Abstract
Summary The conformation of sequenced RNA molecules can be analysed by partial RNAse digestion and two-dimensional acrylamide gel electrophoresis: in the first dimension (neutral acrylamide gel) fragments which are not held together by hydrogen bonds dissociate; thanks to the second dimension (8M urea-acrylamide gel) hidden breaks present in the fragments are revealed. Each spot of the resulting two-dimensional map can then be characterized by elution and fingerprinting. The method yields information both on the existence of particularly exposed regions in the molecule and on the pairing state of some parts of the sequence. New results obtained by the application of this method to the analysis of T1 RNAse partial digests of E. coli 5S RNA are described.
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