Literature DB >> 15465050

Relative flexibility of DNA and RNA: a molecular dynamics study.

Agnes Noy1, Alberto Pérez, Filip Lankas, F Javier Luque, Modesto Orozco.   

Abstract

State of the art molecular dynamics simulations are used to study the structure, dynamics, molecular interaction properties and flexibility of DNA and RNA duplexes in aqueous solution. Special attention is paid to the deformability of both types of structures, revisiting concepts on the relative flexibility of DNA and RNA duplexes. Our simulations strongly suggest that the concepts of flexibility, rigidity and deformability are much more complex than usually believed, and that it is not always true that DNA is more flexible than RNA.

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Year:  2004        PMID: 15465050     DOI: 10.1016/j.jmb.2004.07.048

Source DB:  PubMed          Journal:  J Mol Biol        ISSN: 0022-2836            Impact factor:   5.469


  22 in total

1.  Toward a consensus view of duplex RNA flexibility.

Authors:  Ignacio Faustino; Alberto Pérez; Modesto Orozco
Journal:  Biophys J       Date:  2010-09-22       Impact factor: 4.033

2.  The relative flexibility of B-DNA and A-RNA duplexes: database analysis.

Authors:  Alberto Pérez; Agnes Noy; Filip Lankas; F Javier Luque; Modesto Orozco
Journal:  Nucleic Acids Res       Date:  2004-11-23       Impact factor: 16.971

3.  The snRNP 15.5K protein folds its cognate K-turn RNA: a combined theoretical and biochemical study.

Authors:  Vlad Cojocaru; Stephanie Nottrott; Reinhard Klement; Thomas M Jovin
Journal:  RNA       Date:  2005-02       Impact factor: 4.942

4.  Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.

Authors:  Elena Cubero; F Javier Luque; Modesto Orozco
Journal:  Biophys J       Date:  2005-11-11       Impact factor: 4.033

5.  Analyzing the flexibility of RNA structures by constraint counting.

Authors:  Simone Fulle; Holger Gohlke
Journal:  Biophys J       Date:  2008-02-15       Impact factor: 4.033

6.  Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.

Authors:  Lei Bao; Xi Zhang; Ya-Zhou Shi; Yuan-Yan Wu; Zhi-Jie Tan
Journal:  Biophys J       Date:  2017-03-28       Impact factor: 4.033

7.  Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters.

Authors:  Marie Zgarbová; F Javier Luque; Jiří Sponer; Thomas E Cheatham; Michal Otyepka; Petr Jurečka
Journal:  J Chem Theory Comput       Date:  2013-05-14       Impact factor: 6.006

8.  Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.

Authors:  Jae Young Lee; Young-Joo Kim; Chanseok Lee; Jae Gyung Lee; Hiromasa Yagyu; Osamu Tabata; Do-Nyun Kim
Journal:  Nucleic Acids Res       Date:  2019-01-10       Impact factor: 16.971

9.  Targeting the blind spot of polycationic nanocarrier-based siRNA delivery.

Authors:  Mengyao Zheng; Giovanni M Pavan; Manuel Neeb; Andreas K Schaper; Andrea Danani; Gerhard Klebe; Olivia M Merkel; Thomas Kissel
Journal:  ACS Nano       Date:  2012-10-09       Impact factor: 15.881

10.  The organization of nucleosomes around splice sites.

Authors:  Wei Chen; Liaofu Luo; Lirong Zhang
Journal:  Nucleic Acids Res       Date:  2010-01-21       Impact factor: 16.971

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