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Literature DB >> 10512802

Sodium and chlorine ions as part of the DNA solvation shell.

Abstract

The distribution of sodium and chlorine ions around DNA is presented from two molecular dynamics simulations of the DNA fragment d(C(5)T(5)). (A(5)G(5)) in explicit solvent with 0.8 M additional NaCl salt. One simulation was carried out for 10 ns with the CHARMM force field that keeps the DNA structure close to A-DNA, the other for 12 ns with the AMBER force field that preferentially stabilizes B-DNA conformations (, Biophys. J. 75:134-149). From radial distributions of sodium and chlorine ions a primary ion shell is defined. The ion counts and residence times of ions within this shell are compared between conformations and with experiment. Ordered sodium ion sites were found in minor and major grooves around both A and B-DNA conformations. Changes in the surrounding hydration structure are analyzed and implications for the stabilization of A-DNA and B-DNA conformations are discussed.

Entities: Chemical

Mesh：

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Year: 1999 PMID： 10512802 PMCID： PMC1300463 DOI： 10.1016/S0006-3495(99)77023-2

Source DB: PubMed Journal: Biophys J ISSN： 0006-3495 Impact factor: 4.033

44 in total

1. Sequence-specific recognition of double helical nucleic acids by proteins.

Authors: N C Seeman; J M Rosenberg; A Rich
Journal: Proc Natl Acad Sci U S A Date: 1976-03 Impact factor: 11.205

2. Relative binding affinities of monovalent cations for double-stranded DNA.

Authors: M L Bleam; C F Anderson; M T Record
Journal: Proc Natl Acad Sci U S A Date: 1980-06 Impact factor: 11.205

3. Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations.

Authors: R M Brunne; E Liepinsh; G Otting; K Wüthrich; W F van Gunsteren
Journal: J Mol Biol Date: 1993-06-20 Impact factor: 5.469

4. The B-DNA dodecamer at high resolution reveals a spine of water on sodium.

Authors: X Shui; L McFail-Isom; G G Hu; L D Williams
Journal: Biochemistry Date: 1998-06-09 Impact factor: 3.162

5. The effect of nucleic acid geometry on counterion association.

Authors: M C Olmsted
Journal: J Biomol Struct Dyn Date: 1996-04

Review 6. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity.

Authors: M T Record; C F Anderson; T M Lohman
Journal: Q Rev Biophys Date: 1978-05 Impact factor: 5.318

7. Sodium ion and solvent nuclear relaxation results in aqueous solutions of DNA.

Authors: L van Dijk; M L Gruwel; W Jesse; J de Bleijser; J C Leyte
Journal: Biopolymers Date: 1987-02 Impact factor: 2.505

8. Valence screening of water in protein crystals reveals potential Na+ binding sites.

Authors: M Nayal; E Di Cera
Journal: J Mol Biol Date: 1996-02-23 Impact factor: 5.469

9. The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn.

Authors: I Baikalov; K Grzeskowiak; K Yanagi; J Quintana; R E Dickerson
Journal: J Mol Biol Date: 1993-06-05 Impact factor: 5.469

10. Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).

Authors: T E Cheatham; P A Kollman
Journal: Structure Date: 1997-10-15 Impact factor: 5.006

58 in total

1. Significance of ligand tails for interaction with the minor groove of B-DNA.

Authors: B Wellenzohn; W Flader; R H Winger; A Hallbrucker; E Mayer; K R Liedl
Journal: Biophys J Date: 2001-09 Impact factor: 4.033

2. Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.

Authors: M Feig; M Zacharias; B M Pettitt
Journal: Biophys J Date: 2001-07 Impact factor: 4.033

Sodium and chlorine ions as part of the DNA solvation shell.

1. Sequence-specific recognition of double helical nucleic acids by proteins.

2. Relative binding affinities of monovalent cations for double-stranded DNA.

3. Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations.

4. The B-DNA dodecamer at high resolution reveals a spine of water on sodium.

5. The effect of nucleic acid geometry on counterion association.

Review 6. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity.

7. Sodium ion and solvent nuclear relaxation results in aqueous solutions of DNA.

8. Valence screening of water in protein crystals reveals potential Na+ binding sites.

9. The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn.

10. Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).

1. Significance of ligand tails for interaction with the minor groove of B-DNA.

2. Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.

3. Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

4. On the truncation of long-range electrostatic interactions in DNA.

5. DNA polymorphism: a comparison of force fields for nucleic acids.

6. Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

7. Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

8. Ion motions in molecular dynamics simulations on DNA.

9. The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.

10. Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore.