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Conformational polymorphism of single stranded oligonucleotides with the opioid peptide dynorphin-encoding sequences: effect of CpG methylation and human pathogenic mutations
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Prof. Georgy Bakalkin)
(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Abstract [en]

Single stranded DNA (ssDNA) is characterized by high conformational flexibility that allows these molecules to adopt a variety of conformations and form non-canonical DNA secondary structures. We here evaluated whether cytosine methylation at CpG sites affects conformational flexibility of short ssDNA molecules using native polyacrylamide gel electrophoresis (PAGE), nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. The 37-nucleotide fragments of exon 4 of the PDYN gene that contain four CpG sites were used as model molecules. Some of the analyzed single stranded oligonucleotides demonstrated formation of non-canonical DNA structures at 4oC that were not evident at 37oC. Cytosine methylation at specific CpG sites interfered with the formation of these structures and promoted formation of other conformers at 4oC. Results obtained by the three methods generally correlated. Thus, cytosine methylation may affect conformational flexibility of ssDNA molecules and therefore their propensity to form non-canonical DNA secondary structures. This effect may be potentially relevant for molecular events in the chromatin context including regulation of gene transcription, and DNA replication and recombination where double stranded DNA is unwinded to ssDNA.

URN: urn:nbn:se:uu:diva-158456OAI: oai:DiVA.org:uu-158456DiVA: diva2:439569
Available from: 2011-09-08 Created: 2011-09-08 Last updated: 2011-09-08Bibliographically approved

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Taqi, Malik Mumtaz
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