Assembly of Recombinant Nucleosomes on Nanofabricated DNA Curtains for Single-Molecule Imaging

Methods in Molecular Biology

Volumn 778, Issue , 2011, Pages 243-258

  Lee, Ja Yil ^a   Greene, Eric C ^a  

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

Author keywords

Chromatin; DNA curtain; Lipid bilayer; Nanofabrication; Nucleosomes; TIRF microscopy

Indexed keywords

DNA;

ARTICLE; CHEMISTRY; FLUORESCENCE MICROSCOPY; LIPID BILAYER; METABOLISM; METHODOLOGY; NANOTECHNOLOGY; NUCLEOSOME;

DNA; LIPID BILAYERS; MICROSCOPY, FLUORESCENCE; NANOTECHNOLOGY; NUCLEOSOMES;

EUKARYOTA;

EID: 80054741771     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-261-8_16     Document Type: Chapter

References (22)

1. Widom, J. (1998) Structure, dynamics, and function of chromatin in vitro. Annu. Rev. Bioph. Biom. 27, 285–327.
2. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997) Crystal structure of the nucleosome core particle at 2.8 angstrom resolution. Nature 389, 251–260.
3. Rando, O. J., and Chang, H. Y. (2009) Genome-Wide Views of Chromatin Structure. Annu. Rev. Biochem. 78, 245–271.
4. Rando, O. J., and Ahmad, K. (2007) Rules and regulation in the primary structure of chromatin. Curr. Opin. Cell Biol. 19, 250–256. Fluctuations Govern the Transcription Dynamics of RNA Polymerase II. Science 325,
5. 626–628.
6. Studitsky, V. M., Clark, D. J., and Felsenfeld, G. (1995) Overcoming a Nucleosomal Barrier to Transcription. Cell 83, 19–27.
7. Groth, A., Rocha, W., Verreault, A., and Almouzni, G. (2007) Chromatin challenges during DNA replication and repair. Cell 128, 721–733.
8. Graneli, A., Yeykal, C. C., Prasad, T. K., and Greene, E. C. (2006) Organized arrays of individual DIVA molecules tethered to supported lipid bilayers. Langmuir 22, 292–299.
9. Hager, G. L., McNally, J. G., and Misteli, T. (2009) Transcription Dynamics. Mol. Cell 35, 741–753. 10. Visnapuu, M. L., Fazio, T., Wind, S., and Greene, E. C. (2008) Parallel arrays of geometric nanowells for assembling curtains of DNA
10. Hodges, C., Bintu, L., Lubkowska, L., Kashlev, M., and Bustamante, C. (2009) Nucleosomal with controlled lateral dispersion. Langmuir 24, 11293–11299.
11. Fazio, T., Visnapuu, M. L., Wind, S., and Greene, E. C. (2008) DNA curtains and nanoscale curtain rods: High-throughput tools for single molecule imaging. Langmuir 24, 10524–10531.
12. Greene, E. C., Wind, S., Fazio, T., Gorman, J., and Visnapuu, M. L. (2010) DNA Curtains for High-Throughput Single-Molecule Optical Imaging, Methods in Enzymology, Vol 472: Single Molecule Tools, Pt A: Fluorescence Based Approaches 472, 293–315.
13. Finkelstein, I. J., and Greene, E. C. (in press) Supported lipid-bilayers and DNA curtains for high-throughput single molecule studies. Methods in Molecular Biology.
14. Gorman, J., Fazio, T., Wang, F., Wind, S., and Greene, E. C. (2010) Nanofabricated Racks of Aligned and Anchored DNA Substrates for Single-Molecule Imaging. Langmuir 26, 1372–1379.
15. Prasad, T. K., Robertson, R. B., Visnapuu, M. L., Chi, P., Sung, P., and Greene, E. C. (2007) A DNA-translocating Snf2 molecular motor: Saccharomyces cerevisiae Rdh5,4 displays processive translocation and extrudes DNA loops. J. Mol. Biol. 369, 940–953.
16. Robertson, R. B., Moses, D. N., Kwon, Y., Chan, P., Zhao, W. X., Chi, P., Klein, H., Sung, P., and Greene, E. C. (2009) Visualizing the Disassembly of S. cerevisiae Rad51 Nucleoprotein Filaments. J. Mol. Biol. 388, 703–720.
17. Visnapuu, M. L., and Greene, E. C. (2009) Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition. Nat. Struct. Mol. Biol. 16, 1056–U1075.
18. Smith, A. M., and Nie, S. (2010) Semiconductor Nanocrystals: Structure, Properties, and Band Gap Engineering. Acc. Chem. Res. 43, 190–200.
19. Segal, E., Fondufe-Mittendorf, Y., Chen, L. Y., Thastrom, A., Field, Y., Moore, I. K., Wang, J. P. Z., and Widom, J. (2006) A genomic code for nucleosome positioning. Nature 442, 772–778.
20. Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A. J., Tillo, D., Field, Y., LeProust, E. M., Hughes, T. R., Lieb, J. D., Widom, J., and Segal, E. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458, 362–U129.
21. Field, Y., Kaplan, N., Fondufe-Mittendorf, Y., Moore, I. K., Sharon, E., Lubling, Y., Widom, J., and Segal, E. (2008) Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals. Plos Comput. Biol. 4, 25.
22. Tillo, D., and Hughes, T. R. (2009) G + C content dominates intrinsic nucleosome occupancy. Bmc Bioinformatics 10, 442.