A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

Richard Lavery, Krystyna Zakrzewska, David Beveridge, Thomas C. Bishop, David A. Case, Thomas Cheatham, Surjit Dixit, B. Jayaram, Filip Lankas, Charles Laughton, John H. Maddocks, Alexis Michon, Roman Osman, Modesto Orozco, Alberto Perez, Tanya Singh, Nada Spackova, Jiri Sponer

Research output: Contribution to journalArticlepeer-review

238 Scopus citations

Abstract

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing information not only on all 10 unique base pair steps, but also on all possible nearest-neighbor effects on these steps. These results are derived from simulations of 50-100 ns on 39 different DNA oligomers in explicit solvent and using a physiological salt concentration. We demonstrate that the simulations are converged in terms of helical and backbone parameters. The results show that nearest-neighbor effects on base pair steps are very significant, implying that dinucleotide models are insufficient for predicting sequence-dependent behavior. Flanking base sequences can notably lead to base pair step parameters in dynamic equilibrium between two conformational sub-states. Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA.

Original languageEnglish (US)
Pages (from-to)299-313
Number of pages15
JournalNucleic acids research
Volume38
Issue number1
DOIs
StatePublished - Nov 6 2009

All Science Journal Classification (ASJC) codes

  • Genetics

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