Abstract
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).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Cilley, C. and Williamson, J. R. (1997) Analysis of bacteriophage N protein and peptide binding to boxB RNA using polyacrylamide gel coelectrophoresis (PACE). RNA 3, 57–67.
Cann, J. R. (1989) Phenomenological theory of gel electrophoresis of protein-nucleic acid complexes. J. Biol. Chem. 264, 17,032–17,040.
Carey, J. (1991) Gel retardation. Methods Enzymol. 208, 103–116.
HorejsĂ, V. (1981) Affinity electrophoresis. Anal. Biochem. 112, 1–8.
Lim, W. A., Sauer, R. T., and Lander, A. D. (1991) Analysis of DNA-protein interactions by affinity coelectrophoresis. Methods Enzymol. 208, 196–210.
Matousek, V. and HorejsĂ, V. (1982) Affinity electrophoresis: a theoretical study of the effect of the kinetics of protein-ligand complex formation and dissociation reactions. J. Chromatogr. 245, 271–291.
Martin, G. And Keller, W. (1998) Tailing and 3′-end labeling of RNA with yeast poly(A) polymerase and various nucleotides. RNA 4, 226–230.
Gill, S. C. and von Hippel, P. H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182, 319–326.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989), in Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, NY, pp. 6.12.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Staining SDS-polyacrylamide gels with Coomassie brilliant blue, in Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, NY, pp. 18.55.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Humana Press Inc.
About this protocol
Cite this protocol
Cilley, C.D., Williamson, J.R. (1999). PACE Analysis of RNA-Peptide Interactions. In: Haynes, S.R. (eds) RNA-Protein Interaction Protocols. Methods in Molecular Biology™, vol 118. Humana Press. https://doi.org/10.1385/1-59259-676-2:129
Download citation
DOI: https://doi.org/10.1385/1-59259-676-2:129
Publisher Name: Humana Press
Print ISBN: 978-0-89603-568-3
Online ISBN: 978-1-59259-676-8
eBook Packages: Springer Protocols