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- W3004535774 abstract "Being the main molecule of life, DNADNA 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 DNADNA as a linear copolymer of four nucleotidesNucleotide enables the formation of an infinite variety of three-dimensional structures depending on the monomer sequence and environmental conditions. Molecular mechanisms, general regularitiesRegularity, and biological importance of the diversity of DNADNA duplexes have been extensively studied by Quantum Mechanics (QMQuantum Mechanics (QM)) and Molecular Mechanics (MMMolecular Mechanics (MM)) methods at the level of simple fragments. Our previous DFTDensity Functional Theory (DFT) studies revealed that the important conformational characteristics of BI, BII, AI, and AII families of Watson-Crick duplexes (WCDWatson-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 regularityRegularity in sequence dependence of neighbour base superposition, namely substantial superposition for purine-purine and purine-pyrimidine sequences, and negligible base overlap in pyrimidine-pyrimidine and pyrimidine-purine sequences. This regularityRegularity matches the experimental data; it can be reproduced by using various computational methods; and distinguishes WCDWatson-Crick Duplexes (WCD) from other polynucleotide duplexes. We concluded that this pattern is a consequence of directionality and presence of preferable regions in the sugar-phosphate torsions combined with the difference of purines from pyrimidines in ring shape. It appears that along with other three-dimensional DNADNA structures, experimentally studied fragments of DNADNA contain variety of cdDMPs with Watson-Crick nucleoside pairs but with one or both dDMPs belonging to conformational families different from A and B. Comprehensive analysis of conformational characteristics of such cdDMPCdDMP belonging to select families by using various computational methods, and the comparison of subunit contributions to their three-dimensional structure formation suggested that the regularitiesRegularity for the most of such cdDMPs differ from those of ‘canonicalCanonical’ WCDWatson-Crick Duplexes (WCD). The geometry of the optimized conformations of those cdDMPs depends on the used computational method, and sometimes departs from the double helix structure. Comparison of the results including those from optimization of cdDMPs, dDMPs, SPBSugar-Phosphate Backbone (SPB), and base-base pairwise interactions against the mutual position of DNADNA subunits in crystals shows that none of the computational methods is able to quantitatively describe all experimental structures of DNADNA, and to correctly reproduce the interaction between its subunits. Analysis of these data produces valuable information about the strengths and limitations of the employed computational methods, and suggests the pathway for their improvement. The work concludes that the complex interplay that exists between the DNADNA subunits requires additional investigations by using multiple computational methods each targeting particular aspects of the system." @default.
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- W3004535774 date "2020-01-01" @default.
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- W3004535774 title "Current Problems in Computer Simulation of Variability of Three-Dimensional Structure of DNA" @default.
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- W3004535774 doi "https://doi.org/10.1007/978-3-030-34941-7_12" @default.
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