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Theoretical modeling of DNA electron hole transport through polypyrimidine sequences: a QM/MM study

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Abstract

The phenomenon of DNA hole transport (HT) has attracted of scientists for several decades, mainly due to its potential application in molecular electronics. As electron holes mostly localize on purine bases in DNA, the majority of scientific effort has been invested into chemically modifying the structures of adenine and guanine in order to increase their HT-mediating properties. In this work we examine an alternative, never yet explored, way of affecting the HT efficiency by forcing electron holes to localize on pyrimidine bases and move between them. Using an enhanced and revised version of our previously developed QM/MM model, we perform simulations of HT through polyadenine, polycytosine, polyguanine, and polythymine stacks according to a multistep hopping mechanism. From these simulations, kinetic parameters for HT are obtained. The results indicate a particularly high efficiency of cytosine→cytosine hopping, which is about ten times higher than the G → G hopping. We also discuss possible improvement of cytosine HT by modifying the oxidoreductive properties of complementary guanine residues.

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Acknowledgments

All calculations were performed using the computational resources provided by the University of Arizona and by the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw (as part of G18-6 grant), for which we are grateful.

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Authors and Affiliations

  1. Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland

    Aleksander P. Woźniak & Andrzej Leś

  2. Pharmaceutical Research Institute, Rydygiera 8, 01-793, Warsaw, Poland

    Andrzej Leś

  3. Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, AZ, 85721, USA

    Ludwik Adamowicz

  4. Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Wileńska 4, 87-100, Toruń, Poland

    Ludwik Adamowicz

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  1. Aleksander P. Woźniak
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Correspondence to Ludwik Adamowicz.

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Woźniak, A.P., Leś, A. & Adamowicz, L. Theoretical modeling of DNA electron hole transport through polypyrimidine sequences: a QM/MM study. J Mol Model 25, 97 (2019). https://doi.org/10.1007/s00894-019-3976-9

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