Just as proteins form distinct structural motifs, certain structures are commonly adopted by RNA molecules. Amongst the most prevalent is the RNA pseudoknot.

The authors note that on page 2572, left column, in line 16 of the second full paragraph of the Results section, the sentence, ''Based on the dye locations and previous biochemical and structural characterization of similar complexes, we infer that ribosome populations primarily in a low-FRET regime correspond to an open state of the L1 stalk with populations primarily in the high-FRET regime in a closed conformation of the L1 stalk in the P/E hybrid state,'' should instead read ''Based on the dye locations and previous biochemical and structural characterization of similar complexes, we infer that the low-FRET population corresponds to an open state of the L1 stalk and the high-FRET population to a closed conformation of the L1 stalk in the P/E hybrid state.'' The authors note that due to a printer's error, on page 2575, left column, in line 4 of the first full paragraph, the sentence, ''After the movement of the L1 stalk, we were able to enrich for populations of half-closed (Ϸ0.4 FRET) complexes by addition of excess deacylated tRNA to classical state (Ϸ0.25 FRET) complexes containing a vacant E site ( Fig. 3 C and E),'' should instead appear as ''Following the movement of the L1 stalk, we were able to enrich for populations of half-closed (Ϸ0.4 FRET) complexes by addition of excess deacylated tRNA to classical state (Ϸ0.25 FRET) complexes containing a vacant E site ( Fig. 3 C and E).'' Additionally, the authors note that in Fig. 6, the y-axis of panel B was labeled incorrectly. The corrected figure and its legend appear below. (9) and L1 stalk movement (this work; Table S1). The dashed lines at K eq ϭ 1 divide the plot into 4 quadrants corresponding to the 4 possible combinations of nonrotated and rotated orientations of the subunits and fully closed and open conformations of the L1 stalk. Filled squares correspond to complexes of pretranslocation ribosomes containing deacylated tRNA in the P site (tRNA Tyr , tRNA Phe , or tRNA fMet ). Open circles correspond to posttranslocation ribosomes containing N-Ac-Phe-tRNA Phe in the P site and a vacant E site. Open triangles correspond to vacant ribosomes with or without EF-G⅐GDPNP bound. (B) Correlation between forward rates: closing of the L1 stalk vs. rotation of subunits from classical to hybrid state. (C) Correlation between reverse rates: opening of the L1 stalk vs. rotation of subunits from hybrid to classical state. Lines represent log-linear fits of the data.

No abstract

The translation of reverse transcriptase and other essential viral proteins from the HIV-1 Pol mRNA requires a programmed -1 ribosomal frameshift. This frameshift is induced by two highly conserved elements within the HIV-1 mRNA: a slippery sequence comprised of a UUUUUUA heptamer, and a downstream stem-loop structure. We have determined the structure of the HIV-1 frameshift inducing RNA stem-loop, using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The 22 nucleotide RNA solution structure [root mean squared deviation (r.m.s.d.) = 1.2 A] was determined from 475 nuclear Overhauser effect (NOE)-derived distance restrains, 20 residual dipolar couplings and direct detection of hydrogen bonds via scalar couplings. We find that the frameshift inducing stem-loop is an A-form helix capped by a structured ACAA tetraloop. The ACAA tetraloop is stabilized by an equilateral 5' and 3' stacking pattern, a sheared A-A pair and a cross-strand hydrogen bond. Unexpectedly, the ACAA tetraloop structure is nearly identical to a known tetraloop fold, previously identified in the RNase III recognition site from Saccharomyces cerevisiae.

Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site.