Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry
Double-stranded DNA (dsDNA) unconstrained by torsion undergoes an overstretching transition at about 65 pN, elongating the DNA to about 1.7-fold. Three possible structural transitions have been debated for the nature of DNA overstretching: (i) “peeling” apart of dsDNA to produce a peeled ssDNA stran...
| Main Authors: | , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
National Academy of Sciences (U.S.)
2013
|
| Online Access: | http://hdl.handle.net/1721.1/80397 |
| _version_ | 1811090536883290112 |
|---|---|
| author | Zhang, Xinghua Chen, Hu Le, Shimin Rouzina, Ioulia Doyle, Patrick S. Yan, Jie |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Zhang, Xinghua Chen, Hu Le, Shimin Rouzina, Ioulia Doyle, Patrick S. Yan, Jie |
| author_sort | Zhang, Xinghua |
| collection | MIT |
| description | Double-stranded DNA (dsDNA) unconstrained by torsion undergoes an overstretching transition at about 65 pN, elongating the DNA to about 1.7-fold. Three possible structural transitions have been debated for the nature of DNA overstretching: (i) “peeling” apart of dsDNA to produce a peeled ssDNA strand under tension while the other strand coils, (ii) “inside-strand separation” of dsDNA to two parallel ssDNA strands that share tension (melting bubbles), and (iii) “B-to-S” transition to a novel dsDNA, termed S-DNA. Here we overstretched an end-opened DNA (with one open end to allow peeling) and an end-closed (i.e., both ends of the linear DNA are covalently closed to prohibit peeling) and torsion-unconstrained DNA. We report that all three structural transitions exist depending on experimental conditions. For the end-opened DNA, the peeling transition and the B-to-S transition were observed; for the end-closed DNA, the inside-strand separation and the B-to-S transition were observed. The peeling transition and the inside-strand separation are hysteretic and have an entropy change of approximately 17 cal/(K⋅mol), whereas the B-to-S transition is nonhysteretic and has an entropy change of approximately −2 cal/(K⋅mol). The force-extension curves of peeled ssDNA, melting bubbles, and S-DNA were characterized by experiments. Our results provide experimental evidence for the formation of DNA melting bubbles driven by high tension and prove the existence of nonmelted S-DNA. Our findings afford a full understanding of three possible force-driven structural transitions of torsion-unconstrained DNA and the resulting three overstretched DNA structures. |
| first_indexed | 2024-09-23T14:47:45Z |
| format | Article |
| id | mit-1721.1/80397 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:47:45Z |
| publishDate | 2013 |
| publisher | National Academy of Sciences (U.S.) |
| record_format | dspace |
| spelling | mit-1721.1/803972022-09-29T10:37:09Z Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry Zhang, Xinghua Chen, Hu Le, Shimin Rouzina, Ioulia Doyle, Patrick S. Yan, Jie Massachusetts Institute of Technology. Department of Chemical Engineering Doyle, Patrick S. Double-stranded DNA (dsDNA) unconstrained by torsion undergoes an overstretching transition at about 65 pN, elongating the DNA to about 1.7-fold. Three possible structural transitions have been debated for the nature of DNA overstretching: (i) “peeling” apart of dsDNA to produce a peeled ssDNA strand under tension while the other strand coils, (ii) “inside-strand separation” of dsDNA to two parallel ssDNA strands that share tension (melting bubbles), and (iii) “B-to-S” transition to a novel dsDNA, termed S-DNA. Here we overstretched an end-opened DNA (with one open end to allow peeling) and an end-closed (i.e., both ends of the linear DNA are covalently closed to prohibit peeling) and torsion-unconstrained DNA. We report that all three structural transitions exist depending on experimental conditions. For the end-opened DNA, the peeling transition and the B-to-S transition were observed; for the end-closed DNA, the inside-strand separation and the B-to-S transition were observed. The peeling transition and the inside-strand separation are hysteretic and have an entropy change of approximately 17 cal/(K⋅mol), whereas the B-to-S transition is nonhysteretic and has an entropy change of approximately −2 cal/(K⋅mol). The force-extension curves of peeled ssDNA, melting bubbles, and S-DNA were characterized by experiments. Our results provide experimental evidence for the formation of DNA melting bubbles driven by high tension and prove the existence of nonmelted S-DNA. Our findings afford a full understanding of three possible force-driven structural transitions of torsion-unconstrained DNA and the resulting three overstretched DNA structures. Singapore-MIT Alliance for Research and Technology 2013-09-11T16:49:13Z 2013-09-11T16:49:13Z 2013-02 2012-08 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/80397 Zhang, X., H. Chen, S. Le, I. Rouzina, P. S. Doyle, and J. Yan. “Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry.” Proceedings of the National Academy of Sciences 110, no. 10 (March 5, 2013): 3865-3870. en_US http://dx.doi.org/10.1073/pnas.1213740110 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) PNAS |
| spellingShingle | Zhang, Xinghua Chen, Hu Le, Shimin Rouzina, Ioulia Doyle, Patrick S. Yan, Jie Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry |
| title | Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry |
| title_full | Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry |
| title_fullStr | Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry |
| title_full_unstemmed | Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry |
| title_short | Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry |
| title_sort | revealing the competition between peeled ssdna melting bubbles and s dna during dna overstretching by single molecule calorimetry |
| url | http://hdl.handle.net/1721.1/80397 |
| work_keys_str_mv | AT zhangxinghua revealingthecompetitionbetweenpeeledssdnameltingbubblesandsdnaduringdnaoverstretchingbysinglemoleculecalorimetry AT chenhu revealingthecompetitionbetweenpeeledssdnameltingbubblesandsdnaduringdnaoverstretchingbysinglemoleculecalorimetry AT leshimin revealingthecompetitionbetweenpeeledssdnameltingbubblesandsdnaduringdnaoverstretchingbysinglemoleculecalorimetry AT rouzinaioulia revealingthecompetitionbetweenpeeledssdnameltingbubblesandsdnaduringdnaoverstretchingbysinglemoleculecalorimetry AT doylepatricks revealingthecompetitionbetweenpeeledssdnameltingbubblesandsdnaduringdnaoverstretchingbysinglemoleculecalorimetry AT yanjie revealingthecompetitionbetweenpeeledssdnameltingbubblesandsdnaduringdnaoverstretchingbysinglemoleculecalorimetry |