Extreme Bendability of Short DNA
Many protein-DNA interactions involve bending and looping of DNA on length scales below 50 nanometers. Therefore, quantifying the intrinsic bendability of DNA at these biologically important length scales is essential for understanding DNA-protein interactions. The classical view of DNA posits that DNA must be stiff below the persistence length (<150 base pair) but recent studies addressing this have yielded contradictory results. Recently researchers at the Center for the Physics of Living Cells developed a fluorescence-based, protein-free, assay for studying the cyclization of single DNA molecules in real time (Vafabakhsh R. et al, Science, 337, 1097, 2012). Using this assay, researchers measured the looping rate for short DNA molecules and showed that this has remarkably weak length dependence between 67 and 106 bps, deviating significantly from the worm-like chain model. Moreover, they used this assay to quantify the effect of defects in the DNA as well as base modifications and protein or ligand binding on the overall bendability of dsDNA with high sensitivity. Many biologically significant protein-DNA interactions that involve looping and bending of DNA below 100 bp likely use this intrinsic bendability of DNA.
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