Real-time tRNA transit on single translating ribosomes at codon resolution (original) (raw)

• Green, R. & Noller, H. F. Ribosomes and translation. Annu. Rev. Biochem. 66, 679–716 (1997)
  Article CAS Google Scholar
• Moazed, D. & Noller, H. F. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342, 142–148 (1989)
  Article ADS CAS Google Scholar
• Hausner, T. P., Geigenmüller, U. & Nierhaus, K. H. The allosteric three-site model for the ribosomal elongation cycle. New insights into the inhibition mechanism of aminoglycosides, thiostrepton, and viomycin. J. Biol. Chem. 263, 13103–13111 (1988)
  CAS PubMed Google Scholar
• Rodnina, M. W. & Wintermeyer, W. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu. Rev. Biochem. 70, 415–435 (2001)
  Article CAS Google Scholar
• Agirrezabala, X. et al. Visualization of the hybrid state of tRNA binding promoted by spontaneous racheting of the ribosome. Mol. Cell 32, 190–197 (2008)
  Article CAS Google Scholar
• Marshall, R. A., Aitken, C. E., Dorywalska, M. & Puglisi, J. D. Translation at the single-molecule level. Annu. Rev. Biochem. 77, 177–203 (2008)
  Article CAS Google Scholar
• Levene, M. J. et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682–686 (2003)
  Article ADS CAS Google Scholar
• Foquet, M. et al. Improved fabrication of zero-mode waveguides for single-molecule detection. J. Appl. Phys. 103, 034301 (2008)
  Article ADS Google Scholar
• Korlach, J. et al. Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc. Natl Acad. Sci. USA 105, 1176–1181 (2008)
  Article ADS CAS Google Scholar
• Lundquist, P. M. et al. Parallel confocal detection of single molecules in real time. Opt. Lett. 33, 1026–1028 (2008)
  Article ADS Google Scholar
• Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009)
  Article ADS CAS Google Scholar
• Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S. & Puglisi, J. D. tRNA selection and kinetic proofreading in translation. Nature Struct. Mol. Biol. 11, 1008–1014 (2004)
  Article CAS Google Scholar
• Blanchard, S. C., Kim, H. D., Gonzalez, R. L., Puglisi, J. D. & Chu, S. tRNA dynamics on the ribosome during translation. Proc. Natl Acad. Sci. USA 101, 12893–12898 (2004)
  Article ADS CAS Google Scholar
• Chan, V., Graves, D. J. & McKenzie, S. E. The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys. J. 69, 2243–2255 (1995)
  Article ADS CAS Google Scholar
• Schlunzen, F. et al. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413, 814–821 (2001)
  Article ADS CAS Google Scholar
• Tenson, T., Lovmar, M. & Ehrenberg, M. The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome. J. Mol. Biol. 330, 1005–1014 (2003)
  Article CAS Google Scholar
• Bodley, J. W. & Godtfredsen, W. O. Studies on translocation. XI. Structure-function relationships of the fusidane-type antibiotics. Biochem. Biophys. Res. Commun. 46, 871–877 (1972)
  Article CAS Google Scholar
• Underwood, K. A., Swartz, J. R. & Puglisi, J. D. Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis. Biotechnol. Bioeng. 91, 425–435 (2005)
  Article CAS Google Scholar
• Marshall, R. A., Aitken, C. E. & Puglisi, J. D. GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Mol. Cell 35, 37–47 (2009)
  Article CAS Google Scholar
• Gao, Y. G. et al. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326, 694–699 (2009)
  Article ADS CAS Google Scholar
• Lill, R. & Wintermeyer, W. Destabilization of codon-anticodon interaction in the ribosomal exit site. J. Mol. Biol. 196, 137–148 (1987)
  Article CAS Google Scholar
• Semenkov, Y. P., Rodnina, M. V. & Wintermeyer, W. The “allosteric three-site model” of elongation cannot be confirmed in a well-defined ribosome system from Escherichia coli . Proc. Natl Acad. Sci. USA 93, 12183–12188 (1996)
  Article ADS CAS Google Scholar
• Cornish, P. V. et al. Following movement of the L1 stalk between three functional states in single ribosomes. Proc. Natl Acad. Sci. USA 106, 2571–2576 (2009)
  Article ADS CAS Google Scholar
• Fei, J., Kosuri, P., MacDougall, D. D. & Gonzalez, R. L. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol. Cell 30, 348–359 (2008)
  Article CAS Google Scholar
• Fei, J. et al. Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc. Natl Acad. Sci. USA 106, 15702–15707 (2009)
  Article ADS CAS Google Scholar
• Sanders, C. L. & Curran, J. F. Genetic analysis of the E site during RF2 programmed frameshifting. RNA 13, 1483–1491 (2007)
  Article CAS Google Scholar
• Aitken, C. E., Marshall, R. A. & Puglisi, J. D. An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys. J. 94, 1826–1835 (2008)
  Article CAS Google Scholar
• Aitken, C. E. & Puglisi, J. D. Following the intersubunit conformation of the ribosome during translation in real time. Nat. Struct. Mol. Biol. (in the press)