Terminal protein-induced stretching of bacteriophage φ29 DNA

Journal of Microscopy

Volumn 213, Issue 2, 2004, Pages 172-179

  Wang, H ^a   Grimes, S ^b   Anderson, D L ^b   Serwer, P ^a  

^a UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Concatemer DNA; Fluorescence microscopy; Single molecule microscopy; Thermal motion; Understretched and overstretched DNA

Indexed keywords

BACTERIOPHAGES; FLUORESCENCE; FLUORESCENCE MICROSCOPY; PROTEINS;

CONCATEMER DNA; COVALENTLY BOUND; DNA MOLECULES; DNA STRETCHING; DNA-PROTEIN COMPLEXES; SINGLE DNA MOLECULES; SINGLE-MOLECULE MICROSCOPY; TERMINAL PROTEIN; THERMAL MOTION; UNDERSTRETCHED AND OVERSTRETCHED DNA;

DNA;

BACTERIAL DNA; DOUBLE STRANDED DNA;

ARTICLE; BACILLUS PHAGE; BIOCHEMISTRY; CONTROLLED STUDY; DNA DETERMINATION; DNA STRETCHING; FLUORESCENCE MICROSCOPY; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; TERMINAL SEQUENCE;

BACTERIA (MICROORGANISMS); UNIDENTIFIED BACTERIOPHAGE;

EID: 1242291871     PISSN: 00222720     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2818.2004.01283.x     Document Type: Article

References (29)

1. Bloomfield, V.A., Crothers, D.M. & Tinoco, I. Jr (1974) Physical Chemistry of Nucleic Acids. Harper & Row, New York.
2. Bulger, M. & Groudine, M. (1999) Looping versus linking: toward a model for long-distance gene activation. Genes Dev. 13, 2465-2477.
3. Bustamante, C., Bryant, Z. & Smith, S.B. (2003) Ten years of tension: single-molecule DNA mechanics. Nature, 421, 423-427.
4. Bustamante, C., Keller, D. & Oster, G. (2001) The physics of molecular motors. Acc. Chem. Res. 34, 412-420.
5. Caburet, S., Conti, C. & Bensimon, A. (2002) Combing the genome for genomic instability. Trends Biotechnol. 20, 344-350.
6. Cantor, C.R. & Schimmel, P.R. (1980) Biophysical Chemistry, W.H. Freeman, San Francisco.
7. Fleer, G.J., Cohen Stuart, M.A., Scheutjens, J.M.H.M., Cosgrove, T. & Vincent, B. (1993) Polymers at Interfaces. Chapman & Hall, London.
8. Fujisawa, H. & Morita, M. (1997) Phage DNA packaging. Genes Cells. 2, 537-545.
9. Grimes, S. & Anderson, D. (1997) The bacteriophage φ29 packaging proteins supercoil the DNA ends. J. Mol. Biol. 266, 901-914.
10. Grimes, S., Jardine, P.J. & Anderson, D. (2002) Bacteriophage φ29 DNA packaging. Adv. Virus Res. 58, 255-294.
11. Gueroni, Z., Place, C., Freyssingeas, E. & Berge, B. (2002) Observation by fluorescence microscopy of transcription on single combed DNA. Proc. Natl Acad. Sci. USA, 99, 6005-6010.
12. Guo, P., Peterson, C. & Anderson, D. (1987) Initiation events in in-vitro packaging of bacteriophage φ29 DNA-gp3. J. Mol. Biol. 197, 219-228.
13. Haber, C., Ruiz, S.A. & Wirtz, D. (2000) Shape anisotropy of a single random-walk polymer. Proc. Natl Acad. Sci. USA, 97, 10792-10795.
14. Harada, Y., Funatsu, T., Murakami, K., Nonoyama, Y., Ishihama, A. & Yanagida, T. (1999) Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys. J. 76, 709-715.
15. Herrick, J. & Bensimon, A. (1999) Single molecule analysis of DNA replication. Biochimie, 81, 859-871.
16. Ishijima, A. & Yanagida, T. (2001) Single molecule nanobioscience. Trends Biochem. Sci. 26, 438-444.
17. Manning, G.S. & Ray, J. (1998) Counterion condensation revisited. J. Biomol. Struct. Dynam. 16, 461-476.
18. Rippe, K., von Hippel, P.H. & Langowski, J. (1995) Action at a distance: DNA-looping and initiation of transcription. Trends Biol. Sci. 20, 500-506.
19. Serwer, P., Estrada, A. & Harris, R.A. (1995) Video light microscopy of 670-kb DNA in a hanging drop: shape of the envelope of DNA. Biophys. J. 69, 2649-2660.
20. Serwer, P. & Hayes, S.J. (2001) Partially condensed DNA conformations observed by single molecule fluorescence microscopy. Biophys. J. 81, 3398-3408.
21. Skordalakes, E. & Berger, J.M. (2003) Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell, 114, 135-146.
22. Smith, S.B. & Bendich, A.J. (1990) Electrophoretic charge density and persistence length of DNA as measured by fluorescence microscopy. Biopolymers, 29, 1167-1173.
23. Smith, D.E., Tans, S.J., Smith, S.B., Grimes, S., Anderson, D.L. & Bustamante, C. (2001) The bacteriophage φ29 portal motor can package DNA against a large internal force. Nature, 413, 748-752.
24. Sun, M., Louie, D. & Serwer, P. (1999) Single event-analysis of the packaging of bacteriophage T7 DNA concatemers in vitro. Biophys. J. 77, 1627-1637.
25. Turnquist, S., Simon, M., Egelman, E. & Anderson, D. (1992) Supercoiled DNA wraps around the bacteriophage φ29 head-tail connector. Proc. Natl Acad. Sci. USA, 89, 10479-10483.
26. Wang, M.D., Schnitzer, M.J., Yin, H., Landick, R., Gelles, J. & Block, S.M. (1998) Force and velocity measured for single molecules of RNA polymerase. Science, 282, 902-907.
27. Wenner, J.R., Williams, M.C., Rouzina, I. & Bloomfield, V.A. (2002) Salt dependence of the elasticity and overstretching transition of single DNA molecules. Biophys. J. 82, 3160-3169.
28. Wuite, G.J.L., Smith, S.B., Young, M., Keller, D. & Bustamante, C. (2000) Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature, 404, 103-106.
29. Yin, H., Artsimovitch, I., Landick, R. & Gelles, J. (1999) Nonequilibrium mechanism of transcription termination from observations of single RNA polymerase molecules. Proc. Natl Acad. Sci. USA, 96, 13124-13129.