EDP Sciences logo
Subscriber Authentication Point
Search
Menu
All issues Volume 5 / No 3 (2010) Math. Model. Nat. Phenom., 5 3 (2010) 206-227 References
Free Access
Issue
Math. Model. Nat. Phenom.
Volume 5, Number 3, 2010
Mathematical modeling in the medical sciences
Page(s) 206 - 227
DOI https://doi.org/10.1051/mmnp/20105313
Published online 28 April 2010
  1. A. Alon. An introduction to systems biology: design principles of biological circuits. Chapman and Hall, Boca Raton, 2007. [Google Scholar]
  2. E. Abbodanzieri, W. Greenleaf, J. Shaevitz, R. Landick, S. Block. Direct observation of base-pair stepping by RNA polymerase. Nature, 438 (2005), 460-465. [CrossRef] [PubMed] [Google Scholar]
  3. L. Bai, R. Fulbright, M. Wang. Mechanochemical kinetics of transcription elongation. Phys. Rev. Lett., 98 (2007), No. 6, 068103. [CrossRef] [PubMed] [Google Scholar]
  4. G. Bar-Nahum, V. Epshtein, A. Ruckenstein, R. Rafikov, A. Mustaev, E. Nudler. A ratchet mechanism of transcription elongation and its control. Cell, 120 (2005), No. 2, 183-193. [CrossRef] [PubMed] [Google Scholar]
  5. A. Blank, J. Gallant, R. Burgess, L. Loeb. An RNA polymerase mutant with reduced accuracy of chain elongation. Biochemistry, 25 (1986), No. 20, 5920-5928. [CrossRef] [PubMed] [Google Scholar]
  6. Y. Chen, D. Chafin, D. Price, A. Greenleaf. Drosophila RNA polymerase II mutants that affect transcription elongation. Jour. Biol. Chem., 271 (1996), No. 11, 5993-5999. [CrossRef] [Google Scholar]
  7. G. Eichhorn, P. Chuknyisky, J. Butzow, R. Beal, C. Garland, C. Janzen, P. Clark, E. Tarien. A structural model for fidelity in transcription. Proc. Natl. Acad. Sci., 91 (1994), No. 16, 7613-7617. [CrossRef] [Google Scholar]
  8. D. Gillespie. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comp. Phys., 22 (1976), No. 4, 403-434. [Google Scholar]
  9. D. Gillespie. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem., 81 (1977), No. 25, 2340-2361. [CrossRef] [Google Scholar]
  10. S. Greive, P. von Hippel. Thinking quantitatively about transcriptional regulation. Nat. Rev. Mol. Cell Biol., 6 (2005), 221-232. [CrossRef] [PubMed] [Google Scholar]
  11. K. Herbert, W. Greenleaf, S. Block. Single-molecule studies of RNA polymerase: motoring along. Annu. Rev. Biochem., 77 (2008), 149-176. [CrossRef] [PubMed] [Google Scholar]
  12. W. Hlavacek, A. Redondo, H. Metzger, C. Wofsy, B. Goldstein. Kinetic proofreading models for cell signaling predict ways to escape kinetic proofreading. Proc. Natl. Acad. Sci., 98 (2001), No. 13, 7295-7300. [CrossRef] [Google Scholar]
  13. S. Holmes, T. Santangelo, C. Cunningham, J. Roberts, D. Erie. Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity. Jour. Biol. Chem., 281(2006), No. 27, 18677-18683. [CrossRef] [Google Scholar]
  14. J. Hopfield. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci., 71 (1974), No. 10, 4135-4139. [CrossRef] [Google Scholar]
  15. K. Howe, C. Kane, A. Ares. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in saccharomyces cerevisiae. RNA, 9 (2003), No. 8, 993-1006. [CrossRef] [PubMed] [Google Scholar]
  16. C. Jeon, K. Agarwal. Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc. Natl. Acad. Sci., 93 (1996), No. 24, 13677-13682. [CrossRef] [Google Scholar]
  17. M. Kireeva, Y. Nedlialkov, G. Cremona, Y. Purtov, L. Lubkowska, F. Malagon, Z. Burton, J. Strathern, M. Kashlev. Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. Mol. Cell, 30 (2008), No. 5, 557-566. [CrossRef] [PubMed] [Google Scholar]
  18. R. Libby, J. Gallant. The role of RNA polymerase in transcriptional fidelity. Mol. Microbiol., 5 (1991), No. 5, 999-1004. [CrossRef] [PubMed] [Google Scholar]
  19. R. Libby, J Gallant. Phosphorolytic error correction during transcription. Mol. Microbiol., 12 (1994), No. 1, 121-129. [CrossRef] [PubMed] [Google Scholar]
  20. R. Libby, L. Nelson, J. Calvo, J. Gallant. Transcriptional proofreading in escherichia coli. EMBO Jour., 8 (1989), No. 10, 3153-3158. [Google Scholar]
  21. F. Malagon, M. Kireeva, B. Shafer, L. Lubkowska, M. Kashlev, J. Strathern. Mutations in the saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-Azauracil. Genetics, 172 (2006), No. 4, 2201-2209. [CrossRef] [PubMed] [Google Scholar]
