Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism
| dc.contributor.author | Shepherd, Dionne N | |
| dc.contributor.author | Martin, Darren P | |
| dc.contributor.author | Varsani, Arvind | |
| dc.contributor.author | Thomson, Jennifer A | |
| dc.contributor.author | Rybicki, Edward P | |
| dc.contributor.author | Klump, Horst H | |
| dc.date.accessioned | 2016-07-26T08:47:28Z | |
| dc.date.available | 2016-07-26T08:47:28Z | |
| dc.date.issued | 2006 | |
| dc.date.updated | 2016-07-15T14:57:35Z | |
| dc.description.abstract | We used in vivo (biological), in silico (computational structure prediction), and in vitro (model sequence folding) analyses of singlestranded DNA sequences to show that nucleic acid folding conservation is the selective principle behind a high-frequency single-nucleotide reversion observed in a three-nucleotide mutated motif of the Maize streak virus replication associated protein (Rep) gene. In silico and in vitro studies showed that the three-nucleotide mutation adversely aVected Rep nucleic acid folding, and that the single-nucleotide reversion [C(601)A] restored wild-type-like folding. In vivo support came from infecting maize with mutant viruses: those with Rep genes containing nucleotide changes predicted to restore a wild-type-like fold [A(601)/G(601)] preferentially accumulated over those predicted to fold diVerently [C(601)/T(601)], which frequently reverted to A(601) and displaced the original population. We propose that the selection of native nucleic acid folding is an epigenetic eVect, which might have broad implications in the evolution of plants and their viruses. | en_ZA |
| dc.identifier | http://dx.doi.org/10.1016/j.abb.2005.12.009 | |
| dc.identifier.apacitation | Shepherd, D. N., Martin, D. P., Varsani, A., Thomson, J. A., Rybicki, E. P., & Klump, H. H. (2006). Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism. <i>Archives of Biochemistry and Biophysics</i>, http://hdl.handle.net/11427/20742 | en_ZA |
| dc.identifier.chicagocitation | Shepherd, Dionne N, Darren P Martin, Arvind Varsani, Jennifer A Thomson, Edward P Rybicki, and Horst H Klump "Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism." <i>Archives of Biochemistry and Biophysics</i> (2006) http://hdl.handle.net/11427/20742 | en_ZA |
| dc.identifier.citation | Shepherd, D. N., Martin, D. P., Varsani, A., Thomson, J. A., Rybicki, E. P., & Klump, H. H. (2006). Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism. Archives of Biochemistry and biophysics, 453(1), 108-122. | en_ZA |
| dc.identifier.issn | 0003-9861 | en_ZA |
| dc.identifier.ris | TY - Journal Article AU - Shepherd, Dionne N AU - Martin, Darren P AU - Varsani, Arvind AU - Thomson, Jennifer A AU - Rybicki, Edward P AU - Klump, Horst H AB - We used in vivo (biological), in silico (computational structure prediction), and in vitro (model sequence folding) analyses of singlestranded DNA sequences to show that nucleic acid folding conservation is the selective principle behind a high-frequency single-nucleotide reversion observed in a three-nucleotide mutated motif of the Maize streak virus replication associated protein (Rep) gene. In silico and in vitro studies showed that the three-nucleotide mutation adversely aVected Rep nucleic acid folding, and that the single-nucleotide reversion [C(601)A] restored wild-type-like folding. In vivo support came from infecting maize with mutant viruses: those with Rep genes containing nucleotide changes predicted to restore a wild-type-like fold [A(601)/G(601)] preferentially accumulated over those predicted to fold diVerently [C(601)/T(601)], which frequently reverted to A(601) and displaced the original population. We propose that the selection of native nucleic acid folding is an epigenetic eVect, which might have broad implications in the evolution of plants and their viruses. DA - 2006 DB - OpenUCT DP - University of Cape Town J1 - Archives of Biochemistry and Biophysics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2006 SM - 0003-9861 T1 - Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism TI - Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism UR - http://hdl.handle.net/11427/20742 ER - | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/11427/20742 | |
| dc.identifier.vancouvercitation | Shepherd DN, Martin DP, Varsani A, Thomson JA, Rybicki EP, Klump HH. Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism. Archives of Biochemistry and Biophysics. 2006; http://hdl.handle.net/11427/20742. | en_ZA |
| dc.language | eng | en_ZA |
| dc.publisher | Elsevier | en_ZA |
| dc.publisher.institution | University of Cape Town | |
| dc.rights | Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) | * |
| dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/4.0/ | en_ZA |
| dc.source | Archives of Biochemistry and Biophysics | en_ZA |
| dc.source.uri | http://www.sciencedirect.com/science/journal/00039861 | |
| dc.subject.other | Geminivirus | |
| dc.subject.other | Maize streak virus | |
| dc.subject.other | Replication associated protein gene | |
| dc.subject.other | Epigenetic | |
| dc.subject.other | Plant | |
| dc.title | Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism | en_ZA |
| dc.type | Journal Article | en_ZA |
| uct.type.filetype | Text | |
| uct.type.filetype | Image | |
| uct.type.publication | Research | en_ZA |
| uct.type.resource | Article | en_ZA |