PROBING SEQUENCE-SPECIFIC RNA RECOGNITION BY THE BACTERIOPHAGE-MS2 COAT PROTEIN

We present the results of in vitro binding studies aimed at defining t he key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein. We have used chemi cally synthesized operators carrying modified functional groups at def ined nucleotide positions, which are essential for recognition by the phage coat protein. These experiments have been complemented with modi fication-binding interference assays. The results confirm that the com plexes which form between TR and RNA-free phage capsids, the X-ray str ucture of which has recently been reported at 3.0 Angstrom, are identi cal to those which form in solution between TR and a single coat prote in dimer. There are also effects on operator affinity which cannot be explained simply by the alteration of direct RNA-protein contacts and may reflect changes in the conformational equilibrium of the unligande d operator. The results also provide support for the approach of using modified oligoribonucleotides to investigate the details of RNA-ligan d interactions.