Please use this identifier to cite or link to this item: https://doi.org/10.1073/pnas.1213740110
Title: Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry
Authors: Zhang, X.
Chen, H. 
Le, S.
Rouzina, I.
Doyle, P.S.
Yan, J. 
Keywords: DNA bubble
Magnetic tweezers
Issue Date: 5-Mar-2013
Source: Zhang, X., Chen, H., Le, S., Rouzina, I., Doyle, P.S., Yan, J. (2013-03-05). 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 of the United States of America 110 (10) : 3865-3870. ScholarBank@NUS Repository. https://doi.org/10.1073/pnas.1213740110
Abstract: 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 tensionwhile 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 transitionwere 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.
Source Title: Proceedings of the National Academy of Sciences of the United States of America
URI: http://scholarbank.nus.edu.sg/handle/10635/113132
ISSN: 00278424
DOI: 10.1073/pnas.1213740110
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