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Effect of phenolic radicals on the geometry and electronic structure of DNA base pairs: computational study

Author

Listed:
  • Mohammad Zarei

    (#x2020;Department of Chemistry, University of Kurdistan, 66177-15177, Sanandaj, Iran)

  • Abdolvahab Seif

    (#x2020;Department of Chemistry, University of Kurdistan, 66177-15177, Sanandaj, Iran)

  • Khaled Azizi

    (#x2020;Department of Chemistry, University of Kurdistan, 66177-15177, Sanandaj, Iran)

  • Mohanna Zarei

    (#x2225;Department of Civil Engineering, University of Kurdistan, 6517-15175, Sanandaj, Iran)

  • Jamil Bahrami

    (#x2225;Department of Civil Engineering, University of Kurdistan, 6517-15175, Sanandaj, Iran)

Abstract

In this paper, we show the reaction of a hydroxyl, phenyl and phenoxy radicals with DNA base pairs by the density functional theory (DFT) calculations. The influence of solvation on the mechanism is also presented by the same DFT calculations under the continuum solvation model. The results showed that hydroxyl, phenyl and phenoxy radicals increase the length of the nearest hydrogen bond of adjacent DNA base pair which is accompanied by decrease in the length of furthest hydrogen bond of DNA base pair. Also, hydroxyl, phenyl and phenoxy radicals influenced the dihedral angle between DNA base pairs. According to the results, hydrogen bond lengths between AT and GC base pairs in water solvent are longer than vacuum. All of presented radicals influenced the structure and geometry of AT and GC base pairs, but phenoxy radical showed more influence on geometry and electronic properties of DNA base pairs compared with the phenyl and hydroxyl radicals.

Suggested Citation

  • Mohammad Zarei & Abdolvahab Seif & Khaled Azizi & Mohanna Zarei & Jamil Bahrami, 2016. "Effect of phenolic radicals on the geometry and electronic structure of DNA base pairs: computational study," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 27(10), pages 1-17, October.
    • Handle: RePEc:wsi:ijmpcx:v:27:y:2016:i:10:n:s0129183116501199
    DOI: 10.1142/S0129183116501199
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