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. Author manuscript; available in PMC: 2016 Jul 1.
Published in final edited form as: Biochimie. 2015 Feb 21;114:90–96. doi: 10.1016/j.biochi.2015.02.007

Figure 2. Selected probes used in recent biophysical studies of −1 programmed frameshifting.

Figure 2

A) Multiple conformational changes of ribosome components are necessary for mRNA-tRNA translocation during the elongation cycle. Opening and closing of the L1 arm is presumed to be associated with mRNA-tRNA translocation. The small ribosomal subunit body (b), head (h) and platform (pl) domains can move independently of one another while rotation of the small subunit (blue) relative to the large subunit (gray) and an orthogonal swiveling of the head domain are necessary for mRNA-tRNA translocation (30S shoulder domain closing is not shown). B) Radiolabeled methionine along with fluorescently labeled (purple star) tRNA (P-site tRNA is orange; A-site tRNA is yellow), EF-G and ribosomal proteins (S13, purple) were used to follow the mechanistic sub-steps of −1 programmed frameshifting on the Infectious Bronchitis Virus (IBV) pseudoknot frameshift signal (29). C) Fluorescent and fluorescence quencher oligonucleotides were hybridized to 16S rRNA helix 44 and 23S rRNA Helix 101 to follow small subunit rotation. tRNA or elongation factor arrival during translation of the dnaX frameshift signal was also followed by fluorescence (46). D) Qin et al. used multiple fluorescently labeled ribosomal proteins (S6 and L9 depicted in purple) to identify conformational states of the ribosome while programmed with the dnaX frameshift signal (45). E) A study by Kim et al. used smFRET between tRNA and ribosomal protein L1 to follow peptide bond formation and tRNA translocation on the dnaX frameshift signal (44).