Codon-dependent tRNA fluctuations monitored with fluorescence polarization

Padmaja P. Mishra, Mohd Tanvir Qureshi, Wenhui Ren, Tae Hee Lee

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


During protein synthesis dictated by the codon sequence of messenger RNA, the ribosome selects aminoacyl-tRNA (aa-tRNA) with high accuracy, the exact mechanism of which remains elusive. By using a single-molecule fluorescence resonance energy transfer method coupled with fluorescence emission anisotropy, we provide evidence of random thermal motion of tRNAs within the ribosome in nanosecond timescale that we refer to as fluctuations. Our results indicate that cognate aa-tRNA fluctuates less frequently than near-cognate. This is counterintuitive because cognate aa-tRNA is expected to fluctuate more frequently to reach the ribosomal A-site faster than near-cognate. In addition, cognate aa-tRNA occupies the same position in the ribosome as near-cognate. These results argue for a mechanism which guides cognate aa-tRNA more accurately toward the A-site as compared to near-cognate. We suggest that a basis for this mechanism is the induced fit of the 30S subunit upon cognate aa-tRNA binding. Our single-molecule fluorescence resonance energy transfer time traces also point to a mechanistic model for GTP hydrolysis on elongation factor Tu mediated by aa-tRNA.

Original languageEnglish (US)
Pages (from-to)3849-3858
Number of pages10
JournalBiophysical journal
Issue number11
StatePublished - Dec 1 2010

All Science Journal Classification (ASJC) codes

  • Biophysics


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