Literature DB >> 1391627

Hydration of DNA bases: analysis of crystallographic data.

B Schneider1, D Cohen, H M Berman.   

Abstract

We present a systematic analysis of water structure around nucleic acid bases. We have examined 28 crystal structures of oligonucleotides, and have studied the patterns of water around the four bases, guanine, cytosine, adenine, and thymine. The geometries of water positions were calculated up to 4.00 A from base atoms. We have found conformation-dependent differences in both the geometry and extent of hydration of the bases.

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Year:  1992        PMID： 1391627     DOI： 10.1002/bip.360320703

Source DB:  PubMed          Journal:  Biopolymers        ISSN： 0006-3525            Impact factor:   2.505


  22 in total

1.  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

2.  Hydration changes in the association of Hoechst 33258 with DNA.

Authors:  John R Kiser; Richard W Monk; Rondey L Smalls; Jeffrey T Petty
Journal:  Biochemistry       Date:  2005-12-27       Impact factor: 3.162

3.  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

4.  Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes.

Authors:  G Hummer; A E García; D M Soumpasis
Journal:  Biophys J       Date:  1995-05       Impact factor: 4.033

5.  Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA.

Authors:  Koen Robeyns; Piet Herdewijn; Luc Van Meervelt
Journal:  Artif DNA PNA XNA       Date:  2010-07

6.  A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.

Authors:  M A Young; G Ravishanker; D L Beveridge
Journal:  Biophys J       Date:  1997-11       Impact factor: 4.033

Review 7.  Structure-based modeling of protein: DNA specificity.

Authors:  Adam P Joyce; Chi Zhang; Philip Bradley; James J Havranek
Journal:  Brief Funct Genomics       Date:  2014-11-19       Impact factor: 4.241

8.  Solvated protein-DNA docking using HADDOCK.

Authors:  Marc van Dijk; Koen M Visscher; Panagiotis L Kastritis; Alexandre M J J Bonvin
Journal:  J Biomol NMR       Date:  2013-04-30       Impact factor: 2.835

9.  UV photoelectron and ab initio quantum mechanical characterization of valence electrons in Na(+)-water-2'-deoxyguanosine 5'-phosphate clusters: electronic influences on DNA alkylation by methylating and ethylating carcinogens.

Authors:  H S Kim; P R LeBreton
Journal:  Proc Natl Acad Sci U S A       Date:  1994-04-26       Impact factor: 11.205

10.  Hydration of drug-DNA complexes: greater water uptake for adriamycin compared to daunomycin.

Authors:  Haijia Yu; Jinsong Ren; Jonathan B Chaires; Xiaogang Qu
Journal:  J Med Chem       Date:  2008-09-13       Impact factor: 7.446
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