Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.

Single-stranded DNA (ssDNA) is characterized by high conformational flexibility that allows these molecules to adopt a variety of conformations. Here we used native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy to sh...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Malik Mumtaz Taqi, Sebastian K T S Wärmländer, Olga Yamskova, Fatemeh Madani, Igor Bazov, Jinghui Luo, Roman Zubarev, Dineke Verbeek, Astrid Gräslund, Georgy Bakalkin
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bce2bed7c35440a0b4d484b5cee7a0fc
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:bce2bed7c35440a0b4d484b5cee7a0fc
record_format	dspace
spelling	oai:doaj.org-article:bce2bed7c35440a0b4d484b5cee7a0fc2021-11-18T07:13:56ZConformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.1932-620310.1371/journal.pone.0039605https://doaj.org/article/bce2bed7c35440a0b4d484b5cee7a0fc2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22768096/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Single-stranded DNA (ssDNA) is characterized by high conformational flexibility that allows these molecules to adopt a variety of conformations. Here we used native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy to show that cytosine methylation at CpG sites affects the conformational flexibility of short ssDNA molecules. The CpG containing 37-nucleotide PDYN (prodynorphin) fragments were used as model molecules. The presence of secondary DNA structures was evident from differences in oligonucleotide mobilities on PAGE, from CD spectra, and from formation of A-T, G-C, and non-canonical G-T base pairs observed by NMR spectroscopy. The oligonucleotides displayed secondary structures at 4°C, and some also at 37°C. Methylation at CpG sites prompted sequence-dependent formation of novel conformations, or shifted the equilibrium between different existing ssDNA conformations. The effects of methylation on gel mobility and base pairing were comparable in strength to the effects induced by point mutations in the DNA sequences. The conformational effects of methylation may be relevant for epigenetic regulatory events in a chromatin context, including DNA-protein or DNA-DNA recognition in the course of gene transcription, and DNA replication and recombination when double-stranded DNA is unwinded to ssDNA.Malik Mumtaz TaqiSebastian K T S WärmländerOlga YamskovaFatemeh MadaniIgor BazovJinghui LuoRoman ZubarevDineke VerbeekAstrid GräslundGeorgy BakalkinPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e39605 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Malik Mumtaz Taqi Sebastian K T S Wärmländer Olga Yamskova Fatemeh Madani Igor Bazov Jinghui Luo Roman Zubarev Dineke Verbeek Astrid Gräslund Georgy Bakalkin Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.
description	Single-stranded DNA (ssDNA) is characterized by high conformational flexibility that allows these molecules to adopt a variety of conformations. Here we used native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy to show that cytosine methylation at CpG sites affects the conformational flexibility of short ssDNA molecules. The CpG containing 37-nucleotide PDYN (prodynorphin) fragments were used as model molecules. The presence of secondary DNA structures was evident from differences in oligonucleotide mobilities on PAGE, from CD spectra, and from formation of A-T, G-C, and non-canonical G-T base pairs observed by NMR spectroscopy. The oligonucleotides displayed secondary structures at 4°C, and some also at 37°C. Methylation at CpG sites prompted sequence-dependent formation of novel conformations, or shifted the equilibrium between different existing ssDNA conformations. The effects of methylation on gel mobility and base pairing were comparable in strength to the effects induced by point mutations in the DNA sequences. The conformational effects of methylation may be relevant for epigenetic regulatory events in a chromatin context, including DNA-protein or DNA-DNA recognition in the course of gene transcription, and DNA replication and recombination when double-stranded DNA is unwinded to ssDNA.
format	article
author	Malik Mumtaz Taqi Sebastian K T S Wärmländer Olga Yamskova Fatemeh Madani Igor Bazov Jinghui Luo Roman Zubarev Dineke Verbeek Astrid Gräslund Georgy Bakalkin
author_facet	Malik Mumtaz Taqi Sebastian K T S Wärmländer Olga Yamskova Fatemeh Madani Igor Bazov Jinghui Luo Roman Zubarev Dineke Verbeek Astrid Gräslund Georgy Bakalkin
author_sort	Malik Mumtaz Taqi
title	Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.
title_short	Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.
title_full	Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.
title_fullStr	Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.
title_full_unstemmed	Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.
title_sort	conformation effects of cpg methylation on single-stranded dna oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/bce2bed7c35440a0b4d484b5cee7a0fc
work_keys_str_mv	AT malikmumtaztaqi conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT sebastianktswarmlander conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT olgayamskova conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT fatemehmadani conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT igorbazov conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT jinghuiluo conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT romanzubarev conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT dinekeverbeek conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT astridgraslund conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences AT georgybakalkin conformationeffectsofcpgmethylationonsinglestrandeddnaoligonucleotidesanalysisoftheopioidpeptidedynorphincodingsequences
_version_	1718423753151479808

Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences.

Ejemplares similares