Fluorescence Anisotropy-Based Salt-Titration Approach to Characterize Protein–Nucleic Acid Interactions
Many proteins bind nucleic acids (NA) via cationic residues that interact electrostatically with the anionic phosphate backbone of RNA or DNA. These electrostatic interactions are often insensitive to NA sequence and structure, but confer strong salt dependence to the binding interactions. In contrast, salt-independent non-electrostatic contacts reflect more specific binding interactions. Proteins with multiple cationic NA-binding domains connected by flexible linkers, such as the HIV-1 Gag polyprotein, may bind different NA molecules in distinct ways. For example, Gag binding to the Psi-packaging signal of the HIV-1 RNA genome optimizes the specific non-electrostatic binding component of this protein–RNA interaction. In contrast, Gag binding to a non-psi RNA optimizes the electrostatic interactions at the expense of specific contacts. Here, we describe a fluorescence anisotropy-based salt-titration approach that allows complete characterization of both electrostatic and non-electrostatic binding components for any protein–NA complex in a quantitative manner within a single assay.
Key wordsFluorescence anisotropy Proteins Nucleic acids Specific binding Nonspecific binding Electrostatic interactions Non-electrostatic interactions HIV-1 Gag Nucleocapsid
We thank Mr. Joseph A. Webb and Drs. Christopher Jones and Leslie Parent for their role in FA-based salt-titration method development and application, Ms. Roopa Comandur for determining the effect of glycerol on the FA signal, and Mr. Erik Olson and Ms. Weixin Wu for critical reading of this chapter prior to submission. This work was supported by NIH GM065056 (K.M.-F.) and T.R.-M. was supported by NIH T32-GM008512.
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