Understanding the Origin of Structural Diversity of DNA Double Helix

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 popul...

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Main Authors: Valeri Poltev, Victor M. Anisimov, Veronica Dominguez, Andrea Ruiz, Alexandra Deriabina, Eduardo Gonzalez, Dolores Garcia, Francisco Rivas
Format: Article
Language:English
Published: MDPI AG 2021-09-01
Series:Computation
Subjects:
Online Access:https://www.mdpi.com/2079-3197/9/9/98
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spelling doaj-7b07c37fd34c4cbfb9e1e64c3f942ea62021-09-25T23:56:42ZengMDPI AGComputation2079-31972021-09-019989810.3390/computation9090098Understanding the Origin of Structural Diversity of DNA Double HelixValeri Poltev0Victor M. Anisimov1Veronica Dominguez2Andrea Ruiz3Alexandra Deriabina4Eduardo Gonzalez5Dolores Garcia6Francisco Rivas7Physics and Mathematics Department, Autonomous University of Puebla, Puebla 72570, MexicoArgonne National Laboratory, Lemont, IL 60439, USAPhysics and Mathematics Department, Autonomous University of Puebla, Puebla 72570, MexicoPhysics and Mathematics Department, Autonomous University of Puebla, Puebla 72570, MexicoPhysics and Mathematics Department, Autonomous University of Puebla, Puebla 72570, MexicoPhysics and Mathematics Department, Autonomous University of Puebla, Puebla 72570, MexicoInstitute of Physics, Autonomous University of Puebla, Puebla 72570, MexicoInstitute of Physics, Autonomous University of Puebla, Puebla 72570, MexicoDeciphering 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.https://www.mdpi.com/2079-3197/9/9/98DNA conformationssequence dependencedensity functional theoryab initio computationsmolecular mechanicsdeoxydinucleoside monophospates
collection DOAJ
language English
format Article
sources DOAJ
author Valeri Poltev
Victor M. Anisimov
Veronica Dominguez
Andrea Ruiz
Alexandra Deriabina
Eduardo Gonzalez
Dolores Garcia
Francisco Rivas
spellingShingle Valeri Poltev
Victor M. Anisimov
Veronica Dominguez
Andrea Ruiz
Alexandra Deriabina
Eduardo Gonzalez
Dolores Garcia
Francisco Rivas
Understanding the Origin of Structural Diversity of DNA Double Helix
Computation
DNA conformations
sequence dependence
density functional theory
ab initio computations
molecular mechanics
deoxydinucleoside monophospates
author_facet Valeri Poltev
Victor M. Anisimov
Veronica Dominguez
Andrea Ruiz
Alexandra Deriabina
Eduardo Gonzalez
Dolores Garcia
Francisco Rivas
author_sort Valeri Poltev
title Understanding the Origin of Structural Diversity of DNA Double Helix
title_short Understanding the Origin of Structural Diversity of DNA Double Helix
title_full Understanding the Origin of Structural Diversity of DNA Double Helix
title_fullStr Understanding the Origin of Structural Diversity of DNA Double Helix
title_full_unstemmed Understanding the Origin of Structural Diversity of DNA Double Helix
title_sort understanding the origin of structural diversity of dna double helix
publisher MDPI AG
series Computation
issn 2079-3197
publishDate 2021-09-01
description 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.
topic DNA conformations
sequence dependence
density functional theory
ab initio computations
molecular mechanics
deoxydinucleoside monophospates
url https://www.mdpi.com/2079-3197/9/9/98
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