Current Problems in Computer Simulation of Variability of Three-Dimensional Structure of DNA

Poltev, V. I.; Anisimov, Victor M.; Domínguez, Verónica; Deriabina, A.; Gonzalez, Emmanuel A.; García, Diosdado Baena; Vázquez-Báez, V.; Rivas, Francisco

doi:10.1007/978-3-030-34941-7_12

Cited by 3 publications

(3 citation statements)

References 29 publications

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“…The molecular systems, the methods of computation, and the computational software used in this work closely resemble those used in our current publication series [6][7][8][9]14]. We consider the minimal fragments of single-strand, deoxydinucleoside monophosphates (dDMP) neutralized with Na ion, complementary parts of a DNA duplex, cdDMPs, and the fragments of sugar-phosphate backbone (SPB) encountered in dDMPs and cdDMPs.…”

Section: Methodsmentioning

confidence: 99%

“…The computation of conformational characteristics of DNA fragments em The choice of computational method for the computer simulation of a 3D structure of nucleic acids is dictated by the need to balance the computational cost with achieving sufficiently accurate accounting of the contribution of various subunits. In our recent publication [14], we discussed the problems in computer simulation of DNA 3D-structure formation and variability, and we explained the choice of computational methods. Here, we only mention a few of those problems and use the results reproducible by several methods to draw conclusions.…”

Section: Methodsmentioning

confidence: 99%

“…In our recent paper [14], we performed computations of several minimal DNA fragments in which the sets of torsion angles are positioned in the regions different from classical BI and AI conformations. In it, we analyzed variations of torsion angles of SPB for different conformational classes and inspected changes in these angles after energy minimization.…”

Section: Introductionmentioning

confidence: 99%

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Understanding the Origin of Structural Diversity of DNA Double Helix

et al. 2021

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Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Understanding the Origin of Structural Diversity of DNA Double Helix

et al. 2021

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Efficiency of Molecular Mechanics as a Tool to Understand the Structural Diversity of Watson–Crick Duplexes

Ruiz

Deriabina

Gonzalez

et al. 2023

Proceedings of Trends in Electronics and Health Informatics

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The marvelous dna macromolecule: computer modeling of dna 3d structure and diversity of watson-crick duplex conformations

Poltev,

Dominguez,

Ruiz

et al. 2023

Biofizika

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The work reviews the development of ideas about the 3D structure of DNA and the mechanisms of its formation, from the discovery of the Double Helix to the present day. It tracks the methods of modeling the 3D structure at different stages of the study of the main molecule of life. The discussion underscores a marvelous expedient in DNA molecular structure and its adaptability to important biological functions based on the results of calculations of the intra- and intermolecular interactions of macromolecule subunits. The work presents new data about substantial contribution of chemically monotonous and conformationally flexible sugarphosphate backbone to the formation of sequence-dependent 3D structure of DNA. The diversity of the conformational possibilities of DNA is visible both in the formation of duplexes (as well as triplexes and quadruplexes) with different geometric parameters for base pairs and in the formation of duplexes with Watson-Crick nucleoside pairs containing local conformations corresponding to different regions of the torsion angles of the sugar-phosphate backbone (different conformational classes). Based on our calculations, these classes can be divided into two groups. The first group includes local conformations in which the torsion angles are close to one of energy minima of its isolated elemental repeating fragment, and the second group consists of conformations with one or more of these angles deviating from that of the nearest energy minimum by more than 30°. The regularities of the formation of the local 3D structure of these two groups differ significantly.

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Current Problems in Computer Simulation of Variability of Three-Dimensional Structure of DNA

Cited by 3 publications

References 29 publications

Understanding the Origin of Structural Diversity of DNA Double Helix

Understanding the Origin of Structural Diversity of DNA Double Helix

Efficiency of Molecular Mechanics as a Tool to Understand the Structural Diversity of Watson–Crick Duplexes

The marvelous dna macromolecule: computer modeling of dna 3d structure and diversity of watson-crick duplex conformations

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