Summary
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.
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Acknowledgments
This work was supported by an operating grant from the Canadian Institutes of Health Research.
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© 2009 Humana Press, a part of Springer Science+Business Media, LLC
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Stefanovsky, V.Y., Moss, T. (2009). The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins that Recognize Bent DNA. In: Leblanc, B., Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 543. Humana Press. https://doi.org/10.1007/978-1-60327-015-1_31
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DOI: https://doi.org/10.1007/978-1-60327-015-1_31
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