Synchronized oscillations in double-helix B-DNA molecules with mirror-symmetric codons

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dc.contributor.authorMaciá Barber, Enrique Alfonso
dc.date.accessioned2023-06-17T09:01:24Z
dc.date.available2023-06-17T09:01:24Z
dc.date.issued2021-02
dc.description© 2021 by the author. Licensee MDPI, Basel, Switzerland.This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution(CC BY) license I sincerely thank Constantinos Simserides for his continued interest in my research works and Evgeni B. Starikov for illuminating conversations on physico-chemical aspects of DNA molecules. I gratefully thank Victoria Hernández for a critical reading of the manuscript.
dc.description.abstractA fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard-Dauxois-Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX'X, X'XX', YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.
dc.description.departmentDepto. de Física de Materiales
dc.description.facultyFac. de Ciencias Físicas
dc.description.refereedTRUE
dc.description.statuspub
dc.eprint.idhttps://eprints.ucm.es/id/eprint/64637
dc.identifier.doi10.3390/sym13020241
dc.identifier.issn2073-8994
dc.identifier.officialurlhttp://dx.doi.org/10.3390/sym13020241
dc.identifier.relatedurlhttps://www.mdpi.com/2073-8994/13/2/241
dc.identifier.urihttps://hdl.handle.net/20.500.14352/7954
dc.issue.number2
dc.journal.titleSymmetry
dc.language.isoeng
dc.publisherMDPI
dc.rightsAtribución 3.0 España
dc.rights.accessRightsopen access
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/es/
dc.subject.cdu538.9
dc.subject.keywordDouble-stranded DNA
dc.subject.keywordDNA dynamical models
dc.subject.keywordCorrelated oscillations in macromolecules
dc.subject.keywordEpigenetic changes
dc.subject.ucmFísica de materiales
dc.subject.ucmFísica del estado sólido
dc.subject.unesco2211 Física del Estado Sólido
dc.titleSynchronized oscillations in double-helix B-DNA molecules with mirror-symmetric codons
dc.typejournal article
dc.volume.number13
dspace.entity.typePublication
relation.isAuthorOfPublicationdd37b3ce-0186-44e8-a4b6-62cef9121754
relation.isAuthorOfPublication.latestForDiscoverydd37b3ce-0186-44e8-a4b6-62cef9121754
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