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Literature DB >> 3863112

A molecular dynamics simulation of double-helical B-DNA including counterions and water.

Abstract

We present the results of an atomic level molecular dynamical simulation of a 5-base-pair fragment of double-helical DNA with inclusion of water and sodium counterions and a complete description of their electrostatic interactions. The shape of the double helix is preserved throughout the simulation, and the helix repeat is calculated to be 10.0, in reasonable agreement with experimental results. The most flexible conformational angles in the structure are the glycosidic angle and the sugar pucker.

Entities: Chemical

Mesh：

Substances：
Ions
Water
DNA

Year: 1985 PMID： 3863112 PMCID： PMC390752 DOI： 10.1073/pnas.82.19.6537

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

7 in total

1. Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions.

Authors: U C Singh; S J Weiner; P Kollman
Journal: Proc Natl Acad Sci U S A Date: 1985-02 Impact factor: 11.205

2. Structure of hydrated Na+ ions around a region of A- or B-DNA helix.

Authors: W K Lee; Y Gao; E W Prohofsky
Journal: Biopolymers Date: 1984-02 Impact factor: 2.505

3. Proton NMR studies on the covalently linked RNA-DNA hybrid r(GCG)d(TATACGC). Assignment of proton resonances by application of the nuclear Overhauser effect.

Authors: J R Mellema; C A Haasnoot; G A van der Marel; G Wille; C A van Boeckel; J H van Boom; C Altona
Journal: Nucleic Acids Res Date: 1983-08-25 Impact factor: 16.971

4. Sequence-dependent variations of B-DNA structure and protein-DNA recognition.

Authors: E N Trifonov
Journal: Cold Spring Harb Symp Quant Biol Date: 1983

5. Ordered water structure around a B-DNA dodecamer. A quantitative study.

Authors: M L Kopka; A V Fratini; H R Drew; R E Dickerson
Journal: J Mol Biol Date: 1983-01-05 Impact factor: 5.469

6. Structure of a B-DNA dodecamer: conformation and dynamics.

Authors: H R Drew; R M Wing; T Takano; C Broka; S Tanaka; K Itakura; R E Dickerson
Journal: Proc Natl Acad Sci U S A Date: 1981-04 Impact factor: 11.205

7. Dynamics of DNA oligomers.

Authors: B Tidor; K K Irikura; B R Brooks; M Karplus
Journal: J Biomol Struct Dyn Date: 1983-10

7 in total

26 in total

1. Evaluation of DNA Force Fields in Implicit Solvation.

Authors: Thomas Gaillard; David A Case
Journal: J Chem Theory Comput Date: 2011-10-11 Impact factor: 6.006

2. Molecular dynamics of an in vacuo model of duplex d(CGCGAATTCGCG) in the B-form based on the amber 3.0 force field.

Authors: J Srinivasan; J M Withka; D L Beveridge
Journal: Biophys J Date: 1990-08 Impact factor: 4.033

3. Computer simulation study of molecular recognition in model DNA microarrays.

Authors: Arthi Jayaraman; Carol K Hall; Jan Genzer
Journal: Biophys J Date: 2006-09-15 Impact factor: 4.033

4. Force field influences in beta-hairpin folding simulations.

Authors: Thu Zar Lwin; Ray Luo
Journal: Protein Sci Date: 2006-11 Impact factor: 6.725

5. Molecular modeling of nucleic acid structure: electrostatics and solvation.

Authors: T E Cheatham; B R Brooks; P A Kollman
Journal: Curr Protoc Nucleic Acid Chem Date: 2001-08

6. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution.

Authors: M A Eriksson; T Härd; L Nilsson
Journal: Biophys J Date: 1995-02 Impact factor: 4.033

7. Interaction of berenil with the tyrT DNA sequence studied by footprinting and molecular modelling. Implications for the design of sequence-specific DNA recognition agents.

Authors: C A Laughton; T C Jenkins; K R Fox; S Neidle
Journal: Nucleic Acids Res Date: 1990-08-11 Impact factor: 16.971