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Published January 16, 2007 | Published
Journal Article Open

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


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.

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.

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August 22, 2023
October 16, 2023