Base pairing in Bacillus subtilis ribosomal 5S RNA as measured by ultraviolet absorption and Fourier-transform infrared spectrometry.

Ultraviolet (260 and 280 nm) and Fourier-transform infrared (FT-IR) spectra of Bacillus subtilis ribosomal 5S RNA have been acquired between 20 and 90 degrees C. In the presence of added Mg2+, the average UV melting midpoint, Tm, is 60 (A260) or 62 degrees C (A280), resolving into two components (Tm = 54 and 68 degrees C). In the presence of 10 mM Mg2+, the normalized A260 increases by about 5%, and the average Tm increases to 70 degrees C (A260 or A280), resolving into components at 63 and 73 degrees C at 260 nm but not resolved at 280 nm. From the difference of the 5S RNA FT-IR spectra between 90 and 30 degrees C, the number of base pairs in B. subtilis 5S RNA was determined by the procedure outlined in the accompanying paper [Li, S.-J., Burkey, K. O., Luoma, G. A., Alben, J. O., & Marshall, A. G. (1984) Biochemistry (preceding paper in this issue)]. Addition of 10 mM Mg2+ increases the number of A-U pairs by 1 (from 11 to 12) and the number of G-C pairs by 2 (from 15 to 17). FT-IR melting curve midpoints show that addition of Mg2+ increases the melting point for both A-U and G-C pairs in B. subtilis 5S RNA. The A-U pairs melt before G-C pairs (56 vs. 64 degrees C) in the absence of Mg2+, but both types of pairs melt at the same temperature (67 vs. 70 degrees C) in the presence of Mg2+.(ABSTRACT TRUNCATED AT 250 WORDS)