Stability of lac repressor-operator complexes in a new agarose-based gel matrix

Rapid agarose gel electrophoretic mobility shift assay for quantitating protein: RNA interactions

Interactions between proteins and nucleic acids are frequently analyzed using electrophoretic mobility shift assays (EMSAs). This technique separates bound protein:nucleic acid complexes from free nucleic acids by electrophoresis, most commonly using polyacrylamide gels. The current study utilizes recent advances in agarose gel electrophoresis technology to develop a new EMSA protocol that is simpler and faster than traditional polyacrylamide methods. Agarose gels are normally run at low voltages (∼10 V/cm) to minimize heating and gel artifacts. In this study we demonstrate that EMSAs performed using agarose gels can be run at high voltages (≥20 V/cm) with 0.5 × TB (Tris-borate) buffer, allowing for short run times while simultaneously yielding high band resolution. Several parameters affecting band and image quality were optimized for the procedure, including gel thickness, agarose percentage, and applied voltage. Association of the siRNA-binding protein p19 with its target RNA was investigated using the new system. The agarose gel and conventional polyacrylamide gel methods generated similar apparent binding constants in side-by-side experiments. A particular advantage of the new approach described here is that the short run times (5-10 min) reduce opportunities for dissociation of bound complexes, an important concern in non-equilibrium nucleic acid binding experiments.

Use of biotin-labeled nucleic acids for protein purification and agarose-based chemiluminescent electromobility shift assays

We have employed biotin-labeled RNA to serve two functions. In one, the biotin tethers the RNA to streptavidin-agarose beads, creating an affinity resin for protein purification. In the other, the biotin functions as a label for use in a modified chemiluminescent electromobility shift assay (EMSA), a technique used to detect the formation of protein-RNA complexes. The EMSA that we describe avoids the use not only of radioactivity but also of neurotoxic acrylamide by using agarose as the gel matrix in which the free nucleic acid is separated from protein-nucleic acid complexes. After separation of free from complexed RNA in agarose, the RNA is electroblotted to positively charged nylon. The biotin-labeled RNA is readily bound by a streptavidin-alkaline phosphatase conjugate, allowing for very sensitive chemiluminescent detection ( approximately 0.1-1.0 fmol limit). Using our system, we were able to purify both known iron-responsive proteins (IRPs) from rat liver and assess their binding affinity to RNA containing the iron-responsive element (IRE) using the same batch of biotinylated RNA. We show data indicating that agarose is especially useful for cases when large complexes are formed, although smaller complexes are even better resolved.

Electrophoretic analysis of multiple protein-DNA interactions

Under favorable conditions, native gel electrophoresis allows the resolution of protein-DNA complexes that differ in stoichiometry, identities of occupied DNA sequences (configuration), and macromolecular conformation. This technique provides a unique opportunity to analyze, in thermodynamic terms, the molecular interactions that govern the equilibrium distributions of species in protein-DNA mixtures. Here we describe a general theoretical approach to the analysis of electrophoretic band intensities, and provide examples of its application to the analysis of several interacting systems.

A quantitative cryogenic gel-shift technique for analysis of protein-DNA binding

A cryogenic gel mobility shift technique was developed in which a mixture of protein and DNA samples at equilibrium is rapidly quenched and electrophoresed at -40 degrees C. The rapid and sustained drop in temperature results in almost complete stabilization of the equilibrium species distribution. Autoradiogram analysis of relative abundances for the bound and free DNA sites is carried out over a range of initial binding ratios to yield the binding curve and equilibrium constant as in the usual gel-shift assay. Validity of this technique for determining equilibrium populations of the interacting species is based upon two testable assumptions: (i) The equilibrium species distribution does not change during the cryogenic quench procedure. (ii) This equilibrium distribution is also constant during electrophoresis of the sample. Evidence supporting these assumptions was obtained using lambda cI repressor and a 570-bp DNA fragment containing the repressor binding site OR1. The resolved free energy for this interaction (delta G1) was shown to be independent of the quench procedure, duration of the quench stage, residence time in the gel wells, and duration of low-temperature electrophoresis. The technique yielded a free energy that was in close agreement with those from filter binding and DNAse footprint titration methods. This cryogenic version of the gel-shift method may prove especially useful in cases like that of lambda cI/OR1 binding, for which conventional gel-shift methodology has not been feasible.