Kinetics of the Triplex-Duplex Transition in DNA
The kinetics of triplex folding/unfolding is investigated by the single-molecule fluorescence resonance energy transfer (FRET) technique. In neutral pH conditions, the average dwell times in both high-FRET (folded) and low-FRET (unfolded) states are comparable, meaning that the triplex is marginally...
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| Veröffentlicht in: | Biophysical journal 2012-12, Vol.103 (12), p.2492-2501 |
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| creator | Lee, Il-Buem Hong, Seok-Cheol Lee, Nam-Kyung Johner, Albert |
| description | The kinetics of triplex folding/unfolding is investigated by the single-molecule fluorescence resonance energy transfer (FRET) technique. In neutral pH conditions, the average dwell times in both high-FRET (folded) and low-FRET (unfolded) states are comparable, meaning that the triplex is marginally stable. The dwell-time distributions are qualitatively different: while the dwell-time distribution of the high-FRET state should be fit with at least a double-exponential function, the dwell-time distribution of the low-FRET state can be fit with a single-exponential function. We propose a model where the folding can be trapped in metastable states, which is consistent with the FRET data. Our model also accounts for the fact that the relevant timescales of triplex folding/unfolding are macroscopic. |
| doi_str_mv | 10.1016/j.bpj.2012.10.029 |
| format | Article |
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In neutral pH conditions, the average dwell times in both high-FRET (folded) and low-FRET (unfolded) states are comparable, meaning that the triplex is marginally stable. The dwell-time distributions are qualitatively different: while the dwell-time distribution of the high-FRET state should be fit with at least a double-exponential function, the dwell-time distribution of the low-FRET state can be fit with a single-exponential function. We propose a model where the folding can be trapped in metastable states, which is consistent with the FRET data. 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All rights reserved.</rights><rights>Copyright Biophysical Society Dec 19, 2012</rights><rights>2012 by the Biophysical Society. 2012 Biophysical Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c602t-f1563e03bac31cf17b5ab581755bddfaf2b732808a2a43c6002b9c7de3d98d9f3</citedby><cites>FETCH-LOGICAL-c602t-f1563e03bac31cf17b5ab581755bddfaf2b732808a2a43c6002b9c7de3d98d9f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525853/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.bpj.2012.10.029$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,886,3551,27929,27930,46000,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23260051$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, Il-Buem</creatorcontrib><creatorcontrib>Hong, Seok-Cheol</creatorcontrib><creatorcontrib>Lee, Nam-Kyung</creatorcontrib><creatorcontrib>Johner, Albert</creatorcontrib><title>Kinetics of the Triplex-Duplex Transition in DNA</title><title>Biophysical journal</title><addtitle>Biophys J</addtitle><description>The kinetics of triplex folding/unfolding is investigated by the single-molecule fluorescence resonance energy transfer (FRET) technique. In neutral pH conditions, the average dwell times in both high-FRET (folded) and low-FRET (unfolded) states are comparable, meaning that the triplex is marginally stable. The dwell-time distributions are qualitatively different: while the dwell-time distribution of the high-FRET state should be fit with at least a double-exponential function, the dwell-time distribution of the low-FRET state can be fit with a single-exponential function. We propose a model where the folding can be trapped in metastable states, which is consistent with the FRET data. Our model also accounts for the fact that the relevant timescales of triplex folding/unfolding are macroscopic.</description><subject>Base Sequence</subject><subject>Biophysics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - chemistry</subject><subject>DNA - genetics</subject><subject>DNA - metabolism</subject><subject>DNA-Directed RNA Polymerases - metabolism</subject><subject>energy transfer</subject><subject>Fluorescence</subject><subject>Fluorescence Resonance Energy Transfer</subject><subject>Hydrogen-Ion Concentration</subject><subject>Kinetics</subject><subject>Molecular physics</subject><subject>Nucleic Acid Conformation</subject><subject>Proteins and Nucleic Acids</subject><issn>0006-3495</issn><issn>1542-0086</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkcFO3DAQhq2qqGyhD9BLG4lLL9mO7ThxVKkSghYQqByAs-U4NjjK2ls7QfTtO6sFRHuoerLG_ubXjD9C3lNYUqD152HZrYclA8qwXgJrX5EFFRUrAWT9miwAoC551Ypd8jbnARAUQN-QXcZZDSDogsC5D3byJhfRFdOdLa6TX4_2oTyeNweWOmQ_-RgKH4rjH4f7ZMfpMdt3j-ceufn-7frotLy4PDk7OrwoTQ1sKh0VNbfAO204NY42ndCdkLQRout7px3rGs4kSM10xbEHWNeapre8b2XfOr5Hvm5z13O3sr2xYUp6VOvkVzr9UlF79edL8HfqNt4rLpiQgmPAp8eAFH_ONk9q5bOx46iDjXNWlElBASoh_wNteCXatqKIHvyFDnFOAX8CqYrVtJEASNEtZVLMOVn3PDcFtVGnBoXq1Ebd5grVYc-Hlws_dzy5QuDjFnA6Kn2bfFY3V5gg0CsuAwKJL1vCoph7b5PKxttgbO-TNZPqo__HAL8BlWewow</recordid><startdate>20121219</startdate><enddate>20121219</enddate><creator>Lee, Il-Buem</creator><creator>Hong, Seok-Cheol</creator><creator>Lee, Nam-Kyung</creator><creator>Johner, Albert</creator><general>Elsevier Inc</general><general>Biophysical Society</general><general>The Biophysical Society</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20121219</creationdate><title>Kinetics of the Triplex-Duplex Transition in DNA</title><author>Lee, Il-Buem ; 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| source | MEDLINE; Cell Press Free Archives; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; ScienceDirect Journals (5 years ago - present); PubMed Central |
| subjects | Base Sequence Biophysics Deoxyribonucleic acid DNA DNA - chemistry DNA - genetics DNA - metabolism DNA-Directed RNA Polymerases - metabolism energy transfer Fluorescence Fluorescence Resonance Energy Transfer Hydrogen-Ion Concentration Kinetics Molecular physics Nucleic Acid Conformation Proteins and Nucleic Acids |
| title | Kinetics of the Triplex-Duplex Transition in DNA |
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