Literature DB >> 8461455

Looking into the grooves of DNA.

N Boutonnet1, X Hui, K Zakrzewska.   

Abstract

The present study is aimed at understanding the effects of DNA sequence, local conformation, and curvature on groove geometry. Energy-optimized structures are obtained by Jumna methodology; groove geometry is analyzed by a recently developed technique that allows an accurate and continuous measurement of width and depth. The mechanics of groove deformations is also studied and analyzed in terms of helicoidal parameters.

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Year:  1993        PMID: 8461455     DOI: 10.1002/bip.360330314

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


  13 in total

1.  Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment.

Authors:  D R Bevan; L Li; L G Pedersen; T A Darden
Journal:  Biophys J       Date:  2000-02       Impact factor: 4.033

Review 2.  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

3.  Minor groove deformability of DNA: a molecular dynamics free energy simulation study.

Authors:  Martin Zacharias
Journal:  Biophys J       Date:  2006-05-12       Impact factor: 4.033

4.  Atomic-level simulations of seeman DNA nanostructures: the paranemic crossover in salt solution.

Authors:  Prabal K Maiti; Tod A Pascal; Nagarajan Vaidehi; Jiyoung Heo; William A Goddard
Journal:  Biophys J       Date:  2006-03-01       Impact factor: 4.033

5.  Sensitivity of NMR internucleotide distances to B-DNA conformation: underlying mechanics.

Authors:  A Lefebvre; S Fermandjian; B Hartmann
Journal:  Nucleic Acids Res       Date:  1997-10-01       Impact factor: 16.971

6.  Modelling extreme stretching of DNA.

Authors:  A Lebrun; R Lavery
Journal:  Nucleic Acids Res       Date:  1996-06-15       Impact factor: 16.971

7.  Common DNA structural features exhibited by eukaryotic ribosomal gene promoters.

Authors:  M Marilley; P Pasero
Journal:  Nucleic Acids Res       Date:  1996-06-15       Impact factor: 16.971

8.  Hydrodynamic properties of a double-helical model for DNA.

Authors:  J Garcia de la Torre; S Navarro; M C Lopez Martinez
Journal:  Biophys J       Date:  1994-05       Impact factor: 4.033

9.  A new approach to DNA bending by polyamines and its implication in DNA condensation.

Authors:  David Pastré; Olivier Piétrement; Fabrice Landousy; Loïc Hamon; Isabelle Sorel; Marie-Odile David; Etienne Delain; Alain Zozime; Eric Le Cam
Journal:  Eur Biophys J       Date:  2005-10-25       Impact factor: 1.733

10.  Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.

Authors:  M Roux-Rouquie; M Marilley
Journal:  Nucleic Acids Res       Date:  2000-09-15       Impact factor: 16.971

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