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DNA folding and melting observed in real time redefine the energy landscape

Ma, Hairong and Wan, Chaozhi and Wu, Aiguo and Zewail, Ahmed H. (2007) DNA folding and melting observed in real time redefine the energy landscape. Proceedings of the National Academy of Sciences of the United States of America, 104 (3). pp. 712-716. ISSN 0027-8424. PMCID PMC1766338. https://resolver.caltech.edu/CaltechAUTHORS:MAHpnas07

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Abstract

We report real-time observations of the folding and melting of DNA by probing two active sites of a hairpin structure, the bases and the stem end, and using an ultrafast T-jump. Studies at different initial temperatures (before, during, and after melting) provide the time scale of water heating (<20 ps), single-strand destacking (700 ps to 2 ns), and hairpin destacking (microseconds and longer) in solutions of various ionic strengths and pH values. The behavior of transient changes gives direct evidence to the existence of intermediate collapsed structures, labile in destacking but compact in nature, and indicates that melting is not a two-state process. We propose a landscape that is defined by these nucleation structures and destacking for efficient folding and melting.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://www.pnas.org/content/104/3/712.longPublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1766338/PubMed CentralArticle
https://doi.org/10.1073/pnas.0610028104UNSPECIFIEDUNSPECIFIED
https://doi.org/10.1073/pnas.0610028104UNSPECIFIEDUNSPECIFIED
ORCID:
AuthorORCID
Wu, Aiguo000-0001-7200-8923
Additional Information:© 2007 by the National Academy of Sciences. Freely available online through the PNAS open access option. Contributed by Ahmed H. Zewail, November 13, 2006 (sent for review November 1, 2006). Published online before print January 10, 2007. This work was supported by the National Science Foundation and the Physical Biology Center for Ultrafast Science and Technology. Author contributions: H.M., C.W., A.W., and A.H.Z. performed research and H.M., C.W., and A.H.Z. wrote the paper. The authors declare no conflict of interest.
Funders:
Funding AgencyGrant Number
NSFUNSPECIFIED
Subject Keywords:biopolymers; macromolecular folding; ultrafast T-jump
Issue or Number:3
PubMed Central ID:PMC1766338
Record Number:CaltechAUTHORS:MAHpnas07
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:MAHpnas07
Official Citation:Hairong Ma, Chaozhi Wan, Aiguo Wu, and Ahmed H. Zewail DNA folding and melting observed in real time redefine the energy landscape PNAS 2007 104 (3) 712-716; published ahead of print January 10, 2007, doi:10.1073/pnas.0610028104
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7156
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:11 Jan 2007
Last Modified:14 Dec 2019 00:14

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