Fast microscopical dissection of action scenes played by Escherichia coli RNA polymerase

FEBS Letters

Volumn 586, Issue 19, 2012, Pages 3187-3192

  Suzuki, Yuki ^a   Shin, Minsang ^a   Yoshida, Aiko ^a   Yoshimura, Shige H ^a   Takeyasu, Kunio ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Atomic force microscopy; Fast scanning atomic force microscopy; Protein DNA interaction; RNA polymerase

Indexed keywords

DNA; NUCLEOTIDE; RNA POLYMERASE;

ARTICLE; ATOMIC FORCE MICROSCOPY; DNA TEMPLATE; ENZYME BINDING; ENZYME LOCALIZATION; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; PROTEIN NUCLEIC ACID INTERACTION; PROTEIN TRANSPORT;

BASE SEQUENCE; DNA PRIMERS; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MICROSCOPY, ATOMIC FORCE; PROMOTER REGIONS, GENETIC;

ESCHERICHIA COLI;

EID: 84866615741     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.06.033     Document Type: Article

References (28)

1. P.H. Richter, and M. Eigen Diffusion controlled reaction rates in spheroidal geometry. Application to repressor-operator association and membrane bound enzymes Biophys. Chem. 2 1974 255 263
2. A.D. Riggs, S. Bourgeois, and M. Cohn The lac repressor-operator interaction. 3. Kinetic studies J. Mol. Biol. 53 1970 401 417
3. O.G. Berg, R.B. Winter, and P.H. von Hippel Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory Biochemistry 20 1981 6929 6948
4. P.H. von Hippel, and O.G. Berg Facilitated target location in biological systems J. Biol. Chem. 264 1989 675 678
5. S.E. Halford An end to 40 years of mistakes in DNA-protein association kinetics? Biochem. Soc. Trans. 37 2009 343 348
6. J.L. Gilmore, Y. Suzuki, G. Tamulaitis, V. Siksnys, K. Takeyasu, and Y.L. Lyubchenko Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy Biochemistry 48 2009 10492 10498
7. M. Yokokawa, S.H. Yoshimura, Y. Naito, T. Ando, A. Yagi, N. Sakai, and K. Takeyasu Fast-scanning atomic force microscopy reveals the molecular mechanism of DNA cleavage by ApaI endonuclease IEE Proc. Nanobiotechnol. 153 2006 60 66
8. M.L. Craig, O.V. Tsodikov, K.L. McQuade, P.E. Schlax Jr.; M.W. Capp, R.M. Saecker, and M.T. Record Jr. DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA J. Mol. Biol. 283 1998 741 756
9. W.C. Suh, W. Ross, and M.T. Record Jr. Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site Science 259 1993 358 361
10. P.H. von Hippel, D.G. Bear, W.D. Morgan, and J.A. McSwiggen Protein-nucleic acid interactions in transcription: a molecular analysis Annu. Rev. Biochem. 53 1984 389 446
11. H. Yin, M.D. Wang, K. Svoboda, R. Landick, S.M. Block, and J. Gelles Transcription against an applied force Science 270 1995 1653 1657
12. Y. Harada, T. Funatsu, K. Murakami, Y. Nonoyama, A. Ishihama, and T. Yanagida Single-molecule imaging of RNA polymerase-DNA interactions in real time Biophys. J. 76 1999 709 715
13. H. Kabata, O. Kurosawa, I. Arai, M. Washizu, S.A. Margarson, R.E. Glass, and N. Shimamoto Visualization of single molecules of RNA polymerase sliding along DNA Science 262 1993 1561 1563
14. M. Guthold Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase Biophys. J. 77 1999 2284 2294
15. S. Kasas Escherichia coli RNA polymerase activity observed using atomic force microscopy Biochemistry 36 1997 461 468
16. H.E. Choy, and S. Adhya RNA polymerase idling and clearance in gal promoters: use of supercoiled minicircle DNA template made in vivo Proc. Natl. Acad. Sci. U S A 90 1993 472 476
17. T. Ando, N. Kodera, E. Takai, D. Maruyama, K. Saito, and A. Toda A high-speed atomic force microscope for studying biological macromolecules Proc. Natl. Acad. Sci. U S A 98 2001 12468 12472
18. N. Crampton, M. Yokokawa, D.T. Dryden, J.M. Edwardson, D.N. Rao, K. Takeyasu, S.H. Yoshimura, and R.M. Henderson Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping Proc. Natl. Acad. Sci. U S A 104 2007 12755 12760
19. M. Yokokawa, C. Wada, T. Ando, N. Sakai, A. Yagi, S.H. Yoshimura, and K. Takeyasu Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL EMBO J. 25 2006 4567 4576
20. 2+-pump captured FEBS J. 278 2011 3025 3031
21. C. Rivetti, M. Guthold, and C. Bustamante Wrapping of DNA around the E. coli RNA polymerase open promoter complex EMBO J. 18 1999 4464 4475
22. C. Rivetti, S. Codeluppi, G. Dieci, and C. Bustamante Visualizing RNA extrusion and DNA wrapping in transcription elongation complexes of bacterial and eukaryotic RNA polymerases J. Mol. Biol. 326 2003 1413 1426
23. O. Givaty, and Y. Levy Protein sliding along DNA: dynamics and structural characterization J. Mol. Biol. 385 2009 1087 1097
24. H.G. Abdelhady, S. Allen, M.C. Davies, C.J. Roberts, S.J. Tendler, and P.M. Williams Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I Nucleic Acids Res. 31 2003 4001 4005
25. M. Guthold, M. Bezanilla, D.A. Erie, B. Jenkins, H.G. Hansma, and C. Bustamante Following the assembly of RNA polymerase-DNA complexes in aqueous solutions with the scanning force microscope Proc. Natl. Acad. Sci. U S A 91 1994 12927 12931
26. Y. Suzuki, Y. Higuchi, K. Hizume, M. Yokokawa, S.H. Yoshimura, K. Yoshikawa, and K. Takeyasu Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy Ultramicroscopy 110 2010 682 688
27. Y. Suzuki, M. Yokokawa, S.H. Yoshimura, and K. Takeyasu Biological Application of Fast-Scanning Atomic Force Microscopy B. Bhushan, Scanning probe Microscopy in Nanoscience and Nanotechnology 2 2011 Springer-Verlag Berlin, Heidelberg 217 246
28. S.J. van Noort, K.O. van der Werf, A.P. Eker, C. Wyman, B.G. de Grooth, N.F. van Hulst, and J. Greve Direct visualization of dynamic protein-DNA interactions with a dedicated atomic force microscope Biophys. J. 74 1998 2840 2849