  22. P. Mason, K. Struhl. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell, 17 (2005), No. 6, 831-840. [CrossRef] [PubMed] [Google Scholar]
  23. M. de la Mata, C. Alonso, S. Kadener, J. Fededa, M. Blaustein, J. Pelisch, P. Cramer, D. Bentley, A. Kornblihtt. A Slow RNA Polymerase II Affects Alternative Splicing in Vivo. Mol. Cell, 12 (2003), No. 2, 525-532. [Google Scholar]
  24. T. McKeithan. Kinetic proofreading in T-cell receptor signal transduction. Proc. Natl. Acad. Sci., 92 (1995), No. 11, 5042-5046. [CrossRef] [Google Scholar]
  25. J. Ninio. Kinetic amplification of enzyme discrimination. Biochimie, 57 (1975), No. 5, 587-595. [CrossRef] [PubMed] [Google Scholar]
  26. J. Roberts, S. Shankar, J. Filter. RNA polymerase elongation Ffactors. Annu. Rev. Microbiol., 62 (2008), 211-233. [CrossRef] [PubMed] [Google Scholar]
  27. J. Roussel, R. Zhu. Stochastic kinetics description of a simple transcription model. Bull. Math. Biol., 68 (2006), No. 7, 1681-1713. [CrossRef] [MathSciNet] [PubMed] [Google Scholar]
  28. J. Shaevitz, E. Abbondanzieri, R. Landick, S. Block. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature, 426 (2003), 684-687. [CrossRef] [PubMed] [Google Scholar]
  29. R. Sims, R. Belotserkovskaya, D. Reinberg. Elongation by RNA polymerase II: the short and long of it. Genes Dev., 18 (2004), 2437-2468. [CrossRef] [PubMed] [Google Scholar]
  30. C. Springgate, L. Loeb. On the fidelity of transcription by escherichia coli ribonucleic acid polymerase. J. Mol. Biol., 97 (1975), No. 4, 577-591. [CrossRef] [PubMed] [Google Scholar]
  31. E. Stepanova, J. Lee, M. Ozerova, E. Semenova, K. Datsenko, B. Wanner, K. Severinov, S. Borukhov. Analysis of promoter targets for Escheichia coli transcription elongation factor GreA in vivo and in vitro. J. Bateriol., 189 (2007), No. 24, 8772-8785. [CrossRef] [Google Scholar]
  32. P. Swain, E. Siggia. The role of proofreading in signal transduction specifity. Biophys. J., 82 (2007), No. 6, 2928-2933. [CrossRef] [Google Scholar]
  33. V. Tadigotla, D. O’Maoileidigh, A. Sengupta, V. Epshtein, R. Ebright, E. Nudler, A. Ruckenstein. Thermodynamic and kinetic modeling of transcriptional pausing. Prof. Natl. Acad. Sci.,103 (2006), No. 12, 4439-4444. [Google Scholar]
  34. J. Thomas, A. Platas, D. Hawley. Transcriptional fidelity and proofreading by RNA polymerase II Cell, 93 (1998), No. 4, 627-637. [CrossRef] [PubMed] [Google Scholar]
  35. T. Tlusty, R. Bar-Ziv, A. Libchaber. High-fidelity DNA sensing by protein binding fluctuations. Phys. Rev. Lett., 93 (2004), No. 25, 2581031. [Google Scholar]
  36. U. Vogel, K. Jensen. The RNA chain elongation rate in escherichia coli depends on the growth rate. J. Bacteriol., 176 (1994), No. 10, 2807-2813. [PubMed] [Google Scholar]
  37. M. Voliotis, N. Cohen, C. Molina-Paris, T. Liverpool. Fluctuations, pauses, and backtracking in DNA transcription. Biophys. J., 94 (2008), No. 2, 334-348. [CrossRef] [PubMed] [Google Scholar]
  38. M. Voliotis, N. Cohen, C. Molina-Paris, T. Liverpool. Backtracking and error correction in DNA transcription in The Art and Science of Statistical Bioinformatics. 104-107, Leeds University Press, Leeds, 2008. [Google Scholar]
  39. P. Xie. A dynamic model for transcription elongation and sequence-dependent short pauses by RNA polymerase. BioSystems, 93 (2008), 199-210. [CrossRef] [PubMed] [Google Scholar]
  40. Y. Yamada, C. Peskin. A chemical kinetic model of transcriptional elongation. LANL ArXiv (2006), q-bio.BM/0603012. [Google Scholar]
  41. Y. Yamada, C. Peskin. A look-ahead model for the elongation dynamics of transcription. Biophys. J., 96 (2009), No. 8, 3015-3031. [CrossRef] [PubMed] [Google Scholar]
  42. N. Zenkin, Y. Yuzenkova, K. Severinov. Transcript-assisted transcriptional proofreading. Science, 313 (2006), No. 5786, 518-520. [CrossRef] [PubMed] [Google Scholar]

Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.

Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.

Initial download of the metrics may take a while.