DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

Valeri I. Poltev, Victor M. Anisimov, Victor I. Danilov, Tanja Van Mourik, Alexandra Deriabina, Eduardo Gonzá Lez, Maria Padua, Dolores Garcia, Francisco Rivas, Nina Polteva

Research output: Contribution to journalArticlepeer-review

Abstract

We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the "classical" B conformation (BI-form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence-dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII-like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA.

Original languageEnglish (US)
Pages (from-to)2548-2559
Number of pages12
JournalInternational Journal of Quantum Chemistry
Volume110
Issue number13
DOIs
StatePublished - Nov 5 2010
Externally publishedYes

Keywords

  • DDMP
  • DFT calculations
  • DNA
  • Nucleoside
  • Nucleoside conformation

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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