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Journal of Biomolecular Structure and Dynamics Volume 26, 2009 - Issue 5
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Original Articles

Dependence of Deformability of Geometries and Characteristics of Intramolecular Hydrogen Bonds in Canonical 2′-Deoxyribonucleotides on DNA Conformations

Gennady V. Palamarchuk SSI “Institute for Single Crystals” National Academy of Science of Ukraine, 60 Lenina Ave., Kharkiv, 61001, Ukraine; Ukrainian-American Laboratory of Computational Chemistry Kharkiv Ukraine and Jackson Mississippi
,
Oleg V. Shishkin SSI “Institute for Single Crystals” National Academy of Science of Ukraine, 60 Lenina Ave., Kharkiv, 61001, Ukraine; Ukrainian-American Laboratory of Computational Chemistry Kharkiv Ukraine and Jackson Mississippi; Computational Center for Molecular Structure and Interactions, Jackson State University
,
Leonid Gorb Ukrainian-American Laboratory of Computational Chemistry Kharkiv Ukraine and Jackson Mississippi; Computational Center for Molecular Structure and Interactions, Jackson State University; Department of Molecular Biophysics, Institute of Molecular Biology and Genetics National Academy of Science of Ukraine, 150 Zabolotnogo str., Kyiv, 03143, Ukraine
&
Jerzy Leszczynski Ukrainian-American Laboratory of Computational Chemistry Kharkiv Ukraine and Jackson Mississippi; Computational Center for Molecular Structure and Interactions, Jackson State University
Pages 653-661 | Received 15 May 2008, Published online: 15 May 2012

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Ahmed A. El-Sayed, A. Tamara Molina, M.C. Álvarez-Ros & M. Alcolea Palafox. (2015) Conformational analysis of the anti-HIV Nikavir prodrug: comparisons with AZT and Thymidine, and establishment of structure–activity relationships/tendencies in other 6′-derivatives. Journal of Biomolecular Structure and Dynamics 33:4, pages 723-748.
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YevgenP. Yurenko, RomanO. Zhurakivsky, SvitlanaP. Samijlenko & DmytroM. Hovorun. (2011) Intramolecular CH…O Hydrogen Bonds in the AI and BI DNA-like Conformers of Canonical Nucleosides and their Watson-Crick Pairs. Quantum Chemical and AIM Analysis. Journal of Biomolecular Structure and Dynamics 29:1, pages 51-65.
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Marianne Rooman, Emilie Cauët, Jacques Liévin & René Wintjens. (2011) Conformations Consistent with Charge Migration Observed in DNA and RNA X-ray Structures. Journal of Biomolecular Structure and Dynamics 28:6, pages 949-954.
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Aditi Borkar, Indira Ghosh & Dhananjay Bhattacharyya. (2010) Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach. Journal of Biomolecular Structure and Dynamics 27:5, pages 695-712.
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Articles from other publishers (18)

Leonid Gorb, Oleg V. Shishkin & Tetiana Zubatiuk. (2023) The structure of DNA fragments: Quantum-chemical modelling. BBA Advances 3, pages 100082.
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D. Kattan, M. Alcolea Palafox, S.K. Rathor & V.K. Rastogi. (2016) A DFT analysis of the molecular structure, vibrational spectra and other molecular properties of 5-nitrouracil and comparison with uracil. Journal of Molecular Structure 1106, pages 300-315.
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Yevgen P. Yurenko, Jan Novotný, Vladimir Sklenář & Radek Marek. (2015) Substituting CF 2 for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions . Chemistry – A European Journal 21:49, pages 17933-17943.
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Tetiana A. Zubatiuk, Gennady V. Palamarchuk, Oleg V. Shishkin, Leonid Gorb & Jerzy Leszczynski. 2014. Application of Computational Techniques in Pharmacy and Medicine. Application of Computational Techniques in Pharmacy and Medicine 137 180 .
Jie Shen, Haijun Wang & Yongmei Xia. (2012) A DFT study of hydrogen bond interactions between oxidative 2′-deoxyadenosine nucleotides and RNA nucleotides. Structural Chemistry 24:2, pages 559-571.
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Gennady V. Palamarchuk, Oleg V. Shishkin, Leonid Gorb & Jerzy Leszczynski. (2013) Nucleic Acid Bases in Anionic 2′-Deoxyribonucleotides: A DFT/B3LYP Study of Structures, Relative Stability, and Proton Affinities. The Journal of Physical Chemistry B 117:10, pages 2841-2849.
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Tetiana A. Zubatiuk, Oleg V. Shishkin, Leonid Gorb, Dmytro M. Hovorun & Jerzy Leszczynski. (2013) B-DNA characteristics are preserved in double stranded d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: conclusions from DFT/M06-2X study. Physical Chemistry Chemical Physics 15:41, pages 18155.
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Arnošt Mládek, Miroslav Krepl, Daniel Svozil, Petr Čech, Michal Otyepka, Pavel Banáš, Marie Zgarbová, Petr Jurečka & Jiří Šponer. (2013) Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory. Physical Chemistry Chemical Physics 15:19, pages 7295.
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Stefan A. P. Lenz, Jennifer L. Kellie & Stacey D. Wetmore. (2012) Glycosidic Bond Cleavage in Deoxynucleotides: Effects of Solvent and the DNA Phosphate Backbone in the Computational Model. The Journal of Physical Chemistry B 116:49, pages 14275-14284.
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Vladimír Sychrovský, Zuzana Sochorová Vokáčová & Lukáš Trantírek. (2012) Guanine Bases in DNA G-Quadruplex Adopt Nonplanar Geometries Owing to Solvation and Base Pairing. The Journal of Physical Chemistry A 116:16, pages 4144-4151.
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Jiří Šponer, Arnošt Mládek, Judit E. Šponer, Daniel Svozil, Marie Zgarbová, Pavel Banáš, Petr Jurečka & Michal Otyepka. (2012) The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Physical Chemistry Chemical Physics 14:44, pages 15257.
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Andrea L. Millen, Breanne L. Kamenz, Fern M. V. Leavens, Richard A. Manderville & Stacey D. Wetmore. (2011) Conformational Flexibility of C8-Phenoxylguanine Adducts in Deoxydinucleoside Monophosphates. The Journal of Physical Chemistry B 115:44, pages 12993-13002.
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Marie Zgarbová, Petr Jurečka, Pavel Banáš, Michal Otyepka, Judit E. Šponer, Neocles B. Leontis, Craig L. Zirbel & Jiří Šponer. (2011) Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations. The Journal of Physical Chemistry A 115:41, pages 11277-11292.
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Cassandra D. M. Churchill & Stacey D. Wetmore. (2011) Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA. Physical Chemistry Chemical Physics 13:36, pages 16373.
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Arnošt MládekJudit E. ŠponerPetr JurečkaPavel BanášMichal OtyepkaDaniel SvozilJiří Šponer. (2010) Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. Journal of Chemical Theory and Computation 6:12, pages 3817-3835.
Crossref
Jiří Šponer, Judit E. Šponer, Anton I. Petrov & Neocles B. Leontis. (2010) Quantum Chemical Studies of Nucleic Acids: Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities?. The Journal of Physical Chemistry B 114:48, pages 15723-15741.
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Andrea L. Millen, Richard A. Manderville & Stacey D. Wetmore. (2010) Conformational Flexibility of C8-Phenoxyl-2′-deoxyguanosine Nucleotide Adducts. The Journal of Physical Chemistry B 114:12, pages 4373-4382.
Crossref
Oleg V. Shishkin, Przemyslaw Dopieralski, Gennady V. Palamarchuk & Zdzislaw Latajka. (2010) Rotation around the glycosidic bond as driving force of proton transfer in protonated 2′-deoxyriboadenosine monophosphate (dAMP). Chemical Physics Letters 490:4-6, pages 221-225.
Crossref

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