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Nucleic Acids Research, 1995, Vol. 23, No. 13 2512-2518
© 1995

RNA

Probing sequence-specific RNA recognition by the bacteriophage MS2 coat protien

Peter G. Stockley*, Nicola J. Stonehouse, James B. Murry, Shona T. S. Goodman{dagger}, Simon J. Talbot§, Chris J. Adams, Lars Lilijas1 and Karin Valegå1

Department of Genetics, University of Leeds Leeds LS2 9JT, UK 1Department of Molecular Biology, Biomedical Centre, Uppsala University Box 590, S-751 24 Uppsala, Sweden

*To whom correspondence should be addressed

Received March 2, 1995. Accepted May 22, 1995.

We present the results of In vitro binding studies aimed at defining the key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein. We have used chemically synthesized operators carrying modified functional groups at defined nucleotide positions, which are essential for recognition by the phage coat protein. These experiments have been complemented with modification-binding Interference assays. The results confirm that the complexes which form between TR and RNA-free phage capsids, the X-ray structure of which has recently been reported at 3.0 Å, are identical to those which form in solution between TR and a single coat protein 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 unliganded operator. The results also provide support for the approach of using modified oligoribonucleotides to investigate the details of RNA-ligand interactions.

{dagger}Present addresses: 9 Malthouse Court, Derham, Norfolk NR 20 USA, UK

§Present addresses: Institute for cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK


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