The cruciform DNA mobility shift assay: a tool to study proteins that recognize bent DNA.
So-called architectural DNA binding proteins such as those of the HMGB-box family induce DNA bending and kinking. However, these proteins often display only a weak sequence preference, making the analysis of their DNA binding characteristics difficult if not impossible in a standard electrophoretic mobility assay (EMSA). In contrast, such proteins often bind prebent DNAs with high affinity and specificity. A synthetic cruciform DNA structure will often provide an ideal binding site for such proteins, allowing their affinities for both bent and linear DNAs to be directly and simply determined by a modified form of EMSA.
Department of Medical Biology, Cancer Research Centre, Hôtel-Dieu de Québec, 9 rue McMahon Québec, QC, Canada G1R 2J6.
Victor Y
VY
Stefanovsky
Tom
T
Moss
D000918:Antibody Specificity; D045566:DNA, Cruciform / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay / Q000379:methods*; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides; D011485:Protein Binding; D011506:Proteins / Q000032:analysis* / Q000378:metabolism*; D013194:Staining and Labeling; D013379:Substrate Specificity
D045566:DNA, Cruciform; D009841:Oligonucleotides; D011506:Proteins