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Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments

  • V. PoltevEmail author
  • V. M. Anisimov
  • V. Dominguez
  • E. Gonzalez
  • A. Deriabina
  • D. Garcia
  • F. Rivas
  • N. A. Polteva
Original Paper
  • 192 Downloads
Part of the following topical collections:
  1. QUITEL 2016

Abstract

Deciphering the mechanism of functioning of DNA as the carrier of genetic information requires identifying inherent factors determining its structure and function. Following this path, our previous DFT studies attributed the origin of unique conformational characteristics of right-handed Watson-Crick duplexes (WCDs) to the conformational profile of deoxydinucleoside monophosphates (dDMPs) serving as the minimal repeating units of DNA strand. According to those findings, the directionality of the sugar-phosphate chain and the characteristic ranges of dihedral angles of energy minima combined with the geometric differences between purines and pyrimidines determine the dependence on base sequence of the three-dimensional (3D) structure of WCDs. This work extends our computational study to complementary deoxydinucleotide-monophosphates (cdDMPs) of non-standard conformation, including those of Z-family, Hoogsteen duplexes, parallel-stranded structures, and duplexes with mispaired bases. For most of these systems, except Z-conformation, computations closely reproduce experimental data within the tolerance of characteristic limits of dihedral parameters for each conformation family. Computation of cdDMPs with Z-conformation reveals that their experimental structures do not correspond to the internal energy minimum. This finding establishes the leading role of external factors in formation of the Z-conformation. Energy minima of cdDMPs of non-Watson-Crick duplexes demonstrate different sequence-dependence features than those known for WCDs. The obtained results provide evidence that the biologically important regularities of 3D structure distinguish WCDs from duplexes having non-Watson-Crick nucleotide pairing.

Keywords

Conformation of biopolymers Sequence dependence Density functional theory Molecular mechanics Quantum mechanics computations 

Notes

Acknowledgments

The authors thankfully acknowledge computer resources, technical advice and support provided by Laboratorio Nacional de Supercomputo del Sureste de Mexico (LNS), a member of the CONACYT national laboratories.

Supplementary material

894_2018_3589_MOESM1_ESM.pdf (464 kb)
ESM 1 (PDF 463 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Autonomous University of PueblaPueblaMexico
  2. 2.National Center for Supercomputing ApplicationsUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  3. 3.Institute of Theoretical and Experimental BiophysicsRussian Academy of SciencesPushchinoRussia

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