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Nucleic Acids Research, 1994, Vol. 22, No. 12 2255-2263
© 1994

RNA

Footprinting RNA-protein complexes following gel retardation assays: application to the R-17-procoat-RNA and tat-TAR interactions

Lori Pearson, C.-h.B. Chen, Richard P. Gaynor+ and David S. Sigman*

Department of Biological Chemistry, School of Medicine, Department of Chemistry and Biochemistry and Molecular Biology Institute University of California, Los Angeles, CA 90024-1570, USA

*To whom correspondence should be addressed

Received March 30, 1994. Accepted April 25, 1994.

RNA-protein complexes isolated following a gel retardation assay can be footprinted within the gel matrix using the chemical nuclease activities of 4,7-dimethyl-, 5,6-dimethyl-, and 3,4,7,8-tetramethyl- 1,10-phenanthroline-copper. These complexes are more reactive than 1,10-phenanthroline-copper but share its reaction preference for bulges and loops. The interaction of the coat protein of R-17 with its viral RNA target and tat- and tat-derived peptides with HIV TAR RNA have been studied. In both cases, the RNA sequence opposite a 2–3 nucleotide bulge are protected. Tat-derived peptides inhibit cleavage at sites which intact tat does not protect. These results are consistent with transcription studies which have suggested that truncation of tat increases nonspecific binding.

+Present address: Department of Internal Medicine, Southwestern Medical School, 5323 Harry Hines Blvd, Dallas, TX 75235, USA


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