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Hydration of counterions interacting with DNA double helix: a molecular dynamics study

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Abstract

In the present work, molecular dynamics simulations have been carried out to study the dependence of counterion distribution around the DNA double helix on the character of ion hydration. The simulated systems consisted of DNA fragment d(CGCGAATTCGCG) in water solution with the counterions Na+, K+, Cs+ or Mg2+. The characteristic binding sites of the counterions with DNA and the changes in their hydration shell have been determined. The results show that due to the interaction with DNA at least two hydration shells of the counterions undergo changes. The first hydration shell of Na+, K+, Cs+, and Mg2+ counterions in the bulk consists of six, seven, ten, and six water molecules, respectively, while the second one has several times higher values. The Mg2+ and Na+ counterions, constraining water molecules of the first hydration shell, mostly form with DNA water-mediated contacts. In this case the coordination numbers of the first hydration shell do not change, while the coordination numbers of the second one decrease about twofold. The Cs+ and K+ counterions that do not constrain surrounding water molecules may be easily dehydrated, and when interacting with DNA their first hydration shell may be decreased by three and five water molecules, respectively. Due to the dehydration effect, these counterions can squeeze through the hydration shell of DNA to the bottom of the double helix grooves. The character of ion hydration establishes the correlation between the coordination numbers of the first and the second hydration shells.

Hydration of counterions interacting with DNA double helix

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Acknowledgments

The author acknowledges the BITP and the HT-CONDOR grid system for providing the computational facilities. The author also thanks Prof. S.N. Volkov and colleagues from the Laboratory of Biophysics of Macromolecules of the BITP for the discussion of the results; Dr. Leonid Belous for support of computational process on HT-CONDOR cluster. The support from GRID Program of the National Academy of Sciences of Ukraine (project 0117 U003429) is gratefully acknowledged.

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  1. Bogolyubov Institute for Theoretical Physics, NAS of Ukraine, 14-b Metrolohichna Str, Kyiv, 03143, Ukraine

    Sergiy Perepelytsya

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Correspondence to Sergiy Perepelytsya.

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Perepelytsya, S. Hydration of counterions interacting with DNA double helix: a molecular dynamics study. J Mol Model 24, 171 (2018). https://doi.org/10.1007/s00894-018-3704-x

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