Current Problems in Computer
Simulation of Variability of
Three-Dimensional Structure of DNA
V. Poltev, V. M. Anisimov, V. Dominguez, A. Deriabina, E. Gonzalez,
D. Garcia, V. Vázquez-Báez and F. Rivas
Abstract Being the main molecule of life, DNA has a simple chemical structure
that is surprisingly fit to the important biological functions that it performs. In spite
of its simplicity, the molecular organization of DNA as a linear copolymer of four
nucleotides enables the formation of an infinite variety of three-dimensional structures depending on the monomer sequence and environmental conditions. Molecular
mechanisms, general regularities, and biological importance of the diversity of DNA
duplexes have been extensively studied by Quantum Mechanics (QM) and Molecular Mechanics (MM) methods at the level of simple fragments. Our previous DFT
studies revealed that the important conformational characteristics of BI, BII, AI, and
AII families of Watson-Crick duplexes (WCD), including sequence dependence of
their three-dimensional structure, preexist in the local energy minima of the elemental single chain fragments, deoxydinucleoside monophosphates (dDMPs), and
in the elemental duplex fragments, complementary dDMPs (cdDMPs). Those computations uncovered the important regularity in sequence dependence of neighbour
base superposition, namely substantial superposition for purine-purine and purinepyrimidine sequences, and negligible base overlap in pyrimidine-pyrimidine and
pyrimidine-purine sequences. This regularity matches the experimental data; it can
be reproduced by using various computational methods; and distinguishes WCD
from other polynucleotide duplexes. We concluded that this pattern is a consequence
V. Poltev (B) · V. Dominguez · A. Deriabina · E. Gonzalez · D. Garcia · V. Vázquez-Báez ·
F. Rivas
Autonomous University of Puebla, Puebla 72570, Mexico
e-mail: poltev@fcfm.buap.mx
E. Gonzalez
e-mail: gonzalez@fcfm.buap.mx
D. Garcia
e-mail: dolores@ifuap.buap.mx
F. Rivas
e-mail: rivas@ifuap.buap.mx
V. M. Anisimov
National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA
© Springer Nature Switzerland AG 2020
L. Mammino et al. (eds.), Advances in Quantum Systems in Chemistry,
Physics, and Biology, Progress in Theoretical Chemistry and Physics 32,
https://doi.org/10.1007/978-3-030-34941-7_12
233
Simulation of Variability of
Three-Dimensional Structure of DNA
V. Poltev, V. M. Anisimov, V. Dominguez, A. Deriabina, E. Gonzalez,
D. Garcia, V. Vázquez-Báez and F. Rivas
Abstract Being the main molecule of life, DNA has a simple chemical structure
that is surprisingly fit to the important biological functions that it performs. In spite
of its simplicity, the molecular organization of DNA as a linear copolymer of four
nucleotides enables the formation of an infinite variety of three-dimensional structures depending on the monomer sequence and environmental conditions. Molecular
mechanisms, general regularities, and biological importance of the diversity of DNA
duplexes have been extensively studied by Quantum Mechanics (QM) and Molecular Mechanics (MM) methods at the level of simple fragments. Our previous DFT
studies revealed that the important conformational characteristics of BI, BII, AI, and
AII families of Watson-Crick duplexes (WCD), including sequence dependence of
their three-dimensional structure, preexist in the local energy minima of the elemental single chain fragments, deoxydinucleoside monophosphates (dDMPs), and
in the elemental duplex fragments, complementary dDMPs (cdDMPs). Those computations uncovered the important regularity in sequence dependence of neighbour
base superposition, namely substantial superposition for purine-purine and purinepyrimidine sequences, and negligible base overlap in pyrimidine-pyrimidine and
pyrimidine-purine sequences. This regularity matches the experimental data; it can
be reproduced by using various computational methods; and distinguishes WCD
from other polynucleotide duplexes. We concluded that this pattern is a consequence
V. Poltev (B) · V. Dominguez · A. Deriabina · E. Gonzalez · D. Garcia · V. Vázquez-Báez ·
F. Rivas
Autonomous University of Puebla, Puebla 72570, Mexico
e-mail: poltev@fcfm.buap.mx
E. Gonzalez
e-mail: gonzalez@fcfm.buap.mx
D. Garcia
e-mail: dolores@ifuap.buap.mx
F. Rivas
e-mail: rivas@ifuap.buap.mx
V. M. Anisimov
National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign,
Urbana, IL 61801, USA
© Springer Nature Switzerland AG 2020
L. Mammino et al. (eds.), Advances in Quantum Systems in Chemistry,
Physics, and Biology, Progress in Theoretical Chemistry and Physics 32,
https://doi.org/10.1007/978-3-030-34941-7_12
233