A look-ahead model for the elongation dynamics of transcription

Biophysical Journal

Volumn 96, Issue 8, 2009, Pages 3015-3031

  Yamada, Yujiro Richard ^a   Peskin, Charles S ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOSIDE TRIPHOSPHATE; NUCLEOTIDE; RNA; RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; RIBONUCLEOTIDE;

ANALYTIC METHOD; ARTICLE; CHEMICAL REACTION KINETICS; DNA BINDING; MATHEMATICAL COMPUTING; PARAMETER; PROTEIN FUNCTION; RNA TRANSCRIPTION; STOCHASTIC MODEL; TRANSCRIPTION INITIATION; ALGORITHM; BIOLOGICAL MODEL; BIOSYNTHESIS; COMPUTER SIMULATION; GENETIC TRANSCRIPTION; KINETICS; METABOLISM; PROBABILITY; STATISTICS;

ALGORITHMS; COMPUTER SIMULATION; DNA; DNA-DIRECTED RNA POLYMERASES; KINETICS; MODELS, GENETIC; PROBABILITY; RIBONUCLEOTIDES; RNA; STOCHASTIC PROCESSES; TRANSCRIPTION, GENETIC;

EID: 67649388550     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.12.3955     Document Type: Article

References (29)

1. Bustamante, C., J. Macosko, and G. Wuite. 2000. Grabbing the cat by the tail: manipulated molecules one by one. Nat. Rev. Mol. Cell Biol. 1:130-136.
2. Strick, T., J. Allemand, V. Croquette, and D. Bensimon. 2001. The manipulation of single biomolecules. Phys. Today. 54:46-51.
3. Bustamante, C., Z. Bryant, and S. Smith. 2003. Ten years of tension: single-molecule DNA mechanics. Nature. 421:423-427.
4. Julicher, F., and R. Bruinsma. 1998. Motion of RNA polymerase along DNA: a stochastic model. Biophys. J. 74:1169-1185.
5. Guajardo, R., and R. Sousa. 1997. A model for the mechanism of polymerase translocation. J. Mol. Biol. 265:8-19.
6. Tadigotla, V., D. Maoileigidh, A. Sengupta, V. Epshtein, R. Ebright, et al. 2006. Thermodynamic and kinetic modeling of transcriptional pausing. Proc. Natl. Acad. Sci. USA. 103:8-19.
7. Bai, L., R. Fulbright, and M. D. Wang. 2007. Mechanochemical kinetics of transcription elongation. Phys. Rev. Lett. 98:068103.
8. Wang, H., T. Elston, A. Mogilner, and G. Oster. 1998. Force generation in RNA polymerase. Biophys. J. 74:1186-1202.
9. Yamada, Y.R., and C.S. Peskin. 2006. A chemical kinetic model of transcriptional elongation. arXiv:q-bio.BM/0603012 v2.
10. Yamada, Y.R. 2007. Quantitative models of transcriptional elongation. (Thesis). Cornell University, Ithaca, NY.
11. Yin, Y., and T. Steitz. 2004. The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell. 116:393-404.
12. Gong, X., C. Zhang, M. Feig, and Z. Burton. 2005. Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol. Cell. 18:461-470.
13. Transcription elongation. In Pausing, Arrest, and Termination: Structure and Mechanism: Lectures at the KITP 2003 Program on Bio-Molecular Networks. 2003. http://online.itp.ucsb.edu/online/bionet03/ebright/.
14. Adelman, K., A. LaPorta, T. Santangelo, J. Lis, J. Roberts, et al. 2002. Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc. Natl. Acad. Sci. USA. 99:13538-13543.
15. Abbodanzieri, E., W. Greenleaf, J. Shaevitz, R. Landick, and S. Block. 2005. Direct observation of base-pair stepping by RNA polymerase. Nature. 438:460-465.
16. Gillespie, G. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22:403-434.
17. Gillespie, G. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361.
18. Manly, B. 1998. Randomization, Bootstrap and Monte Carlo Methods in Biology Chapman and Hall, London, UK.
19. Neuman, K., E. Abbondanzieri, R. Landick, J. Gelles, and S. Block. 2003. Ubiquitous transcriptional pausing is independent of RNA polymerase pausing. Cell. 115:437-447.
20. Nudler, E., A. Mustaev, E. Lukhtanov, and A. Goldfarb. 1997. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell. 89:33-41.
21. Forde, N., D. Izhaky, G. Woodcock, G. Wuite, and C. Bustamante. 2002. Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by E. coli RNA polymerase. Proc. Natl. Acad. Sci. USA. 99:11682-11687.
22. Davenport, J., G. Wuite, R. Landick, and C. Bustamante. 2000. Single molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science. 287:2497-2500.
23. Bai, L., A. Shundrovsky, and M. Wang. 2004. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J. Mol. Biol. 344:335-349.
24. Shaevitz, J., E. Abbodanzieri, R. Landick, and S. Block. 2003. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature. 426:684-687.
25. Herbert, K., A. LaPorta, B. Wong, R. Mooney, K. Neuman, et al. 2006. Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell. 125:1083-1094.
26. Chamberlin, M. 1995. New models for the mechanism of transcription elongation and its regulation. In The Harvey Lectures.. Wiley, New York.
27. Vassylyev, D., M. Vassylyeva, A. Perederina, T. Tahirov, and I. Artsimovitch. 2007. Structural basis for transcription elongation by bacterial RNA polymerase. Nature. 448:157-162.
28. Galburt, E., S. Grill, A. Wiedmann, L. Lubkowska, J. Choy, et al. 2007. Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature. 446:820-823.
29. Tolic-Norrelykke, S., A. Engh, R. Landick, and J. Gelles. 2004. Diversity in the rates of transcript elongation by single RNA polymerase molecules. J. Biol. Chem. 279:3292-3299.