Solution structure of a DNA duplex containing a formamide-adenine base pair

2002 ◽  
Vol 80 (7) ◽  
pp. 609-617 ◽  
Author(s):  
Corinne Maufrais ◽  
Yves Boulard
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Hydrogen Bond ◽  
Base Pair ◽  
Solution Structure ◽  
Side Chain ◽  
Key Words Dna ◽  
Anti Conformation ◽  
Adenine Base ◽  
Cis Isomer

The N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide residue results from a ring fragmentation product of thymine or cytosine. The presence of a formamide-adenine base pair in the sequence 5'd(AGGAACCACG).d(CGTGGFTCCT) has been studied by 1H and 31P nuclear magnetic resonance (NMR) and molecular dynamics. There are two possible isomers for the formamide side chain, either cis or trans. For each isomer, we observed an equilibrium in solution between two forms. First, a species where the formamide is intrahelical and paired with the facing adenine. For the cis isomer, the formamide is in a syn conformation and two hydrogen bonds with adenine are formed. The trans isomer is in an anti conformation and a single hydrogen bond is observed. In the second form, whatever the isomer, the formamide is rejected outside the helix, whereas the adenine remains inside. Key words: DNA structure, mutagenesis, NMR, molecular dynamics, formamide.

Refinement of the solution structure of the DNA dodecamer 5'd(CGCGPATTCGCG)2 containing a stable purine-thymine base pair: combined use of nuclear magnetic resonance and restrained molecular dynamics

Biochemistry ◽  
1988 ◽  
Vol 27 (11) ◽  
pp. 4185-4197 ◽  
Author(s):  
G. Marius Clore ◽  
Hartmut Oschkinat ◽  
Larry W. McLaughlin ◽  
Fritz Benseler ◽  
Claudia Scalfi Happ ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Base Pair ◽  
Solution Structure ◽  
Combined Use ◽  
Dna Dodecamer ◽  
Restrained Molecular Dynamics ◽  
Nuclear Magnetic

Solution structure of FK506 from nuclear magnetic resonance and molecular dynamics

1990 ◽  
Vol 112 (25) ◽  
pp. 9434-9436 ◽  
Author(s):  
Peter Karuso ◽  
Horst Kessler ◽  
Dale F. Mierke
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Solution Structure ◽  
Nuclear Magnetic

scholarly journals Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

2021 ◽  
Vol 8 ◽  
Author(s):  
Lorenzo Di Rienzo ◽  
Mattia Miotto ◽  
Leonardo Bò ◽  
Giancarlo Ruocco ◽  
Domenico Raimondo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Computational Method ◽  
Side Chain ◽  
Water Molecules ◽  
Amino Acid Side Chain ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Protein Environment

Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.

Solution Structure of two Mismatches A . A and T . T in the K-ras Gene Context by Nuclear Magnetic Resonance and Molecular Dynamics

1995 ◽  
Vol 228 (2) ◽  
pp. 279-290 ◽  
Author(s):  
Virginie Gervais ◽  
Jean A. H. Cognet ◽  
Marc Bret ◽  
Lawrence C. Sowers ◽  
G. Victor Fazakerley
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Solution Structure ◽  
Ras Gene ◽  
Nuclear Magnetic

A study of secondary and tertiary solution structure of yeast tRNAAspby nuclear magnetic resonance. Assignment of G.cntdot.U ring imidogen and hydrogen-bonded base pair proton resonances

Biochemistry ◽  
1976 ◽  
Vol 15 (9) ◽  
pp. 1883-1888 ◽  
Author(s):  
George T. Robillard ◽  
C. W. Hilbers ◽  
Brian R. Reid ◽  
Jean Gangloff ◽  
Guy Dirheimer ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Resonance Assignment ◽  
Base Pair ◽  
Solution Structure ◽  
Proton Resonances ◽  
Nuclear Magnetic ◽  
Hydrogen Bonded

scholarly journals Gramicidin A Backbone and Side Chain Dynamics Evaluated by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Experiments. II: Nuclear Magnetic Resonance Experiments

2011 ◽  
Vol 115 (22) ◽  
pp. 7427-7432 ◽  
Author(s):  
Vitaly V. Vostrikov ◽  
Hong Gu ◽  
Helgi I. Ingólfsson ◽  
James F. Hinton ◽  
Olaf S. Andersen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Molecular Dynamics Simulations ◽  
Gramicidin A ◽  
Side Chain ◽  
Chain Dynamics ◽  
Dynamics Simulations ◽  
Side Chain Dynamics ◽  
Nuclear Magnetic

Refinement of the solution structure of the DNA decamer 5'd(CTGGATCCAG)2: combined use of nuclear magnetic resonance and restrained molecular dynamics

Biochemistry ◽  
1987 ◽  
Vol 26 (12) ◽  
pp. 3734-3744 ◽  
Author(s):  
Michael Nilges ◽  
G. Marius Clore ◽  
Angela M. Gronenborn ◽  
Norbert Piel ◽  
Larry W. McLaughlin
Keyword(s):  
Molecular Dynamics ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Solution Structure ◽  
Combined Use ◽  
Restrained Molecular Dynamics ◽  
Nuclear Magnetic
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