pages 1-89.
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D. B. Tippin & M. Sundaralingam. (1997) Comparison of Major Groove Hydration in Isomorphous A-DNA Octamers and Dependence on Base Sequence and Local Helix Geometry. Biochemistry 36:3, pages 536-543.
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Markus C. Wahl & Muttaiya Sundaralingam. (1999) Crystal structures of A‐DNA duplexes. Biopolymers 44:1, pages 45-63.
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Helen M. Berman, Anke Gelbin & John Westbrook. (1996) Nucleic acid crystallography: A view from the nucleic acid database. Progress in Biophysics and Molecular Biology 66:3, pages 255-288.
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Stefan Portmann, Nassim Usman & Martin Egli. (2002) The Crystal Structure of r(CCCCGGGG) in Two Distinct Lattices. Biochemistry 34:23, pages 7569-7575.
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