Literature DB >> 12071727

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

Péter Várnai1, Richard Lavery.   

Abstract

Carrying out chemistry on the bases of DNA, necessary for biological processes such as methylation or repair, requires flipping the base into an accessible position. In this work, molecular dynamics simulations are used to generate a free energy profile for flipping a cytosine base out of its helical stack in double-stranded DNA. The results shed light on the mechanics of this process by comparing routes for base flipping via the minor and major grooves.

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Year:  2002        PMID： 12071727     DOI： 10.1021/ja025980x

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN： 0002-7863            Impact factor:   15.419


  33 in total

1.  Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.

Authors:  Emmanuel Giudice; Péter Várnai; Richard Lavery
Journal:  Nucleic Acids Res       Date:  2003-03-01       Impact factor: 16.971

2.  Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

Authors:  Kamila Réblová; Nad'a Spacková; Richard Stefl; Kristina Csaszar; Jaroslav Koca; Neocles B Leontis; Jirí Sponer
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

3.  Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

Authors:  Niu Huang; Nilesh K Banavali; Alexander D MacKerell
Journal:  Proc Natl Acad Sci U S A       Date:  2002-12-27       Impact factor: 11.205

4.  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

5.  Base-flipping mechanism in postmismatch recognition by MutS.

Authors:  Sean M Law; Michael Feig
Journal:  Biophys J       Date:  2011-11-01       Impact factor: 4.033

6.  Stationary solutions for a modified Peyrard-Bishop DNA model with up to third-neighbor interactions.

Authors:  Z Rapti
Journal:  Eur Phys J E Soft Matter       Date:  2010-06-17       Impact factor: 1.890

7.  Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping.

Authors:  Jia Luo; Thomas C Bruice
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-19       Impact factor: 11.205

8.  Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix.

Authors:  Nilesh K Banavali; Niu Huang; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2006-06-08       Impact factor: 2.991

9.  NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

Authors:  U Deva Priyakumar; Alexander D Mackerell
Journal:  J Am Chem Soc       Date:  2006-01-25       Impact factor: 15.419

10.  Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study.

Authors:  André Barthel; Martin Zacharias
Journal:  Biophys J       Date:  2006-01-06       Impact factor: 4.033
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