DNA thermodynamic pressure: A potential contributor to genome evolution

Descripción del Articulo

This work was supported by a grant from CONCYTEC. We are very grateful to Holger Valqui and Oscar Moran for their critical comments, and to ClaudiaMachicado and Jose Choufor their comments and help in compiling and analysing part of the DNA sequences that support this work. Thanks also to Arman- do...

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Detalles Bibliográficos
Autores: Zimic M.J., Guerra D., Arévalo J.
Formato: artículo
Fecha de Publicación:2002
Institución:Consejo Nacional de Ciencia Tecnología e Innovación
Repositorio:CONCYTEC-Institucional
Lenguaje:inglés
OAI Identifier:oai:repositorio.concytec.gob.pe:20.500.12390/770
Enlace del recurso:https://hdl.handle.net/20.500.12390/770
https://doi.org/10.1016/s0035-9203(02)90046-5
Nivel de acceso:acceso abierto
Materia:thymine
adenine
cytosine
guanine
protozoal DNA
https://purl.org/pe-repo/ocde/ford#1.06.07
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oai_identifier_str oai:repositorio.concytec.gob.pe:20.500.12390/770
network_acronym_str CONC
network_name_str CONCYTEC-Institucional
repository_id_str 4689
dc.title.none.fl_str_mv DNA thermodynamic pressure: A potential contributor to genome evolution
title DNA thermodynamic pressure: A potential contributor to genome evolution
spellingShingle DNA thermodynamic pressure: A potential contributor to genome evolution
Zimic M.J.
thymine
adenine
cytosine
guanine
protozoal DNA
protozoal DNA
protozoal DNA
https://purl.org/pe-repo/ocde/ford#1.06.07
title_short DNA thermodynamic pressure: A potential contributor to genome evolution
title_full DNA thermodynamic pressure: A potential contributor to genome evolution
title_fullStr DNA thermodynamic pressure: A potential contributor to genome evolution
title_full_unstemmed DNA thermodynamic pressure: A potential contributor to genome evolution
title_sort DNA thermodynamic pressure: A potential contributor to genome evolution
author Zimic M.J.
author_facet Zimic M.J.
Guerra D.
Arévalo J.
author_role author
author2 Guerra D.
Arévalo J.
author2_role author
author
dc.contributor.author.fl_str_mv Zimic M.J.
Guerra D.
Arévalo J.
dc.subject.none.fl_str_mv thymine
topic thymine
adenine
cytosine
guanine
protozoal DNA
protozoal DNA
protozoal DNA
https://purl.org/pe-repo/ocde/ford#1.06.07
dc.subject.es_PE.fl_str_mv adenine
cytosine
guanine
protozoal DNA
protozoal DNA
protozoal DNA
dc.subject.ocde.none.fl_str_mv https://purl.org/pe-repo/ocde/ford#1.06.07
description This work was supported by a grant from CONCYTEC. We are very grateful to Holger Valqui and Oscar Moran for their critical comments, and to ClaudiaMachicado and Jose Choufor their comments and help in compiling and analysing part of the DNA sequences that support this work. Thanks also to Arman- do Bernui, Javier Espinoza, Jairzhinho Ramos, Luis Marky and Cristian Orrego, for their contribution to discussions, and especially to Mrs Ellen M. Pragen for her editorial work.
publishDate 2002
dc.date.accessioned.none.fl_str_mv 2024-05-30T23:13:38Z
dc.date.available.none.fl_str_mv 2024-05-30T23:13:38Z
dc.date.issued.fl_str_mv 2002
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12390/770
dc.identifier.doi.none.fl_str_mv https://doi.org/10.1016/s0035-9203(02)90046-5
dc.identifier.scopus.none.fl_str_mv 2-s2.0-0036324733
url https://hdl.handle.net/20.500.12390/770
https://doi.org/10.1016/s0035-9203(02)90046-5
identifier_str_mv 2-s2.0-0036324733
dc.language.iso.none.fl_str_mv eng
language eng
dc.relation.ispartof.none.fl_str_mv Transactions of the Royal Society of Tropical Medicine and Hygiene
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Royal Society of Tropical Medicine and Hygiene
publisher.none.fl_str_mv Royal Society of Tropical Medicine and Hygiene
dc.source.none.fl_str_mv reponame:CONCYTEC-Institucional
instname:Consejo Nacional de Ciencia Tecnología e Innovación
instacron:CONCYTEC
instname_str Consejo Nacional de Ciencia Tecnología e Innovación
instacron_str CONCYTEC
institution CONCYTEC
reponame_str CONCYTEC-Institucional
collection CONCYTEC-Institucional
repository.name.fl_str_mv Repositorio Institucional CONCYTEC
repository.mail.fl_str_mv repositorio@concytec.gob.pe
_version_ 1844883001183305728
