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Literature DB >> 12708848

Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.

Abstract

Molecular dynamics free-energy calculations of base pair opening within double helical DNA and RNA are used to explain why A-tracts (oligo-adenine repeats) greatly increase the lifetimes of AT base pairs, whereas the structural and the chemical changes involved in passing from B-DNA to A-RNA have comparatively small effects.

Entities: Chemical

Mesh：

Substances：
RNA
DNA

Year: 2003 PMID： 12708848 DOI： 10.1021/ja034095r

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

Keyword Cloud
Cited

15 in total

1. Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.

Authors: Yongping Pan; Alexander D MacKerell
Journal: Nucleic Acids Res Date: 2003-12-15 Impact factor: 16.971

2. DNA dynamically directs its own transcription initiation.

Authors: Chu H Choi; George Kalosakas; Kim O Rasmussen; Makoto Hiromura; Alan R Bishop; Anny Usheva
Journal: Nucleic Acids Res Date: 2004-03-05 Impact factor: 16.971

3. Sequence-dependent base pair opening in DNA double helix.

Authors: Andrew Krueger; Ekaterina Protozanova; Maxim D Frank-Kamenetskii
Journal: Biophys J Date: 2006-02-24 Impact factor: 4.033

4. 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

9. Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process.

Authors: Lin-Tai Da; Jin Yu
Journal: Nucleic Acids Res Date: 2018-06-20 Impact factor: 16.971

10. Free energy calculation of modified base-pair formation in explicit solvent: A predictive model.

Authors: Franck A P Vendeix; Antonio M Munoz; Paul F Agris
Journal: RNA Date: 2009-10-27 Impact factor: 4.942

Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.

1. Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.

2. DNA dynamically directs its own transcription initiation.

3. Sequence-dependent base pair opening in DNA double helix.

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

5. A molecular dynamics study of slow base flipping in DNA using conformational flooding.

6. Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

7. Dynamic behavior of DNA base pairs containing 8-oxoguanine.

8. A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA.

9. Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process.

10. Free energy calculation of modified base-pair formation in explicit solvent: A predictive model.