Literature DB >> 8599672

Hydration of the DNA bases is local.

B Schneider1, H M Berman.   

Abstract

Ordered hydration sites were determined for the nucleotide bases in B-type conformations using the crystal structure data on 14 B-DNA decamer structures. A method of density representation was extended so that positions, occupancies, and distributions of the hydration sites were predicted around a B-DNA double helix by a method analogous to crystallographic refinement. The predicted hydration sites correctly reproduce the main features of hydration around the B-DNA dodecamer. In contrast to the previous observations, the newly available crystal data show the same extent of hydration of guanine and adenine, and of cytosine and thymine.

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Year:  1995        PMID： 8599672      PMCID： PMC1236503          DOI： 10.1016/S0006-3495(95)80136-0

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


  28 in total

1.  Dielectric study on hydration of B-, A-, and Z-DNA.

Authors:  T Umehara; S Kuwabara; S Mashimo; S Yagihara
Journal:  Biopolymers       Date:  1990       Impact factor: 2.505

2.  Crystallographic study of one turn of G/C-rich B-DNA.

Authors:  U Heinemann; C Alings
Journal:  J Mol Biol       Date:  1989-11-20       Impact factor: 5.469

3.  A systematic study of patterns of hydration in nucleic acids:(I) guanine and cytosine.

Authors:  H M Berman; A Sowri; S Ginell; D Beveridge
Journal:  J Biomol Struct Dyn       Date:  1988-04

4.  Evidence for heterogeneity in DNA-associated solvent mobility from acridine phosphorescence spectra.

Authors:  J G Milton; W C Galley
Journal:  Biopolymers       Date:  1986-09       Impact factor: 2.505

5.  On the hydration of DNA. II. Base composition dependence of the net hydration of DNA.

Authors:  M J Unis; J E Hearst
Journal:  Biopolymers       Date:  1968       Impact factor: 2.505

6.  Structure of a B-DNA dodecamer. III. Geometry of hydration.

Authors:  H R Drew; R E Dickerson
Journal:  J Mol Biol       Date:  1981-09-25       Impact factor: 5.469

Review 7.  Helix geometry, hydration, and G.A mismatch in a B-DNA decamer.

Authors:  G G Privé; U Heinemann; S Chandrasegaran; L S Kan; M L Kopka; R E Dickerson
Journal:  Science       Date:  1987-10-23       Impact factor: 47.728

8.  Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G.

Authors:  G G Privé; K Yanagi; R E Dickerson
Journal:  J Mol Biol       Date:  1991-01-05       Impact factor: 5.469

9.  Water structure in cubic insulin crystals.

Authors:  J Badger; D L Caspar
Journal:  Proc Natl Acad Sci U S A       Date:  1991-01-15       Impact factor: 11.205

10.  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
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  40 in total

1.  Internal dynamics in a DNA triple helix probed by (1)H-(15)N-NMR spectroscopy.

Authors:  Lihong Jiang; Irina M Russu
Journal:  Biophys J       Date:  2002-06       Impact factor: 4.033

2.  Solvation of nucleosides in aqueous mixtures of organic solvents: relevance to DNA open basepairs.

Authors:  Anas M Ababneh; C C Large; S Georghiou
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

3.  Hydration changes upon DNA folding studied by osmotic stress experiments.

Authors:  Shu-ichi Nakano; Daisuke Yamaguchi; Hisae Tateishi-Karimata; Daisuke Miyoshi; Naoki Sugimoto
Journal:  Biophys J       Date:  2012-06-19       Impact factor: 4.033

4.  Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

Authors:  Surjit B Dixit; Mihaly Mezei; David L Beveridge
Journal:  J Biosci       Date:  2012-07       Impact factor: 1.826

5.  Dependence of nucleotide physical properties on their placement in codons and determinative degree.

Authors:  A Y Berezhnoy; S A Duplij
Journal:  J Zhejiang Univ Sci B       Date:  2005-10       Impact factor: 3.066

6.  Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.

Authors:  Monika Fuxreiter; Mihaly Mezei; István Simon; Roman Osman
Journal:  Biophys J       Date:  2005-05-13       Impact factor: 4.033

7.  DNA sequence representation by trianders and determinative degree of nucleotides.

Authors:  Diana Duplij; Steven Duplij
Journal:  J Zhejiang Univ Sci B       Date:  2005-08       Impact factor: 3.066

8.  The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation.

Authors:  Mika A Kastenholz; Thomas U Schwartz; Philippe H Hünenberger
Journal:  Biophys J       Date:  2006-10-15       Impact factor: 4.033

9.  Microhydration of protonated nucleic acid bases and protonated nucleosides in the gas phase.

Authors:  Henryk Wincel
Journal:  J Am Soc Mass Spectrom       Date:  2009-07-10       Impact factor: 3.109

10.  Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

Authors:  Bao Linh Nguyen; B Montgomery Pettitt
Journal:  J Chem Theory Comput       Date:  2015-04-14       Impact factor: 6.006
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