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Journal of Biomolecular Structure and Dynamics Volume 16, 1998 - Issue 3
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Original Articles

The Solution Conformation of a Carbocyclic Analog of the Dickerson-Drew Dodecamer: Comparison with its own X-ray Structure and that of the NMR Structure of the Native Counterpart

Aleksej Yu. Denisov Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23, Uppsala, Sweden
,
E. V. Zamaratski Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23, Uppsala, Sweden
,
Tatiana V. Maltseva Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23, Uppsala, Sweden
,
Anders Sandström Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23, Uppsala, Sweden
,
Somer Bekiroglu Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23, Uppsala, Sweden
,
Karl-Heinz Altmann Department of Oncology, Novartis Pharma Inc., CH-4002, Basel, Switzerland
,
Martin Egli Drug Discovery Program, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, Chicago, IL, 60611-3008, USA
&
Jyoti Chattopadhyaya Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23, Uppsala, Sweden
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Pages 547-568 | Received 16 Jun 1998, Published online: 21 May 2012

Citations (20)

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J. Isaksson, O. Plashkevych, P.I. Pradeepkumar, S. Chatterjee, J. Barman, W. Pathmasiri, P. Shrivastava, C. Petit & J. Chattopadhyaya. (2005) Oxetane Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions—An NMR Structure and Hydration Study. Journal of Biomolecular Structure and Dynamics 23:3, pages 299-330.
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D. Djuranovic & B. Hartmann. (2003) Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states. Journal of Biomolecular Structure and Dynamics 20:6, pages 771-788.
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J. Isaksson, E. Zamaratski, T.V. Maltseva, P. Agback, A. Kumar & J. Chattopadhyaya. (2001) The First Example of a Hoogsteen Basepaired DNA Duplex in Dynamic Equilibrium with a Watson-Crick Basepaired Duplex—A Structural (NMR), Kinetic and Thermodynamic Study. Journal of Biomolecular Structure and Dynamics 18:6, pages 783-806.
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Articles from other publishers (17)

Sudakshina Ganguly, N. Arul Murugan, Debasis Ghosh, Nagarjun Narayanaswamy, Thimmaiah Govindaraju & Gautam Basu. (2021) DNA Minor Groove-Induced cis – trans Isomerization of a Near-Infrared Fluorescent Probe . Biochemistry 60:26, pages 2084-2097.
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Ilektra‐Chara Giassa, Andrea Vavrinská, Jiří Zelinka, Jakub Šebera, Vladimír Sychrovský, Rolf Boelens, Radovan Fiala & Lukáš Trantírek. (2020) HERMES – A Software Tool for the Prediction and Analysis of Magnetic‐Field‐Induced Residual Dipolar Couplings in Nucleic Acids. ChemPlusChem 85:9, pages 2177-2185.
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Alexey Y. Denisov, Francis P. McManus, Derek K. O'Flaherty, Anne M. Noronha & Christopher J. Wilds. (2017) Structural basis of interstrand cross-link repair by O 6 -alkylguanine DNA alkyltransferase . Organic & Biomolecular Chemistry 15:39, pages 8361-8370.
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Guohui Li, Hujun Shen, Dinglin Zhang, Yan Li & Honglei Wang. (2016) Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay–Berne and Electric Multipole Potentials. Journal of Chemical Theory and Computation 12:2, pages 676-693.
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Alexander A. Lomzov, Yury N. Vorobjev & Dmitrii V. Pyshnyi. (2015) Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation. The Journal of Physical Chemistry B 119:49, pages 15221-15234.
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Eric Largy & Jean-Louis Mergny. (2014) Shape matters: size-exclusion HPLC for the study of nucleic acid structural polymorphism. Nucleic Acids Research 42:19, pages e149-e149.
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Rohit Singh & Robert Vince. (2012) 2-Azabicyclo[2.2.1]hept-5-en-3-one: Chemical Profile of a Versatile Synthetic Building Block and its Impact on the Development of Therapeutics. Chemical Reviews 112:8, pages 4642-4686.
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Pablo Peñalver, Filipa MarceloJesús Jiménez‐BarberoCristina Vicent. (2011) Carbohydrate Recognition at the Minor‐Groove of the Self‐Complementary Duplex d(CGCGAATTCGCG) 2 by a Synthetic Glyco‐oligoamide . Chemistry – A European Journal 17:16, pages 4561-4570.
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Pablo D. Dans, Ari Zeida, Matías R. Machado & Sergio Pantano. (2010) A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. Journal of Chemical Theory and Computation 6:5, pages 1711-1725.
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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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Mark Lukin & Carlos de los Santos. (2006) NMR Structures of Damaged DNA. Chemical Reviews 106:2, pages 607-686.
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J. Isaksson & J. Chattopadhyaya. (2005) A Uniform Mechanism Correlating Dangling-End Stabilization and Stacking Geometry. Biochemistry 44:14, pages 5390-5401.
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D. Djuranovic & B. Hartmann. (2004) DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations. Biopolymers 73:3, pages 356-368.
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Jérôme Boisbouvier, Frank Delaglio & Ad Bax. (2003) Direct observation of dipolar couplings between distant protons in weakly aligned nucleic acids. Proceedings of the National Academy of Sciences 100:20, pages 11333-11338.
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Haribabu Arthanari, Kevin J. McConnell, Richard Beger, Matthew A. Young, D. L. Beveridge & Philip H. Bolton. (2002) Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants. Biopolymers 68:1, pages 3-15.
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Bernd Wellenzohn, Wolfgang Flader, Rudolf H. Winger, Andreas Hallbrucker, Erwin Mayer & Klaus R. Liedl. (2002) Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2. Biopolymers 61:4, pages 276-286.
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Nico Tjandra, Shin-ichi Tate, Akira Ono, Masatsune Kainosho & Ad Bax. (2000) The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase. Journal of the American Chemical Society 122:26, pages 6190-6200.
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