Nucleic Acid Base Pair Dynamics: The Impact of Sequence and Structure Using Free-Energy Calculations

Journal of the American Chemical Society ◽

10.1021/ja034095r ◽

2003 ◽

Vol 125 (17) ◽

pp. 4998-4999 ◽

Author(s):

Emmanuel Giudice ◽

Richard Lavery

Keyword(s):

Free Energy ◽

Nucleic Acid ◽

Base Pair ◽

Free Energy Calculations ◽

Acid Base ◽

Energy Calculations ◽

Nucleic Acid Base ◽

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A standard reference frame for the description of nucleic acid base-pair geometry 1 1Edited by P. E. Wright 2 2This is a document of the Nomenclature Committee of IUBMB (NC-IUBMB)/IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN), whose members are R. Cammack (chairman), A. Bairoch, H.M. Berman, S. Boyce, C.R. Cantor, K. Elliott, D. Horton, M. Kanehisa, A. Kotyk, G.P. Moss, N. Sharon and K.F. Tipton.

Journal of Molecular Biology ◽

10.1006/jmbi.2001.4987 ◽

2001 ◽

Vol 313 (1) ◽

pp. 229-237 ◽

Author(s):

Wilma K Olson ◽

Manju Bansal ◽

Stephen K Burley ◽

Richard E Dickerson ◽

Mark Gerstein ◽

...

Keyword(s):

Nucleic Acid ◽

Reference Frame ◽

Base Pair ◽

Joint Commission ◽

Acid Base ◽

Nomenclature Committee ◽

Biochemical Nomenclature ◽

Nucleic Acid Base

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ChemInform Abstract: Synthesis and X-Ray Crystal Structure of a Novel Tetrathiafulvalene Dimethyl(2,4-dioxo(1H,3H)pyrimido)tetrathiafulvalene, Able to Form Intermolecular Hydrogen Bonds of Nucleic Acid Base-Pair Type.

10.1002/chin.199527161 ◽

2010 ◽

Vol 26 (27) ◽

pp. no-no

Author(s):

O. NEILANDS ◽

S. BELYAKOV ◽

V. TILIKA ◽

A. EDZINA

Keyword(s):

Crystal Structure ◽

Nucleic Acid ◽

Hydrogen Bonds ◽

Base Pair ◽

Pair Type ◽

Acid Base ◽

Intermolecular Hydrogen Bonds ◽

X Ray ◽

Nucleic Acid Base

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Flexibly capped β-cyclodextrins by the hydrogen-bonded nucleic acid base pair. The pH-control of binding ability by an on-off-switched capping

Tetrahedron Letters ◽

10.1016/s0040-4039(00)98325-4 ◽

1985 ◽

Vol 26 (14) ◽

pp. 1735-1738 ◽

Author(s):

Katuyuki Nagai ◽

Shigeo Ukal ◽

Kenji Hayakawa ◽

Ken Kanematsu

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Acid Base ◽

Binding Ability ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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Nucleobase difunctionalized .beta.-cyclodextrins. Preparation and spectral observation of base stacking and the hydrogen-bonded nucleic acid base pair

The Journal of Organic Chemistry ◽

10.1021/jo00371a003 ◽

1986 ◽

Vol 51 (21) ◽

pp. 3931-3939 ◽

Author(s):

Katsuyuki Nagai ◽

Kenji Hayakawa ◽

Shigeo Ukai ◽

Ken Kanematsu

Keyword(s):

Nucleic Acid ◽

Base Pair ◽

Spectral Observation ◽

Base Stacking ◽

Acid Base ◽

Nucleic Acid Base ◽

Hydrogen Bonded

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Calculating stacking interactions in nucleic acid base-pair steps using spin-component scaling and local second order Møller–Plesset perturbation theory

Physical Chemistry Chemical Physics ◽

10.1039/b718691f ◽

2008 ◽

Vol 10 (19) ◽

pp. 2785 ◽

Author(s):

J. Grant Hill ◽

James A. Platts

Keyword(s):

Perturbation Theory ◽

Nucleic Acid ◽

Base Pair ◽

Second Order ◽

Spin Component ◽

Stacking Interactions ◽

Acid Base ◽

Nucleic Acid Base ◽

Moller Plesset ◽

Plesset Perturbation Theory

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Free energy increments for hydrogen bonds in nucleic acid base pairs

Journal of the American Chemical Society ◽

10.1021/ja00246a047 ◽

1987 ◽

Vol 109 (12) ◽

pp. 3783-3785 ◽

Author(s):

Douglas H. Turner ◽

Naoki Sugimoto ◽

Ryszard Kierzek ◽

Scott D. Dreiker

Keyword(s):

Free Energy ◽

Nucleic Acid ◽

Hydrogen Bonds ◽

Acid Base ◽

Nucleic Acid Base

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Biological agent identification by nucleic acid base-pair analysis using surface-enhanced Raman spectroscopy

10.1117/12.336858 ◽

1999 ◽

Author(s):

Stuart Farquharson ◽

Wayne W. Smith ◽

Susan Elliott ◽

Jay F. Sperry

Keyword(s):

Raman Spectroscopy ◽

Nucleic Acid ◽

Base Pair ◽

Surface Enhanced Raman Spectroscopy ◽

Biological Agent ◽

Acid Base ◽

Surface Enhanced ◽

Nucleic Acid Base ◽

Surface Enhanced Raman ◽

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Potential Energy and Free Energy Surfaces of All Ten Canonical and Methylated Nucleic Acid Base Pairs: Molecular Dynamics and Quantum Chemical ab Initio Studies

The Journal of Physical Chemistry B ◽

10.1021/jp0104886 ◽

2001 ◽

Vol 105 (24) ◽

pp. 5804-5817 ◽

Author(s):

Martin Kabeláč ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Nucleic Acid ◽

Potential Energy ◽

Ab Initio ◽

Quantum Chemical ◽

Acid Base ◽

Nucleic Acid Base ◽

Energy Surfaces

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Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes

Computational Studies of RNA and DNA ◽

10.1007/978-1-4020-4851-3_8 ◽

2006 ◽

pp. 211-234

Author(s):

David L. Beveridge ◽

Surjit B. Dixit ◽

Bethany L. Kormos ◽

Anne M. Baranger ◽

B. Jayaram

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Nucleic Acid ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Energy Calculations ◽

Protein Nucleic Acid ◽

Dynamics Simulations

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Artificial Reaction Coordinate “Tunneling” In Free Energy Calculations: Nucleic Acid Cleavage By Ribonuclease-H

Biophysical Journal ◽

10.1016/j.bpj.2008.12.3750 ◽

2009 ◽

Vol 96 (3) ◽

pp. 573a

Author(s):

Edina Rosta ◽

H. Lee Woodcock ◽

Bernard R. Brooks ◽

Gerhard Hummer

Keyword(s):

Free Energy ◽

Nucleic Acid ◽

Free Energy Calculations ◽

Reaction Coordinate ◽

Ribonuclease H ◽

Energy Calculations ◽

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