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Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)(n) Repeats by PNA or LNA Targeting

Expansion of (GAA)(n) repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)(n) expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epige...

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Autores principales: Bergquist, Helen, Rocha, Cristina S. J., Álvarez-Asencio, Rubén, Nguyen, Chi-Hung, Rutland, Mark. W., Smith, C. I. Edvard, Good, Liam, Nielsen, Peter E., Zain, Rula
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112992/
https://www.ncbi.nlm.nih.gov/pubmed/27846236
http://dx.doi.org/10.1371/journal.pone.0165788
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author Bergquist, Helen
Rocha, Cristina S. J.
Álvarez-Asencio, Rubén
Nguyen, Chi-Hung
Rutland, Mark. W.
Smith, C. I. Edvard
Good, Liam
Nielsen, Peter E.
Zain, Rula
author_facet Bergquist, Helen
Rocha, Cristina S. J.
Álvarez-Asencio, Rubén
Nguyen, Chi-Hung
Rutland, Mark. W.
Smith, C. I. Edvard
Good, Liam
Nielsen, Peter E.
Zain, Rula
author_sort Bergquist, Helen
collection PubMed
description Expansion of (GAA)(n) repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)(n) expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)(n) expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)(n) repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)(4)-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)(5)-PNA did not. We present evidence that (GAA)(4)-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)(5)-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression.
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spelling pubmed-51129922016-12-08 Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)(n) Repeats by PNA or LNA Targeting Bergquist, Helen Rocha, Cristina S. J. Álvarez-Asencio, Rubén Nguyen, Chi-Hung Rutland, Mark. W. Smith, C. I. Edvard Good, Liam Nielsen, Peter E. Zain, Rula PLoS One Research Article Expansion of (GAA)(n) repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)(n) expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)(n) expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)(n) repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)(4)-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)(5)-PNA did not. We present evidence that (GAA)(4)-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)(5)-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression. Public Library of Science 2016-11-15 /pmc/articles/PMC5112992/ /pubmed/27846236 http://dx.doi.org/10.1371/journal.pone.0165788 Text en © 2016 Bergquist 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 (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Bergquist, Helen
Rocha, Cristina S. J.
Álvarez-Asencio, Rubén
Nguyen, Chi-Hung
Rutland, Mark. W.
Smith, C. I. Edvard
Good, Liam
Nielsen, Peter E.
Zain, Rula
Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)(n) Repeats by PNA or LNA Targeting
title Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)(n) Repeats by PNA or LNA Targeting
title_full Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)(n) Repeats by PNA or LNA Targeting
title_fullStr Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)(n) Repeats by PNA or LNA Targeting
title_full_unstemmed Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)(n) Repeats by PNA or LNA Targeting
title_short Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)(n) Repeats by PNA or LNA Targeting
title_sort disruption of higher order dna structures in friedreich’s ataxia (gaa)(n) repeats by pna or lna targeting
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112992/
https://www.ncbi.nlm.nih.gov/pubmed/27846236
http://dx.doi.org/10.1371/journal.pone.0165788
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