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Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER

We have designed a dodecamer d-AGATCTAGATCT (RY12) with alternate oligopurines and oligopyrimidines tracts and its homologous 28 bp hairpin oligomer (RY28) that forms a triple helix only in the presence of a pentapeptide REWER. An intermolecular triplex is formed by the single strand invasion of the...

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Autores principales: Das, Amrita, Saha, Tapas, Ahmad, Faizan, Roy, Kunal B., Rishi, Vikas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660596/
https://www.ncbi.nlm.nih.gov/pubmed/23705027
http://dx.doi.org/10.1371/journal.pone.0065010
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author Das, Amrita
Saha, Tapas
Ahmad, Faizan
Roy, Kunal B.
Rishi, Vikas
author_facet Das, Amrita
Saha, Tapas
Ahmad, Faizan
Roy, Kunal B.
Rishi, Vikas
author_sort Das, Amrita
collection PubMed
description We have designed a dodecamer d-AGATCTAGATCT (RY12) with alternate oligopurines and oligopyrimidines tracts and its homologous 28 bp hairpin oligomer (RY28) that forms a triple helix only in the presence of a pentapeptide REWER. An intermolecular triplex is formed by the single strand invasion of the RY28 duplex by RY12 in the presence of REWER. 5′- oligopurine end of RY12 binds to oligopurine sequence of RY28 in a parallel orientation and its oligopyrimidine stretch then changes strand and adopts an antiparallel orientation with the other strand of the duplex. Evidence for the formation of the triplex come from our studies of the UV melting curves, UV mixing curves, gel retardation assay, and chemical sequencing of 1∶1 mixture of dodecamer and hairpin oligonucleotides in the presence and absence of the peptide REWER. RY12 exists as a duplex that melts at 35°C. The hairpin (RY28) melts at 68°C. 1∶1 mixture of RY12 and RY28 in the absence of REWER gives a biphasic transition curve with thermodynamic properties corresponding to those of the melting of the duplex of RY12 and the hairpin RY28. However, the melting curve of this mixture is triphasic in the presence of the REWER; the thermodynamic parameters associated with the first phase (melting of the duplex of RY12), second phase (melting of the triplex) and the third phase (melting of the hairpin) show dependence on the molar ratio of peptide to oligonucleotides. Under appropriate conditions, gel retardation assay showed a shifted band that corresponds to a possible triplex. Chemical sequencing of KMnO(4) and DEPC treated mixture of RY12, RY28 and REWER revealed the footprint of triplex.
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spelling pubmed-36605962013-05-23 Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER Das, Amrita Saha, Tapas Ahmad, Faizan Roy, Kunal B. Rishi, Vikas PLoS One Research Article We have designed a dodecamer d-AGATCTAGATCT (RY12) with alternate oligopurines and oligopyrimidines tracts and its homologous 28 bp hairpin oligomer (RY28) that forms a triple helix only in the presence of a pentapeptide REWER. An intermolecular triplex is formed by the single strand invasion of the RY28 duplex by RY12 in the presence of REWER. 5′- oligopurine end of RY12 binds to oligopurine sequence of RY28 in a parallel orientation and its oligopyrimidine stretch then changes strand and adopts an antiparallel orientation with the other strand of the duplex. Evidence for the formation of the triplex come from our studies of the UV melting curves, UV mixing curves, gel retardation assay, and chemical sequencing of 1∶1 mixture of dodecamer and hairpin oligonucleotides in the presence and absence of the peptide REWER. RY12 exists as a duplex that melts at 35°C. The hairpin (RY28) melts at 68°C. 1∶1 mixture of RY12 and RY28 in the absence of REWER gives a biphasic transition curve with thermodynamic properties corresponding to those of the melting of the duplex of RY12 and the hairpin RY28. However, the melting curve of this mixture is triphasic in the presence of the REWER; the thermodynamic parameters associated with the first phase (melting of the duplex of RY12), second phase (melting of the triplex) and the third phase (melting of the hairpin) show dependence on the molar ratio of peptide to oligonucleotides. Under appropriate conditions, gel retardation assay showed a shifted band that corresponds to a possible triplex. Chemical sequencing of KMnO(4) and DEPC treated mixture of RY12, RY28 and REWER revealed the footprint of triplex. Public Library of Science 2013-05-21 /pmc/articles/PMC3660596/ /pubmed/23705027 http://dx.doi.org/10.1371/journal.pone.0065010 Text en © 2013 Das et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Das, Amrita
Saha, Tapas
Ahmad, Faizan
Roy, Kunal B.
Rishi, Vikas
Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER
title Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER
title_full Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER
title_fullStr Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER
title_full_unstemmed Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER
title_short Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER
title_sort dodecamer d-agatctagatct and a homologous hairpin form triplex in the presence of peptide rewer
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660596/
https://www.ncbi.nlm.nih.gov/pubmed/23705027
http://dx.doi.org/10.1371/journal.pone.0065010
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