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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/56300
Ver los metadatos del registro completo
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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 Técnicas2025-09-29T10:42:00Zoai: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:34982025-09-29 10:42:00.75CONICET 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 |
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reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
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CONICET Digital (CONICET) |
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CONICET Digital (CONICET) |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
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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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13.070432 |