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Updated: Apr 23, 2026

Studying RNA Interactors of Protein Kinase RNA-Activated during the Mammalian Cell Cycle
Published on: March 5, 2019
Studying the affinity, kinetic stability, and specificity of RNA/protein interactions: SINE ncRNA/Pol II complexes as
James A Goodrich1, Jennifer F Kugel
1Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, CO, 80309-0215, USA.
Abstract:
The number of documented interactions between proteins and noncoding RNAs (ncRNA) of all types has grown rapidly in the past several years. A current challenge is to experimentally characterize these interactions to ultimately understand their biological roles at a mechanistic level, which will require a combination of multiple experimental techniques. One such category of techniques is biochemical assays that determine the affinity, kinetic stability, and specificity of ncRNA/protein complexes. Here we describe how to experimentally determine these important parameters using electrophoretic mobility shift assays (EMSAs). The interaction between mammalian SINE-encoded ncRNAs and human RNA polymerase II is presented as a model system; however, the experiments could be readily adapted to other ncRNA/protein complexes.
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