PACE Analysis of RNA-Peptide Interactions

The PACE assay is a relatively new addition to the arsenal of techniques used to examine quantitatively the interactions of proteins and peptides with DNA and RNA (1 ). Polyacrylamide coelectrophoresis (PACE) involves electrophoresis of a labeled nucleic acid through a gel medium that contains the target peptide or protein ligand. In this way, the nucleic acid is maintained in a constant concentration of the ligand throughout the electrophoresis, and the conditions for binding equilibrium are maintained throughout the experiment. This avoids the requirement for formation of complexes that are kinetically stable under the nonequilibrium conditions typical of a gel mobility shift experiment. A particularly powerful aspect of the PACE experiment is the ability to probe interactions that are too weak to be observed in other binding assays such as gel shift or filter binding (see Chapters 9 and 10 ).