Studies on 5 s RNA conformation by partial ribonuclease hydrolysis

Abstract

32P-labeled native 5 s RNA from Escherichia coli was digested under mild conditions with T 1 or pancreatic RNases; the hydrolysate was analysed on an acrylamide gel slab in non-denaturing conditions and was resolved into a small number of discrete bands, which were eluted and characterized by fingerprinting. Definite sequences can be assigned to the corresponding fragments; exposed, singlestranded regions can be defined and self-paired nucleotide stretches are identified. 8 m-urea-acrylamide gel electrophoresis of molecules containing “hidden breaks” was used to define the most accessible of these exposed regions, which is located around position 44 in the sequence. The same procedure applied to denatured 5 s RNA yielded very different results which demonstrate a difference with respect to the pairing scheme between native and denatured forms of the molecule. These data restrict considerably the range of possible models and in particular exclude all the previously published ones, but do not allow the specification of a unique pairing scheme. They do however suggest the possibility that 5 s RNA is involved in an interaction with transfer RNA since the sequence of the most accessible region of the molecule is complementary to the universal transfer RNA G-T- Ψ-C- G A sequence.