DNA curtains: Novel tools for imaging protein-nucleic acid interactions at the single-molecule level

Methods in Cell Biology

Volumn 123, Issue , 2014, Pages 217-234

  Collins, Bridget E ^a   Ye, Ling F ^a   Duzdevich, Daniel ^a   Greene, Eric C ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

Lipid bilayer; Nanofabrication; One dimensional diffusion; Single molecule; Single stranded DNA; Total internal reflection fluorescence microscopy; Translocation

Indexed keywords

DNA BINDING PROTEIN; IMMOBILIZED NUCLEIC ACID; LIPID BILAYER; PROTEIN BINDING;

CHEMISTRY; DEVICES; DIFFUSION; ENZYME ASSAY; FLUORESCENCE MICROSCOPY; GENETIC PROCEDURES; LIPID BILAYER; MICROFLUIDIC ANALYSIS; PROCEDURES;

BIOSENSING TECHNIQUES; DIFFUSION; DNA-BINDING PROTEINS; ENZYME ASSAYS; IMMOBILIZED NUCLEIC ACIDS; LIPID BILAYERS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MICROSCOPY, FLUORESCENCE; PROTEIN BINDING;

EID: 84902952646     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-420138-5.00012-4     Document Type: Chapter

References (23)

1. Aussel L., Barre F., Aroyo M., Stasiak A., Stasiak A., Sherratt D. FtsK Is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell 2002, 108:195-205.
2. Axelrod D. Total internal reflection fluorescence microscopy. Methods in Cell Biology 1989, 30:245-270.
3. Barre F. FtsK and SpoIIIE: The tale of the conserved tails. Molecular Microbiology 2007, 66:1051-1055.
4. Bianco P.R., Brewer L.R., Corzett M., Balhorn R., Yeh Y., Kowalczykowski S.C., et al. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 2001, 409:374-378.
5. Courtemanche N., Lee J.Y., Pollard T.D., Greene E.C. Tension modulates actin filament polymerization mediated by formin and profilin. Proceedings of the National Academy of Sciences of the United States of America 2013, 110:9752-9757.
6. Dillingham M.S., Kowalczykowski S.C. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiology and Molecular Biology Reviews 2008, 72:642-671. Table of Contents.
7. Fazio T., Visnapuu M.L., Wind S., Greene E.C. DNA curtains and nanoscale curtain rods: High-throughput tools for single molecule imaging. Langmuir 2008, 24:10524-10531.
8. Finkelstein I., Visnapuu M.-L., Greene E. Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase. Nature 2010, 468:983-987.
9. Gibb B., Silverstein T.D., Finkelstein I.J., Greene E.C. Single-stranded DNA curtains for real-time single-molecule visualization of protein-nucleic acid interactions. Analytical Chemistry 2012, 84:7607-7612.
10. Gorman J., Chowdhury A., Surtees J.A., Shimada J., Reichman D.R., Alani E., et al. Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Molecular Cell 2007, 28:359-370.
11. Gorman J., Fazio T., Wang F., Wind S., Greene E. Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging. Langmuir 2010, 26:1372-1379.
12. Gorman J., Plys A., Visnapuu M., Alani E., Greene E. Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice. Nature Structural and Molecular Biology 2010, 17:932-938.
13. Gorman J., Wang F., Redding S., Plys A.J., Fazio T., Wind S., et al. Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair. Proceedings of the National Academy of Sciences of the United States of America 2012, 109:E3074-E3083.
14. Greene E., Wind S., Fazio T., Gorman J., Visnapuu M.-L. DNA curtains for high-throughput single-molecule optical imaging. Methods in Enzymology 2010, 472:293-315.
15. Ha T., Kozlov A., Lohman T. Single-molecule views of protein movement on single-stranded DNA. Annual Review of Biophysics 2012, 41:295-319.
16. Lee J.Y., Finkelstein I.J., Crozat E., Sherratt D.J., Greene E.C. Single-molecule imaging of DNA curtains reveals mechanisms of KOPS sequence targeting by the DNA translocase FtsK. Proceedings of the National Academy of Sciences of the United States of America 2012, 109:6531-6536.
17. Sarkar S.K., Bumb A., Mills M., Neuman K.C. SnapShot: Single-molecule fluorescence. Cell 2013, 153:1408-1408.e1.
18. Spies M. There and back again: New single-molecule insights in the motion of DNA repair proteins. Current Opinion in Structural Biology 2013, 23:154-160.
19. van Oijen A.M. Single-molecule approaches to characterizing kinetics of biomolecular interactions. Current Opinion in Biotechnology 2011, 22:75-80.
20. Visnapuu M.L., Fazio T., Wind S., Greene E.C. Parallel arrays of geometric nanowells for assembling curtains of DNA with controlled lateral dispersion. Langmuir 2008, 24:11293-11299.
21. Visnapuu M.-L., Greene E. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition. Nature Structural and Molecular Biology 2009, 16:1056-1062.
22. von Hippel P., Berg O. Facilitated target location in biological systems. The Journal of Biological Chemistry 1989, 264:675-678.
23. Wang F., Redding S., Finkelstein I.J., Gorman J., Reichman D.R., Greene E.C. The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion. Nature Structural and Molecular Biology 2013, 20:174-181.