spelling Publicationrp01981600rp01316500rp01883500Zimic M.J.Guerra D.Arévalo J.2024-05-30T23:13:38Z2024-05-30T23:13:38Z2002https://hdl.handle.net/20.500.12390/770https://doi.org/10.1016/s0035-9203(02)90046-52-s2.0-0036324733This work was supported by a grant from CONCYTEC. We are very grateful to Holger Valqui and Oscar Moran for their critical comments, and to ClaudiaMachicado and Jose Choufor their comments and help in compiling and analysing part of the DNA sequences that support this work. Thanks also to Arman- do Bernui, Javier Espinoza, Jairzhinho Ramos, Luis Marky and Cristian Orrego, for their contribution to discussions, and especially to Mrs Ellen M. Pragen for her editorial work.Codon usage bias is a feature of living organisms. The origin of this bias might be explained not only by external factors but also by the nature of the structure of deoxyribonucleic acid (DNA) itself. We have developed a point mutation simulation program of coding sequences, in which nucleotide replacement follows thermodynamic criteria. For this purpose we calculated the hydrogen bond-like and electrostatic energies of non-canonical base pairs in a 5 bp neighbourhood. Although the rate of non-canonical base pair formation is extremely low, such pairs occur with a preference towards a guanine (G) or cytosine (C) rather than an adenine (A) or thymine (T) replacement due to thermodynamic considerations. This feature, according to the simulation program, should result in an increase in the GC content of the genome over evolutionary time. In addition, codon bias towards a higher GC usage is also predicted. DNA sequence analysis of genes of the Trypanosomatidae lineage supported the hypothesis that DNA thermodynamic pressure is a driving force that impels increases in GC content and GC codon bias.Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica - ConcytecengRoyal Society of Tropical Medicine and HygieneTransactions of the Royal Society of Tropical Medicine and Hygieneinfo:eu-repo/semantics/openAccessthymineadenine-1cytosine-1guanine-1protozoal DNA-1protozoal DNA-1protozoal DNA-1https://purl.org/pe-repo/ocde/ford#1.06.07-1DNA thermodynamic pressure: A potential contributor to genome evolutioninfo:eu-repo/semantics/articlereponame:CONCYTEC-Institucionalinstname:Consejo Nacional de Ciencia Tecnología e Innovacióninstacron:CONCYTEC#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#20.500.12390/770oai:repositorio.concytec.gob.pe:20.500.12390/7702024-05-30 15:36:03.742http://purl.org/coar/access_right/c_14cbinfo:eu-repo/semantics/closedAccessmetadata only accesshttps://repositorio.concytec.gob.peRepositorio Institucional CONCYTECrepositorio@concytec.gob.pe#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#<Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="920e23f4-188f-45d0-a175-fb6fc0cdf0df"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>DNA thermodynamic pressure: A potential contributor to genome evolution</Title> <PublishedIn> <Publication> <Title>Transactions of the Royal Society of Tropical Medicine and Hygiene</Title> </Publication> </PublishedIn> <PublicationDate>2002</PublicationDate> <DOI>https://doi.org/10.1016/s0035-9203(02)90046-5</DOI> <SCP-Number>2-s2.0-0036324733</SCP-Number> <Authors> <Author> <DisplayName>Zimic M.J.</DisplayName> <Person id="rp01981" /> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> <Author> <DisplayName>Guerra D.</DisplayName> <Person id="rp01316" /> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> <Author> <DisplayName>Arévalo J.</DisplayName> <Person id="rp01883" /> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Royal Society of Tropical Medicine and Hygiene</DisplayName> <OrgUnit /> </Publisher> </Publishers> <Keyword>thymine</Keyword> <Keyword>adenine</Keyword> <Keyword>cytosine</Keyword> <Keyword>guanine</Keyword> <Keyword>protozoal DNA</Keyword> <Keyword>protozoal DNA</Keyword> <Keyword>protozoal DNA</Keyword> <Abstract>Codon usage bias is a feature of living organisms. The origin of this bias might be explained not only by external factors but also by the nature of the structure of deoxyribonucleic acid (DNA) itself. We have developed a point mutation simulation program of coding sequences, in which nucleotide replacement follows thermodynamic criteria. For this purpose we calculated the hydrogen bond-like and electrostatic energies of non-canonical base pairs in a 5 bp neighbourhood. Although the rate of non-canonical base pair formation is extremely low, such pairs occur with a preference towards a guanine (G) or cytosine (C) rather than an adenine (A) or thymine (T) replacement due to thermodynamic considerations. This feature, according to the simulation program, should result in an increase in the GC content of the genome over evolutionary time. In addition, codon bias towards a higher GC usage is also predicted. DNA sequence analysis of genes of the Trypanosomatidae lineage supported the hypothesis that DNA thermodynamic pressure is a driving force that impels increases in GC content and GC codon bias.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication> -1
score 13.394457
DNA thermodynamic pressure: A potential contributor to genome evolution
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