The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures

Valeri Poltev, Victor M. Anisimov, Victor I. Danilov, Dolores Garcia, Carolina Sanchez, Alexandra Deriabina, Eduardo Gonzalez, Francisco Rivas, Nina Polteva

Research output: Contribution to journalArticle

Abstract

Our previous DFT computations of deoxydinucleoside monophosphate complexes with Na+-ions (dDMPs) have demonstrated that the main characteristics of Watson-Crick (WC) right-handed duplex families are predefined in the local energy minima of dDMPs. In this work, we study the mechanisms of contribution of chemically monotonous sugar-phosphate backbone and the bases into the double helix irregularity. Geometry optimization of sugar-phosphate backbone produces energy minima matching the WC DNA conformations. Studying the conformational variability of dDMPs in response to sequence permutation, we found that simple replacement of bases in the previously fully optimized dDMPs, e.g. by constructing Pyr-Pur from Pur-Pyr, and Pur-Pyr from Pyr-Pur sequences, while retaining the backbone geometry, automatically produces the mutual base position characteristic of the target sequence. Based on that, we infer that the directionality and the preferable regions of the sugar-phosphate torsions, combined with the difference of purines from pyrimidines in ring shape, determines the sequence dependence of the structure of WC DNA. No such sequence dependence exists in dDMPs corresponding to other DNA conformations (e.g., Z-family and Hoogsteen duplexes). Unlike other duplexes, WC helix is unique by its ability to match the local energy minima of the free single strand to the preferable conformations of the duplex.

Original languageEnglish (US)
Pages (from-to)640-650
Number of pages11
JournalBiopolymers
Volume101
Issue number6
DOIs
StatePublished - Jun 2014

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Keywords

  • DFT computations
  • DNA conformation families
  • DNA sequence dependence
  • deoxydinucleoside monophospates
  • single-strand interactions

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

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