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In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents

A SELEX approach has been developed in order to select oligonucleotides that bind double-stranded DNA in the presence of a triplex-stabilizing agent, and was applied to a target sequence containing an oligopurine–oligopyrimidine stretch. After only seven rounds of selection, the process led to the i...

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Detalles Bibliográficos
Autores principales: Ayel, Elodie, Escudé, Christophe
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836567/
https://www.ncbi.nlm.nih.gov/pubmed/20007154
http://dx.doi.org/10.1093/nar/gkp1139
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author Ayel, Elodie
Escudé, Christophe
author_facet Ayel, Elodie
Escudé, Christophe
author_sort Ayel, Elodie
collection PubMed
description A SELEX approach has been developed in order to select oligonucleotides that bind double-stranded DNA in the presence of a triplex-stabilizing agent, and was applied to a target sequence containing an oligopurine–oligopyrimidine stretch. After only seven rounds of selection, the process led to the identification of oligonucleotides that were able to form triple helices within the antiparallel motif. Inspection of the selected sequences revealed that, contrary to GC base pair which were always recognized by guanines, recognition of AT base pair could be achieved by either adenine or thymine, depending on the sequence context. While thymines are strongly preferred for several positions, some others can accommodate the presence of adenines. These results contribute to set the rules for designing oligonucleotides that form stable triple helices in the presence of triplex-stabilizing agents at physiological pH. They set the basis for further experiments regarding extension of potential target sequences for triple-helix formation or recognition of ligand–DNA complexes.
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spelling pubmed-28365672010-03-11 In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents Ayel, Elodie Escudé, Christophe Nucleic Acids Res Methods Online A SELEX approach has been developed in order to select oligonucleotides that bind double-stranded DNA in the presence of a triplex-stabilizing agent, and was applied to a target sequence containing an oligopurine–oligopyrimidine stretch. After only seven rounds of selection, the process led to the identification of oligonucleotides that were able to form triple helices within the antiparallel motif. Inspection of the selected sequences revealed that, contrary to GC base pair which were always recognized by guanines, recognition of AT base pair could be achieved by either adenine or thymine, depending on the sequence context. While thymines are strongly preferred for several positions, some others can accommodate the presence of adenines. These results contribute to set the rules for designing oligonucleotides that form stable triple helices in the presence of triplex-stabilizing agents at physiological pH. They set the basis for further experiments regarding extension of potential target sequences for triple-helix formation or recognition of ligand–DNA complexes. Oxford University Press 2010-03 2009-12-08 /pmc/articles/PMC2836567/ /pubmed/20007154 http://dx.doi.org/10.1093/nar/gkp1139 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Ayel, Elodie
Escudé, Christophe
In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents
title In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents
title_full In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents
title_fullStr In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents
title_full_unstemmed In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents
title_short In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents
title_sort in vitro selection of oligonucleotides that bind double-stranded dna in the presence of triplex-stabilizing agents
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836567/
https://www.ncbi.nlm.nih.gov/pubmed/20007154
http://dx.doi.org/10.1093/nar/gkp1139
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