BIOPHYSICS. For the article “Specificity of RNA–RNA helix recognition,” by Daniel J. Battle and Jennifer A. Doudna, which appeared in number 18, September 3, 2002, of Proc. Natl. Acad. Sci. USA (99, 11676–11681; First Published August 20, 2002; 10.1073/pnas.182221799), Figs. 2 and 4 appeared incorrectly. The correct figures and their legends appear below.
Fig 2.
P4–P6 folding assay. (a) Constructs used in the assay. The J5/5a-bp construct contains mutations causing the J5/5a hinge region between the P5abc subdomain and the P456 region to base pair, forming a linear molecule unable to make tertiary contacts between P5abc and P456 at any magnesium concentration (8). (b) P4–P6 domain variants with mutations of the C109-G212 base pair to all 16 possible base-pair combinations were incubated at various magnesium concentrations and subjected to native gel electrophoresis at constant temperature. As magnesium concentration increased, the molecules folded, resulting in increased mobility relative to the J5/5a control molecule. (c) Plots of electrophoretic mobility of P4–P6 domain variants with Watson–Crick base pairs at the 109–212 receptor position relative to the J5/5a-bp unfolded control molecule vs. magnesium concentration.
Fig 4.
Native gel folding assays conducted with P4–P6 domain variants. P4–P6 domain variants with mutations of the C109-G212 base pair to all 12 possible base mismatches were incubated at various magnesium concentrations and subjected to native gel electrophoresis at constant temperature. Shown are plots of electrophoretic mobility relative to the J5/5a-bp unfolded control molecule vs. magnesium concentration. Values for the Hill coefficient (n), the apparent equilibrium magnesium concentration required for folding of one-half of the molecules ([Mg2+]1/2) and ΔGapparent were calculated as described. (a) Plots of relative electrophoretic mobility vs. magnesium concentration for P4–P6 domain variants with pyrimidine–pyrimidine mismatches at the 109–212 position. (b) Plots of relative electrophoretic mobility vs. magnesium concentration for P4–P6 domain variants with purine-purine mismatches at the 109–212 position. (c) Plots of relative electrophoretic mobility vs. magnesium concentration for P4–P6 domain variants with wobble base pairs at the 109–212 position. (d) Model for the effects of mutation of the receptor base pair to G-U or U-G. Wobble base pairs adapted from an oligonucleotide crystal structure (PDB entry code ) (16) were superimposed on the P4–P6 wild-type structure by alignment on the phosphate backbone with the program O (12). Arrows represent some likely areas of steric conflict between the model base pairs and A184.