RNA Structure, Free and on the Ribosome, as Revealed by Chemical and Enzymatic Studies

At present, various chemical and enzymatic probes are the experimental techniques capable of providing large amounts of data on the structure and arrangement of large RNA molecules. Direct reactivity measurements yield information on accessibility, while cross-linking provides information on proximity. Taken together with secondary structure estimates derived from analysis of base pairing potential and phylogenetic variations, the results of chemical and enzymatic studies can help evaluate specific models for RNA structures and interactions. It is unlikely that a precise three-dimensional structure could result from this approach. However, it should be possible, through accumulation of a large enough data set, to provide reasonably accurate secondary structures and approximate models of how the secondary structure is arranged in space, alone, or in concert with proteins. A unique advantage of this approach is that it is suited to the detection of conformational changes in RNA molecules. Thus, it will be very useful in establishing functional aspects of altered RNA structures where they exist.