Motion of RNA polymerase along DNA: A stochastic model

Biophysical Journal

Volumn 74, Issue 3, 1998, Pages 1169-1185

  Jülicher, Frank ^a   Bruinsma, Robijn ^b  

^a INSTITUT CURIE   (France)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA POLYMERASE;

ARTICLE; DNA FOOTPRINTING; ENZYME MECHANISM; GENETIC TRANSCRIPTION; POLYMERIZATION; SIMULATION; STOCHASTIC MODEL;

EID: 0142127778     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77833-6     Document Type: Article

References (34)

1. Alexander, S., J. Bernasconi, W. R. Schneider, and R. Orbach. 1981. Excitation dynamics in random one-dimensional systems. Rev. Mod. Phys. 53:175-198.
2. Bernasconi, J., and W. R. Schneider. 1982. Diffusion in a one-dimensional lattice with random asymmetric transition rates. J. Phys. A Math. Gen. 15:L729-L734.
3. Chamberlin, M. J. 1995. New models for the mechanism of transcription elongation and its regulation. Harvey Lect. (Ser. 88): 1-21.
4. Chan, C. L., and R. Landick. 1994. New perspectives on RNA chain elongation and termination by E. coli RNA polymerase. In Transcription: Mechanisms and Regulation. R. C. Conavay and J. W. Conaway, editors. Raven Press, New York. 297-321.
5. Creighton, S., and M. F. Goodman. 1995. Gel kinetic analysis of DNA polymerase fidelity in the presence of proofreading using bacteriophage T4 DNA polymerase. J. Biol. Chem. 270:4759-4774.
6. Derényi, I., and T. Vicsek. 1996. The kinesin walk: a dynamic model with elastically coupled heads. Proc. Natl. Acad. Sci. USA. 93:6775-6779.
7. Duke, T., and S. Leibler. 1996. Motor protein mechanics: a stochastic model with minimal mechanochemical coupling. Biophys. J. 71: 1235-1247.
8. Erie, D. A., T. D. Yager, and P. H. von Hippel. 1992. The single-nucleotide addition cycle in transcription: a biophysical and biochemical perspective. Annu. Rev. Biophys. Biomol. Struct. 21:379-415.
9. Hua, W., E. C. Young, M. L. Fleming, and J. Gelles. 1997. Coupling of kinesin steps to ATP hydrolysis. Nature. 388:390-393.
10. Jülicher, F., A. Ajdari, and J. Prost. 1997. Modelling molecular motors. Rev. Mod. Phys. 69:1269-1282.
11. Komissarova, N., and M. Kashlev. 1997. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl. Acad. Sci. USA. 94:1755-1760.
12. Krummel, B., and M. J. Chamberlin. 1992. Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Desoxyribonuclease I footprinting of individual complexes along different transcription units. J. Mol. Biol. 225:239-250.
13. Landick, R. 1997. RNA polymerase slides home: pause and termination site recognition. Cell. 88:741-744.
14. Leibler, S., and D. Huse. 1993. Porters versus rowers: a unified stochastic model. J. Cell Biol. 121:1357-1368.
15. Lewis, B., Genes V. Oxford University Press, Oxford, 1994.
16. Marinani, E., G. Parisi, D. Ruelle, and P. Windey. 1983. Random walk in a random environment and 1/f noise. Phys. Rev. Lett. 50:1223-1225.
17. Metzger, W. M., P. Schicktor, and H. Heumann. 1989. A cinematographic view of Escherichia coli RNA polymerase translocation. EMBO J. 8:2745-2754.
18. Meyhöfer, E., and J. Howard. 1995. The force generated by a single kinesin molecule against an elastic load. Proc. Natl. Acad. Sci. USA. 92: 574-578.
19. Monod, J., J. Wyman, and J. P. Changeux. 1965. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:88-118.
20. Mustaev, A., M. Kashlev, E. Zaychikov, M. Grachev, and A. Goldfarb. 1993. Active center rearrangement in RNA polymerase initiation complex. J. Biol. Chem. 268:19185-19187.
21. Nudler, E., A. Goldfarb, and M. Kashlev. 1994. Discontinuous mechanism of transcription elongation. Science. 265:793-796.
22. Nudler, E., M. Kashlev, V. Nikiforov, and A. Goldfarb. 1995. Coupling between transcription elongation and RNA polymerase inchworming. Cell. 81:351-357.
23. Oosawa, F., and S. Asakura. 1975. Thermodynamics of the Polymerization of Proteins. Academic Press, London, New York.
24. Peskin, C. S., G. B. Ermentrout, and G. F. Oster. 1994. The correlation ratche: a novel mechanism for generating directed motion by ATP hydrolysis. In Cell Mechanics and Cellular Engineering, V. C. Mow, F. Guilak, R. Tran-Son-Tay and R. Hochmuth, editors. Springer Verlag, New York. 479-489.
25. Peskin, C. S., and G. F. Oster. 1995. Coordinated hydrolysis explains the mechanical behavior of kinesin. Biophys. J. 68:202-210.
26. Prost, J., J. F. Chauwin, L. Peliti, and A. Ajdari. 1994. Asymmetric pumping of particles. Phys. Rev. Lett. 72:2652-2655.
27. Reeder, T. C., and D. K. Hawley. 1996. Promotor proximal sequences modulate RNA polymerase II elongation by a novel mechanism. Cell. 87:767-777.
28. Rice, G. A., C. M. Kane, and M. J. Chamberlin. 1991. Footprinting analysis of mammalian RNA polymerase II along its transcript: an alternative view of transcript elongation. Prot. Natl. Acad. Sci. USA. 88:4245-4249.
29. Schnitzer, M., and S. Block. 1997. Kinesin hydrolyses one ATP per 8-nm step. Nature. 388:386-390.
30. Stryer, L. 1988. Biochemistry. W. H. Freeman, New York.
31. Svoboda, K., P. Mitra, and S. Block. 1994. Fluctuation analysis of motor protein movement and single enzyme kinetics. Proc. Natl. Acad. Sci. USA. 91:11782-11786.
32. Wang, D., T. Meier, C. Chan, G. Feng, D. Lee, and R. Landick. 1995. Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex. Cell. 81: 341-350.
33. Yager, T. D., and P. H. von Hippel. 1987. Transcript elongation and termination in Escherichia coli. In Escherichia coli and Salmonella typhimurium. F. C. Neidhard, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger, editors. American Society for Microbiology, Washington, DC, 1241-1275.
34. Yin, H., M. D. Wang, K. Svoboda, R. Landick, S. M. Block, and J. Gelles. 1995. Transcription against an applied force. Science. 270:1653-1657.