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Measuring DNA–Protein Binding Affinity on a Single Molecule Using Optical Tweezers

  • ️Sat Jan 01 2011

References

  1. Ashkin, A., Schutze, K., Dziedzic, J. M., Euteneuer, U., and Schliwa, M. (1990) Force generation of organelle transport measured in vivo by an infrared laser trap, Nature 348, 346–348.

    Article  CAS  Google Scholar 

  2. Bustamante, C., Bryant, Z., and Smith, S. B. (2003) Ten years of tension: single-molecule DNA mechanics, Nature 421, 423–427.

    Article  Google Scholar 

  3. McCauley, M. J., and Williams, M. C. (2009) Optical tweezers experiments resolve distinct modes of DNA-protein binding, Biopolymers 91, 265–282.

    Article  CAS  Google Scholar 

  4. Neuman, K. C., and Block, S. M. (2004) Optical trapping, Rev Sci Instrum 75, 2787–2809.

    Article  CAS  Google Scholar 

  5. Marko, J. F., and Siggia, E. D. (1995) Stretching DNA., Macromolecules 28, 8759–8770.

    Article  CAS  Google Scholar 

  6. Cluzel, P., Lebrun, A., Heller, C., Lavery, R., Viovy, J.-L., Chatenay, D., and Caron, F. (1996) DNA: An extensible molecule, Science 271, 792–794.

    Article  CAS  Google Scholar 

  7. Smith, S. B., Cui, Y., and Bustamante, C. (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules, Science 271, 795–799.

    Article  CAS  Google Scholar 

  8. Williams, M. C., Rouzina, I., and Bloomfield, V. A. (2002) Thermodynamics of DNA interactions from single molecule stretching experiments, Acc Chem Res 35, 159–166.

    Article  CAS  Google Scholar 

  9. van Mameren, J., Gross, P., Farge, G., Hooijman, P., Modesti, M., Falkenberg, M., Wuite, G., and Peterman, E. (2009) Unraveling the structure of DNA during overs-tretching using multicolor, single-molecule fluorescence imaging, Proc Natl Acad Sci USA, 10.1073/PNAS.0904322106.

    Google Scholar 

  10. Shokri, L., McCauley, M. J., Rouzina, I., and Williams, M. C. (2008) DNA overstretching in the presence of glyoxal: Structural evidence of force-induced melting, Biophys J 95, 1248–1255.

    Article  CAS  Google Scholar 

  11. Rouzina, I., and Bloomfield, V. A. (2001) Force-induced melting of the DNA double helix. 2. Effect of solution conditions, Biophys J 80, 894–900.

    Article  CAS  Google Scholar 

  12. Rouzina, I., and Bloomfield, V. A. (2001) Force-induced melting of the DNA double helix 1. Thermodynamic analysis, Biophys J 80, 882–893.

    Article  CAS  Google Scholar 

  13. Cruceanu, M., Urbaneja, M. A., Hixson, C. V., Johnson, D. G., Datta, S. A., Fivash, M. J., Stephen, A. G., Fisher, R. J., Gorelick, R. J., Casas-Finet, J. R., Rein, A., Rouzina, I., and Williams, M. C. (2006) Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins, Nucleic Acids Res 34, 593–605.

    Article  CAS  Google Scholar 

  14. Pant, K., Karpel, R. L., Rouzina, I., and Williams, M. C. (2005) Salt dependent binding of T4 gene 32 protein to single- and double-stranded DNA: Single molecule force spectroscopy measurements, J Mol Bio 349, 317–330.

    Article  CAS  Google Scholar 

  15. Vladescu, I., McCauley, M., Nunez, M. E., Rouzina, I., and Williams, M. C. (2007) Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching, Nature Methods 4, 517–522.

    Article  CAS  Google Scholar 

  16. Smith, S. B., Cui, Y., and Bustamante, C. (2003) Optical-trap force transducer that operates by direct measurement of light momentum, Methods Enzymol 361, 134–162.

    Article  CAS  Google Scholar 

  17. Wang, M. D., Yin, H., Landick, R., Gelles, J., and Block, S. M. (1997) Stretching DNA With Optical Tweezers, Biophys J 72, 1335–1346.

    Article  CAS  Google Scholar 

  18. Wenner, J. R., Williams, M. C., Rouzina, I., and Bloomfield, V. A. (2002) Salt Dependence of the Elasticity and Overstretching Transition of Single DNA Molecules, Biophys J 82, 3160–3169.

    Article  CAS  Google Scholar 

  19. McCauley, M. J., Shokri, L., Sefcikova, J., Venclovas, C., Beuning, P. J., and Williams, M. C. (2008) Distinct Double- and Single-Stranded DNA Binding of E. coli Replicative DNA Polymerase III alpha Subunit, ACS Chem Biol 3, 577–587.

    Article  CAS  Google Scholar 

  20. McCauley, M. J., Zimmerman, J., Maher, L. J., 3rd, and Williams, M. C. (2007) HMGB binding to DNA: single and double box motifs, J Mol Biol 374, 993–1004.

    Article  CAS  Google Scholar 

  21. McGhee, J. D., and von Hippel, P. H. (1974) Theoretical aspects of DNA-protein interactions: Cooperative and non-cooperative binding of large ligands to a one-dimensional homogeneous lattice. Journal of Molecular Biology 86, 469–489.

    Article  CAS  Google Scholar 

  22. McCauley, M., Hardwidge, P. R., Maher, L. J., 3rd, and Williams, M. C. (2005) Dual binding modes for an HMG domain from human HMGB2 on DNA, Biophys J 89, 353–364.

    Article  CAS  Google Scholar 

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