Stretching submicron biomolecules with constant-force axial optical tweezers

Biophysical Journal

Volumn 96, Issue 11, 2009, Pages 4701-4708

  Chen, Yih Fan ^a   Blab, Gerhard A ^a   Meiners, Jens Christian ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; DNA;

ARTICLE; ARTIFACT; BIOMEDICAL ENGINEERING; FEEDBACK SYSTEM; FORCE; LASER; OPTICAL TWEEZERS; PARTICLE SIZE; STEREOSPECIFICITY; TENSION; ALGORITHM; CALIBRATION; CHEMISTRY; ELASTICITY; METHODOLOGY; NANOTECHNOLOGY;

ALGORITHMS; CALIBRATION; DNA; ELASTICITY; NANOTECHNOLOGY; OPTICAL TWEEZERS;

EID: 68949114442     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.03.009     Document Type: Article

References (32)

1. Meiners, J.-C., and S. R. Quake. 2000. Femtonewton force spectroscopy of single extended DNA molecules. Phys. Rev. Lett. 84:5014-5017.
2. Revyakin, A., R. H. Ebright, and T. R. Strick. 2005. Single-molecule DNA nanomanipulation: improved resolution through use of shorter DNA fragments. Nat. Methods. 2:127-138.
3. Wang, M. D., M. J. Schnitzer, H. Yin, R. Landick, J. Gelles, et al. 1998. Force and velocity measured for single molecules of RNA polymerase. Science. 282:902-907.
4. Smith, D. E., S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, et al. 2001. The bacteriophage ø29 portal motor can package DNA against a large internal force. Nature. 413:748-752.
5. Brower-Toland, B. D., C. L. Smith, R. C. Yeh, J. T. Lis, C. L. Peterson, et al. 2002. Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl. Acad. Sci. USA. 99:1960-1965.
6. Liesfeld, B., R. Nambiar, and J.-C. Meiners. 2003. Particle transport in asymmetric scanning-line optical tweezers. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 68:051907.
7. Nambiar, R., A. Gajraj, and J.-C. Meiners. 2004. All-optical constantforce laser tweezers. Biophys. J. 87:1972-1980.
8. Greenleaf, W. J., M. T. Woodside, E. A. Abbondanzieri, and S. M. Block. 2005. Passive all-optical force clamp for high-resolution laser trapping. Phys. Rev. Lett. 95:208102.
9. Abbondanzieri, E. A., W. J. Greenleaf, J. W. Shaevitz, R. Landick, and S. M. Block. 2005. Direct observation of base-pair stepping by RNA polymerase. Nature. 438:460-465.
10. Meiners, J.-C., and S. R. Quake. 1999. Direct measurement of hydrodynamic cross correlations between two particles in an external potential. Phys. Rev. Lett. 82:2211.
11. Rohrbach, A., and E. H. K. Stelzer. 2002. Three-dimensional position detection of optically trapped dielectric particles. J. Appl. Phys. 91:5474-5488.
12. Deufel, C., and M. D. Wang. 2006. Detection of forces and displacements along the axial direction in an optical trap. Biophys. J. 90:657-667.
13. Finzi, L., and J. Gelles. 1995. Measurement of lactose repressormediated loop formation and breakdown in single DNA-molecules. Science. 267:378-380.
14. Vanzi, F., C. Broggio, L. Sacconi, and F. S. Pavone. 2006. Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion. Nucleic Acids Res. 34:3409-3420.
15. Hsieh, W. T., P. A. Whitson, K. S. Matthews, and R. D. Wells. 1987. Influence of sequence and distance between two operators on interaction with the lac repressor. J. Biol. Chem. 262:14583-14591.
16. Revyakin, A., J. F.Allemand, V. Croquette, R.H. Ebright, and T. R. Strick. 2003. Single-molecule DNA nanomanipulation: detection of promoterunwinding events by RNA polymerase. Methods Enzymol. 370:577-598.
17. Viana, N. B., R. T. Freire, and O. N. Mesquita. 2002. Dynamic light scattering from an optically trapped microsphere. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65:041921.
18. Rocha, M. S., N. B. Viana, and O. N. Mesquita. 2004. DNA-psoralen interaction: a singlemolecule experiment. J.Chem. Phys. 121:9679-9683.
19. Rohrbach, A. 2005. Switching and measuring a force of 25 femtoNewtons with an optical trap. Opt. Express. 13:9695-9701.
20. Brenner, H. 1961. The slow motion of a sphere through a viscous fluid towards a plane surface. Chem. Eng. Sci. 16:242-251.
21. Neuman, K. C., and S. M. Block. 2004. Optical trapping. Rev. Sci. Instrum. 75:2787-2809.
22. Neuman, K. C., E. A. Abbondanzieri, and S. M. Block. 2005. Measurement of the effective focal shift in an optical trap. Opt. Lett. 30:1318-1320.
23. Gouesbet, G., B. Maheu, and G. Gréhan. 1988. Light scattering from a sphere arbitrarily located in a Gaussian beam, using a Bromwich formulation. J. Opt. Soc. Am. A. 5:1427-1443.
24. Harada, Y., and T. Asakura. 1996. Radiation forces on a dielectric sphere in the Rayleigh scattering regime. Opt. Commun. 124:529-541.
25. Nieminen, T. A., V. L. Y. Loke, A. B. Stilgoe, G. Knoner, A. M. Branczyk, et al. 2007. Optical tweezers computational toolbox. J. Opt. Pure Appl. Opt. 9:S196-S203.
26. Smith, S. B., L. Finzi, and C. Bustamante. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 258:1122-1126.
27. Wang, M. D., H. Yin, R. Landick, J. Gelles, and S. M. Block. 1997. Stretching DNA with optical tweezers. Biophys. J. 72:1335-1346.
28. Seol, Y., J. Li, P. C. Nelson, T. T. Perkins, and M. D. Betterton. 2007. Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 mm. Biophys. J. 93:4360-4373.
29. Segall, D. E., P. C. Nelson, and R. Phillips. 2006. Volume-exclusion effects in tethered-particle experiments: bead size matters. Phys. Rev. Lett. 96:088306.
30. Marko, J. F., and E. D. Siggia. 1995. Stretching DNA. Macromolecules. 28:8759-8770.
31. Bustamante, C., J. F. Marko, E. D. Siggia, and S. B. Smith. 1994. Entropic elasticity of l-phage DNA. Science. 265:1599-1600.
32. Bouchiat, C., M. D. Wang, J. F. Allemand, T. Strick, S. M. Block, et al. 1999. Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys. J. 76:409-413.