From Unfolded Sequences to Structural Motifs

Autores
Niel, Blanca Isabel; Reartes, Cesar Walter; Brignole, Nélida Beatriz
Año de publicación
2011
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
We consider that the biopolymer chain forms intramolecular contacts at the expense of losing conformational freedom. By means of a cohesive arithmetic method we have analysed the feasible base pairing contact patterns in nucleotide subsequences from untangled to knotted biopolymer chains. The procedure associates complementary integers to each of the two W-C base pairings of the four bases that integrate the homologous sequences. Given the number of the basic building blocks and the quantities of each of the nucleotides in the biopolymer, the unfolded sequence is obtained searching for the admissible Hamiltonian paths of different lengths under the penalisation of any zipping and/or stacking of base pairing processes. Finally, by comparing backward and forward readings in the obtained unfolded sequences we could individualize certain structural features of biological interest which are deployed in scientific papers about nucleic acids (J. P. Sheehy et. al., RNA, 16(2):417-429 (2010); A. Fernández, B. Niel and T. Burastero, Biophysical Chemistry, 74(2):89-98 ( 1998)).
Fil: Niel, Blanca Isabel. Universidad Nacional del Sur; Argentina
Fil: Reartes, Cesar Walter. Universidad Nacional del Sur; Argentina
Fil: Brignole, Nélida Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina
Materia
BIOPOLYMER FOLDING
PALINDROMES
HOMOLOGOUS SEQUENCES
HAIRPIN LOOPS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/56300
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/56300
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling From Unfolded Sequences to Structural MotifsNiel, Blanca IsabelReartes, Cesar WalterBrignole, Nélida BeatrizBIOPOLYMER FOLDINGPALINDROMESHOMOLOGOUS SEQUENCESHAIRPIN LOOPShttps://purl.org/becyt/ford/1.1https://purl.org/becyt/ford/1We consider that the biopolymer chain forms intramolecular contacts at the expense of losing conformational freedom. By means of a cohesive arithmetic method we have analysed the feasible base pairing contact patterns in nucleotide subsequences from untangled to knotted biopolymer chains. The procedure associates complementary integers to each of the two W-C base pairings of the four bases that integrate the homologous sequences. Given the number of the basic building blocks and the quantities of each of the nucleotides in the biopolymer, the unfolded sequence is obtained searching for the admissible Hamiltonian paths of different lengths under the penalisation of any zipping and/or stacking of base pairing processes. Finally, by comparing backward and forward readings in the obtained unfolded sequences we could individualize certain structural features of biological interest which are deployed in scientific papers about nucleic acids (J. P. Sheehy et. al., RNA, 16(2):417-429 (2010); A. Fernández, B. Niel and T. Burastero, Biophysical Chemistry, 74(2):89-98 ( 1998)).Fil: Niel, Blanca Isabel. Universidad Nacional del Sur; ArgentinaFil: Reartes, Cesar Walter. Universidad Nacional del Sur; ArgentinaFil: Brignole, Nélida Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; ArgentinaAsociación Argentina de Mecánica Computacional2011-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/56300Niel, Blanca Isabel; Reartes, Cesar Walter; Brignole, Nélida Beatriz; From Unfolded Sequences to Structural Motifs; Asociación Argentina de Mecánica Computacional; Mecánica Computacional; XXX; 37; 11-2011; 2853-28622591-3522CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://cimec.org.ar/ojs/index.php/mc/article/view/3956info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T12:14:39Zoai:ri.conicet.gov.ar:11336/56300instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 12:14:39.339CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv From Unfolded Sequences to Structural Motifs
title From Unfolded Sequences to Structural Motifs
spellingShingle From Unfolded Sequences to Structural Motifs
Niel, Blanca Isabel
BIOPOLYMER FOLDING
PALINDROMES
HOMOLOGOUS SEQUENCES
HAIRPIN LOOPS
title_short From Unfolded Sequences to Structural Motifs
