Literature DB >> 2586615

The conformation of the DNA double helix in the crystal is dependent on its environment.

Z Shakked1, G Guerstein-Guzikevich, M Eisenstein, F Frolow, D Rabinovich.   

Abstract

Studies of the crystal structures of more than 30 synthetic DNA fragments have provided structural information about three basic forms of the double helix: A-, B- and Z-form DNA. These studies have demonstrated that the DNA double helix adopts a highly variable structure which is related to its base sequence. The extent to which such observed structures are influenced by the crystalline environment can be found by studying the same molecule in different crystalline forms. We have recently crystallized one particular oligomer in various crystal forms. Here we report the results of structural analyses of the different crystal structures and demonstrate that the DNA double helix can adopt a range of conformations in the crystalline state depending on hydration, molecular packing and temperature. These results have implications on our understanding of the influence of the environment on DNA structure, and on the modes of DNA recognition by proteins.

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Year:  1989        PMID: 2586615     DOI: 10.1038/342456a0

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  23 in total

1.  The influence of packing on free radical yields in solid-state DNA: film compared to lyophilized frozen solution.

Authors:  M T Milano; W A Bernhard
Journal:  Radiat Res       Date:  1999-08       Impact factor: 2.841

2.  B-form to A-form conversion by a 3'-terminal ribose: crystal structure of the chimera d(CCACTAGTG)r(G).

Authors:  M C Wahl; M Sundaralingam
Journal:  Nucleic Acids Res       Date:  2000-11-01       Impact factor: 16.971

3.  3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.

Authors:  Xiang-Jun Lu; Wilma K Olson
Journal:  Nucleic Acids Res       Date:  2003-09-01       Impact factor: 16.971

4.  Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.

Authors:  David L Beveridge; Gabriela Barreiro; K Suzie Byun; David A Case; Thomas E Cheatham; Surjit B Dixit; Emmanuel Giudice; Filip Lankas; Richard Lavery; John H Maddocks; Roman Osman; Eleanore Seibert; Heinz Sklenar; Gautier Stoll; Kelly M Thayer; Péter Varnai; Matthew A Young
Journal:  Biophys J       Date:  2004-08-23       Impact factor: 4.033

5.  Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix.

Authors:  U Heinemann; L N Rudolph; C Alings; M Morr; W Heikens; R Frank; H Blöcker
Journal:  Nucleic Acids Res       Date:  1991-02-11       Impact factor: 16.971

Review 6.  Origins of specificity in protein-DNA recognition.

Authors:  Remo Rohs; Xiangshu Jin; Sean M West; Rohit Joshi; Barry Honig; Richard S Mann
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

7.  Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability.

Authors:  I Berger; V Tereshko; H Ikeda; V E Marquez; M Egli
Journal:  Nucleic Acids Res       Date:  1998-05-15       Impact factor: 16.971

8.  Hydration of the phosphate group in double-helical DNA.

Authors:  B Schneider; K Patel; H M Berman
Journal:  Biophys J       Date:  1998-11       Impact factor: 4.033

9.  The effect of packing and conformation on free radical yields in films of variably hydrated DNA.

Authors:  M T Milano; W A Bernhard
Journal:  Radiat Res       Date:  1999-01       Impact factor: 2.841

10.  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

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