Structural transitions and elasticity from torque measurements on DNA

Nature

Volumn 424, Issue 6946, 2003, Pages 338-341

  Bryant, Zev ^a   Stone, Michael D ^a   Gore, Jeff ^a   Smith, Steven B ^a   Cozzarelli, Nicholas R ^a   Bustamante, Carlos ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELASTICITY; ENZYMES; MOLECULES; POLYMERS; STRAIN; TORQUE MEASUREMENT; TORSIONAL STRESS;

STRUCTURAL TRANSITIONS;

DNA;

DNA; POLYMER;

DNA;

ARTICLE; CALIBRATION; DNA STRUCTURE; ELASTICITY; FORCE; MEASUREMENT; MECHANICAL STRESS; PRIORITY JOURNAL; ROTATION; TORQUE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; TEMPERATURE;

DNA; ELASTICITY; NUCLEIC ACID CONFORMATION; TEMPERATURE; TORQUE;

EID: 0041305824     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature01810     Document Type: Article

References (29)

1. Smith, S. B., Finzi, L. & Bustamante, C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258, 1122-1126 (1992).
2. Strick, T. R., Allemand, J. F., Bensimon, D., Bensimon, A. & Croquette, V. The elasticity of a single supercoiled DNA molecule. Science 271, 1835-1837 (1996).
3. Smith, S. B., Cui, Y. & Bustamante, C. Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795-799 (1996).
4. Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. Entropic elasticity of lambda-phage DNA. Science 265, 1599-1600 (1994).
5. Cluzel, P. et al. DNA: An extensible molecule. Science 271, 792-794 (1996).
6. Allemand, J. F., Bensimon, D., Lavery, R. & Croquette, V. Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc. Natl Acad. Sci. USA 95, 14152-14157 (1998).
7. Leger, J. F. et al. Structural transitions of a twisted and stretched DNA molecule. Phys. Rev. Lett. 83, 1066-1069 (1999).
8. Bustamante, C., Bryant, Z. & Smith, S. B. Ten years of tension: Single-molecule DNA mechanics. Nature 421, 423-427 (2003).
9. Bouchiat, C. & Mezard, M. Elasticity model of a supercoiled DNA molecule. Phys. Rev. Lett. 80, 1556-1559 (1998).
10. Sarkar, A., Leger, J. F., Chatenay, D. & Marko, J. F. Structural transitions in DNA driven by external force and torque. Phys. Rev. E 63, 051903 (2001).
11. Smith, S. B., Cui, Y. & Bustamante, C. Optical-trap force transducer that operates by direct measurement oflight momentum. Methods Enzymol. 361, 134-162 (2003).
12. Strick, T. R., Bensimon, D. & Croquette, V. Micro-mechanical measurement of the torsional modulus of DNA. Genetica 106, 57-62 (1999).
13. Selvin, P. R. et al. Torsional rigidity of positively and negatively supercoiled DNA. Science 255, 82-85 (1992).
14. Millar, D. P., Bobbins, R. J. & Zewail, A. H. Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy. Proc Natl Acad. Sci. USA 77, 5593-5597 (1980).
15. Heath, P. J., Clendenning, J. B., Fujimoto, B. S. & Schurr, J. M. Effect of bending strain on the torsion elastic constant of DNA. J. Mol. Biol. 260, 718-730 (1996).
16. Horowitz, D. S. & Wang, J. C. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Mol. Biol. 173, 75-91 (1984).
17. Shore, D. & Baldwin, R. L. Energetics of DNA twisting. II. Topoisomer analysis. J. Mol. Biol. 170, 983-1007 (1983).
18. Crothers, D. M., Drak, J., Kahn, J. D. & Levene, S. D. DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods Enzymol. 212, 3-29 (1992).
19. Vologodskii, A. V. & Marko, J. F. Extension of torsionally stressed DNA by external force. Biophys. J. 73, 123-132 (1997).
20. Moroz, J. D. & Nelson, P. Entropic elasticity of twist-storing polymers. Macromolecules 31, 6333-6347 (1998).
21. Yasuda, R., Miyata, H. & Kinosita, K. Jr Direct measurement of the torsional rigidity of single actin filaments. J. Mol. Biol. 263, 227-236 (1996).
22. Williams, M. C., Rouzina, I. & Bloomfield, V. A. Thermodynamics of DNA interactions from single molecule stretching experiments. Acc. Chem. Res. 35, 159-166 (2002).
23. Soong, R. K. et al. Powering an inorganic nanodevice with a biomolecular motor. Science 290, 1555-1558 (2000).
24. Yasuda, R., Noji, H., Kinosita, K. Jr & Yoshida, M. Fl-ATPase is a highly efficient molecular motor that rotates with discrete 120 degree steps. Cell 93, 1117-1124 (1998).
25. Seaman, N. C. DNA in a material world. Nature 421, 427-431 (2003).
26. Harada, Y. et al. Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature 409, 113-115 (2001).
27. Wobbe, C. R., Dean, F., Weissbach, L. & Hurwitz, J. In vitro replication of duplex circular DNA containing the simian virus 40 DNA origin site. Proc. Natl Acad. Sci. USA 82, 5710-5714 (1985).
28. Davenport, R. J., Wuite, G. J., Landick, R. & Bustamante, C. Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science 287, 2497-2500 (2000).
29. Davis, M. H. The slow translation and rotation of two unequal spheres in a viscous fluid. Chem. Eng. Sci. 24, 1769-1776 (1969).