title_full From Unfolded Sequences to Structural Motifs
title_fullStr From Unfolded Sequences to Structural Motifs
title_full_unstemmed From Unfolded Sequences to Structural Motifs
title_sort From Unfolded Sequences to Structural Motifs
dc.creator.none.fl_str_mv Niel, Blanca Isabel
Reartes, Cesar Walter
Brignole, Nélida Beatriz
author Niel, Blanca Isabel
author_facet Niel, Blanca Isabel
Reartes, Cesar Walter
Brignole, Nélida Beatriz
author_role author
author2 Reartes, Cesar Walter
Brignole, Nélida Beatriz
author2_role author
author
dc.subject.none.fl_str_mv BIOPOLYMER FOLDING
PALINDROMES
HOMOLOGOUS SEQUENCES
HAIRPIN LOOPS
topic BIOPOLYMER FOLDING
PALINDROMES
HOMOLOGOUS SEQUENCES
HAIRPIN LOOPS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.1
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv We consider that the biopolymer chain forms intramolecular contacts at the expense of losing conformational freedom. By means of a cohesive arithmetic method we have analysed the feasible base pairing contact patterns in nucleotide subsequences from untangled to knotted biopolymer chains. The procedure associates complementary integers to each of the two W-C base pairings of the four bases that integrate the homologous sequences. Given the number of the basic building blocks and the quantities of each of the nucleotides in the biopolymer, the unfolded sequence is obtained searching for the admissible Hamiltonian paths of different lengths under the penalisation of any zipping and/or stacking of base pairing processes. Finally, by comparing backward and forward readings in the obtained unfolded sequences we could individualize certain structural features of biological interest which are deployed in scientific papers about nucleic acids (J. P. Sheehy et. al., RNA, 16(2):417-429 (2010); A. Fernández, B. Niel and T. Burastero, Biophysical Chemistry, 74(2):89-98 ( 1998)).
Fil: Niel, Blanca Isabel. Universidad Nacional del Sur; Argentina
Fil: Reartes, Cesar Walter. Universidad Nacional del Sur; Argentina
Fil: Brignole, Nélida Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentina
description We consider that the biopolymer chain forms intramolecular contacts at the expense of losing conformational freedom. By means of a cohesive arithmetic method we have analysed the feasible base pairing contact patterns in nucleotide subsequences from untangled to knotted biopolymer chains. The procedure associates complementary integers to each of the two W-C base pairings of the four bases that integrate the homologous sequences. Given the number of the basic building blocks and the quantities of each of the nucleotides in the biopolymer, the unfolded sequence is obtained searching for the admissible Hamiltonian paths of different lengths under the penalisation of any zipping and/or stacking of base pairing processes. Finally, by comparing backward and forward readings in the obtained unfolded sequences we could individualize certain structural features of biological interest which are deployed in scientific papers about nucleic acids (J. P. Sheehy et. al., RNA, 16(2):417-429 (2010); A. Fernández, B. Niel and T. Burastero, Biophysical Chemistry, 74(2):89-98 ( 1998)).
publishDate 2011
dc.date.none.fl_str_mv 2011-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/56300
Niel, Blanca Isabel; Reartes, Cesar Walter; Brignole, Nélida Beatriz; From Unfolded Sequences to Structural Motifs; Asociación Argentina de Mecánica Computacional; Mecánica Computacional; XXX; 37; 11-2011; 2853-2862
2591-3522
CONICET Digital
CONICET
url http://hdl.handle.net/11336/56300
identifier_str_mv Niel, Blanca Isabel; Reartes, Cesar Walter; Brignole, Nélida Beatriz; From Unfolded Sequences to Structural Motifs; Asociación Argentina de Mecánica Computacional; Mecánica Computacional; XXX; 37; 11-2011; 2853-2862
2591-3522
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://cimec.org.ar/ojs/index.php/mc/article/view/3956
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Asociación Argentina de Mecánica Computacional
publisher.none.fl_str_mv Asociación Argentina de Mecánica Computacional
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.982451

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