Current Problems in Computer Simulation of Variability …
251
with the use of dispersion corrected PW91-ulg functional except the distance between
stacked bases where PW91 predicts considerably larger values than those predicted
by the PW91-ulg functional and observed in the experiment. Examples of the latter
are cdDMP structures of experimental fragments of DNA duplexes deposited in NDB
(in cdDMPs with two chains being in BI conformation). We failed to reproduce these
results with GAUSSIAN software despite trying various basis sets.
6 Conclusions
Due to DNA being the principal molecule of life, deciphering the molecular mechanisms of its 3D structure organization represents one of the important tasks of
natural science. In spite of extensive study of the structure of DNA including that of
its fragments of various complexity quantitative evaluation of the contribution of the
subunits into the macromolecule structure remains an open challenge. The presented
work summarizes the results of previous investigations of simple fragments of DNA
duplex and its separate chains conducted by using quantum mechanics and molecular
mechanics methods. The exact and reliable approaches of quantum mechanics remain
too computationally demanding to be applicable to the simplest DNA fragments. The
less reliable but more affordable MP2 level of theory may produce physically inadequate structures that have shortened atom-atom contacts. Application of the Density
Functional Theory methods using simple functionals has revealed interesting regularities in 3D structure formation of Watson-Crick duplexes, but failed to predict
regularities for duplexes that have two complementary chains belonging to different
conformation families. Existing classical molecular mechanics force fields cannot
reproduce many experimental data on simple DNA fragments and require adjustment of the parameters. The study of variability of three-dimensional structure of
DNA simple fragments provides the pathway to improvement of approximate computational methods for elucidation of nucleic acid biomolecular organization and
biological functions.
Acknowledgements The authors thankfully acknowledge the computer resources and technical
expertise and support provided by the Laboratorio Nacional de Supercómputo del Sureste de México
(grant# 201901015C) and Autonomous University of Puebla (grant# 100261355-V1EP2019).
References
1. Watson JD, Crick FHC (1953) Nat 171:964–967
2. Poltev VI, Anisimov VM, Danilov VI, Deriabina A, Gonzalez E, Jurkiewicz A, Le´ s A, Polteva
N (2008) J Biomol Struct Dyn 25:563–571
3. Poltev VI, Anisimov VM, Danilov VI, Deriabina A, Gonzalez E, Garcia D, Rivas F, Jurkiewicz
A, Le´ s A, Polteva NA (2009) J Mol Struct: THEOCHEM 912:53–59
251
with the use of dispersion corrected PW91-ulg functional except the distance between
stacked bases where PW91 predicts considerably larger values than those predicted
by the PW91-ulg functional and observed in the experiment. Examples of the latter
are cdDMP structures of experimental fragments of DNA duplexes deposited in NDB
(in cdDMPs with two chains being in BI conformation). We failed to reproduce these
results with GAUSSIAN software despite trying various basis sets.
6 Conclusions
Due to DNA being the principal molecule of life, deciphering the molecular mechanisms of its 3D structure organization represents one of the important tasks of
natural science. In spite of extensive study of the structure of DNA including that of
its fragments of various complexity quantitative evaluation of the contribution of the
subunits into the macromolecule structure remains an open challenge. The presented
work summarizes the results of previous investigations of simple fragments of DNA
duplex and its separate chains conducted by using quantum mechanics and molecular
mechanics methods. The exact and reliable approaches of quantum mechanics remain
too computationally demanding to be applicable to the simplest DNA fragments. The
less reliable but more affordable MP2 level of theory may produce physically inadequate structures that have shortened atom-atom contacts. Application of the Density
Functional Theory methods using simple functionals has revealed interesting regularities in 3D structure formation of Watson-Crick duplexes, but failed to predict
regularities for duplexes that have two complementary chains belonging to different
conformation families. Existing classical molecular mechanics force fields cannot
reproduce many experimental data on simple DNA fragments and require adjustment of the parameters. The study of variability of three-dimensional structure of
DNA simple fragments provides the pathway to improvement of approximate computational methods for elucidation of nucleic acid biomolecular organization and
biological functions.
Acknowledgements The authors thankfully acknowledge the computer resources and technical
expertise and support provided by the Laboratorio Nacional de Supercómputo del Sureste de México
(grant# 201901015C) and Autonomous University of Puebla (grant# 100261355-V1EP2019).
References
1. Watson JD, Crick FHC (1953) Nat 171:964–967
2. Poltev VI, Anisimov VM, Danilov VI, Deriabina A, Gonzalez E, Jurkiewicz A, Le´ s A, Polteva
N (2008) J Biomol Struct Dyn 25:563–571
3. Poltev VI, Anisimov VM, Danilov VI, Deriabina A, Gonzalez E, Garcia D, Rivas F, Jurkiewicz
A, Le´ s A, Polteva NA (2009) J Mol Struct: THEOCHEM 912:53–59