Introduction to Regulatory RNA

Key concept
- Small RNAs can function as regulators by base pairing to specific target RNAs and to proteins by several different mechanisms.
Regulation via RNA uses changes in secondary structure base pairing as the guiding principle. The ability of an RNA to shift between different conformations with regulatory consequences is the nucleic acid’s alternative to the allosteric changes in protein enzymatic conformation. The changes in structure may result from either intramolecular or intermolecular interactions.

The most common role for intramolecular changes is for an RNA molecule to assume alternative secondary structures by utilizing different schemes for base pairing. The properties of the alternative conformations may be different. Changes in the secondary structure of an mRNA can result in a change in its ability to be translated. In intermolecular interactions, an RNA regulator recognizes its target by the familiar principle of complementary base pairing.
FIGURE .1 shows that the regulator is usually a small RNA molecule with extensive secondary structure, but with a singlestranded region(s) that is complementary to a single-stranded region in its target. The formation of a double-helical region between the regulator and the target can have two types of consequence:
- Formation of the double-helical structure may itself be sufficient for regulatory purposes. In some cases, a protein can bind only to the single-stranded form of the target sequence and is therefore prevented from acting by duplex formation. In other cases, the duplex region becomes a target for binding—for example, by nucleases that degrade the RNA and therefore prevent its expression.
- Duplex formation may be important because it sequesters a region of the target RNA that would otherwise participate in some alternative secondary structure.

FIGURE .1 A regulator RNA is a small RNA with a singlestranded region that can pair with a single-stranded region in a target RNA.