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Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

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Abstract

Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the observed water and ion atmosphere around the DNA sequences is the MD simulation is in good agreement with experimental observations.

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Acknowledgements

We gratefully acknowledge support from MRAC award CHE050040P, SDSC account WEU202, NIH grant GM37909 to DLB, The Keck Center for Integrative Genomics at Wesleyan University and the HHMI grant 52005211. We thank the participants of the Ascona B-DNA Consortium for kindly sharing with us the trajectories of the 39 DNA sequences. DLB acknowledges support from Dr Joshua Boger and the WE Coffman family.

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  1. Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, CT, 06457, USA

    Surjit B Dixit & David L Beveridge

  2. Department of Structural and Chemical Biology, The Mount Sinai School of Medicine, New York, NY, 10029, USA

    Mihaly Mezei

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  1. Surjit B Dixit
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[Dixit SB, Mezei M and Beveridge DL 2012 Studies of base pair sequence effects on DNA salvation based on all-atom molecular dynamics simulations. J. Biosci. 37 1–23] DOI 10.1007/s12038-012-9223-5

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Dixit, S.B., Mezei, M. & Beveridge, D.L. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations. J Biosci 37, 399–421 (2012). https://doi.org/10.1007/s12038-012-9223-5

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