Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 10 November 2006:
Vol. 314. no. 5801, pp. 1001 - 1004
DOI: 10.1126/science.1133601
Prev | Table of Contents | Next

Reports

Direct Measurement of the Full, Sequence-Dependent Folding Landscape of a Nucleic Acid

Michael T. Woodside,1,2 Peter C. Anthony,3 William M. Behnke-Parks,2 Kevan Larizadeh,2 Daniel Herschlag,4 Steven M. Block2,5*

Nucleic acid hairpins provide a powerful model system for understanding macromolecular folding, with free-energy landscapes that can be readily manipulated by changing the hairpin sequence. The full shapes of energy landscapes for the reversible folding of DNA hairpins under controlled loads exerted by an optical force clamp were obtained by deconvolution from high-resolution, single-molecule trajectories. The locations and heights of the energy barriers for hairpin folding could be tuned by adjusting the number and location of G:C base pairs, and the presence and position of folding intermediates were controlled by introducing single-nucleotide mismatches.

1 National Institute for Nanotechnology, National Research Council of Canada, Edmonton AB, Canada, T6G 2M9.
2 Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.
3 Biophysics Program, Stanford University, Stanford, CA 94305, USA.
4 Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
5 Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.

* To whom correspondence should be addressed. E-mail: sblock{at}stanford.edu

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis.
E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo (2009)
PNAS 106, 18125-18130
   Abstract »    Full Text »    PDF »
DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases.
J. Volker, H. H. Klump, and K. J. Breslauer (2008)
PNAS 105, 18326-18330
   Abstract »    Full Text »    PDF »
End-joining long nucleic acid polymers.
M. van den Hout, S. Hage, C. Dekker, and N. H. Dekker (2008)
Nucleic Acids Res. 36, e104
   Abstract »    Full Text »    PDF »
Loop dependence of the stability and dynamics of nucleic acid hairpins.
S. V. Kuznetsov, C.-C. Ren, S. A. Woodson, and A. Ansari (2008)
Nucleic Acids Res. 36, 1098-1112
   Abstract »    Full Text »    PDF »
Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers.
W. J. Greenleaf, K. L. Frieda, D. A. N. Foster, M. T. Woodside, and S. M. Block (2008)
Science 319, 630-633
   Abstract »    Full Text »    PDF »
Single-molecule biophysics: at the interface of biology, physics and chemistry.
A. A Deniz, S. Mukhopadhyay, and E. A Lemke (2008)
J R Soc Interface 5, 15-45
   Abstract »    Full Text »    PDF »
Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA.
G. Chen, J.-D. Wen, and I. Tinoco Jr (2007)
RNA 13, 2175-2188
   Abstract »    Full Text »    PDF »
Fluorescence-Force Spectroscopy Maps Two-Dimensional Reaction Landscape of the Holliday Junction.
S. Hohng, R. Zhou, M. K. Nahas, J. Yu, K. Schulten, D. M. J. Lilley, and T. Ha (2007)
Science 318, 279-283
   Abstract »    Full Text »    PDF »
Real-time control of the energy landscape by force directs the folding of RNA molecules.
P. T. X. Li, C. Bustamante, and I. Tinoco Jr. (2007)
PNAS 104, 7039-7044
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)