Literature DB >> 8441668

BI-BII transitions in B-DNA.

B Hartmann1, D Piazzola, R Lavery.   

Abstract

Molecular modelling is used to study the conformational and energetic aspects of BI-BII transitions within the backbone of a B-DNA dodecamer d(CATGACGTCATG) whose fine structure has previously been determined by molecular modelling combined with NMR spectroscopy. It is shown that while the dodecamer under investigation does not contain any BII junctions, the central CpG step can most easily undergo the transition. More generally, it is also found that the base sequence and hence the backbone geometry of a DNA segment, strongly influences both the conformational impact of the transition, the associated energy barrier and the stability of the resulting BII state.

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Year:  1993        PMID： 8441668      PMCID： PMC309153          DOI： 10.1093/nar/21.3.561

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  22 in total

1.  Static and dynamic conformational properties of AT sequences in B-DNA.

Authors:  K Zakrzewska
Journal:  J Biomol Struct Dyn       Date:  1992-02

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.  Effect of crystal packing environment on conformation of the DNA duplex. Molecular structure of the A-DNA octamer d(G-T-G-T-A-C-A-C) in two crystal forms.

Authors:  S Jain; M Sundaralingam
Journal:  J Biol Chem       Date:  1989-08-05       Impact factor: 5.157

4.  Theoretical prediction of base sequence effects in DNA. Experimental reactivity of Z-DNA and B-Z transition enthalpies.

Authors:  B Hartmann; B Malfoy; R Lavery
Journal:  J Mol Biol       Date:  1989-05-20       Impact factor: 5.469

5.  Energetic coupling between DNA bending and base pair opening.

Authors:  J Ramstein; R Lavery
Journal:  Proc Natl Acad Sci U S A       Date:  1988-10       Impact factor: 11.205

6.  A general approach to the optimization of the conformation of ring molecules with an application to valinomycin.

Authors:  R Lavery; I Parker; J Kendrick
Journal:  J Biomol Struct Dyn       Date:  1986-12

7.  Definitions and nomenclature of nucleic acid structure parameters.

Authors: 
Journal:  J Mol Biol       Date:  1989-02-20       Impact factor: 5.469

8.  Conformational flexibility of DNA: polymorphism and handedness.

Authors:  G Gupta; M Bansal; V Sasisekharan
Journal:  Proc Natl Acad Sci U S A       Date:  1980-11       Impact factor: 11.205

Review 9.  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

10.  The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA.

Authors:  R Lavery; H Sklenar; K Zakrzewska; B Pullman
Journal:  J Biomol Struct Dyn       Date:  1986-04
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  47 in total

1.  Alpha/gamma transitions in the B-DNA backbone.

Authors:  Péter Várnai; Dragana Djuranovic; Richard Lavery; Brigitte Hartmann
Journal:  Nucleic Acids Res       Date:  2002-12-15       Impact factor: 16.971

2.  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

3.  Structure of d(CGGGTACCCG)4 as a four-way Holliday junction.

Authors:  P K Mandal; S Venkadesh; N Gautham
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-11-29

4.  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

5.  Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove.

Authors:  Difei Wang; Nikolai B Ulyanov; Victor B Zhurkin
Journal:  J Biomol Struct Dyn       Date:  2010-06

6.  Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism.

Authors:  D Djuranovic; B Hartmann
Journal:  Biophys J       Date:  2005-07-29       Impact factor: 4.033

7.  Theoretical studies of DNA-RNA hybrid conformations.

Authors:  S R Sanghani; R Lavery
Journal:  Nucleic Acids Res       Date:  1994-04-25       Impact factor: 16.971

8.  Structural equilibrium of DNA represented with different force fields.

Authors:  M Feig; B M Pettitt
Journal:  Biophys J       Date:  1998-07       Impact factor: 4.033

9.  Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.

Authors:  David R Gruber; Joanna J Toner; Heather L Miears; Andrey V Shernyukov; Alexey S Kiryutin; Alexander A Lomzov; Anton V Endutkin; Inga R Grin; Darya V Petrova; Maxim S Kupryushkin; Alexandra V Yurkovskaya; Eric C Johnson; Mark Okon; Elena G Bagryanskaya; Dmitry O Zharkov; Serge L Smirnov
Journal:  Nucleic Acids Res       Date:  2018-11-16       Impact factor: 16.971

10.  Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2015-08-26       Impact factor: 6.006
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