Methods for Analyzing DNA Bending

DNA bending is observed in all DNA transactions, including replication, transcription, recombination, repair, and packaging. DNA bending can be sequence-directed, as in kinetoplast minicircle DNA and many synthetic sequences, or protein-induced, as in the nucleosome and in protein–DNA complexes formed with the catabolite activator protein (CAP), the TATA binding protein (TBP), and the integration host factor (IHF). In addition, the “bendability” of DNA is sequence-dependent; that is, some sequences demonstrate an increased propensity to adopt a bent conformation under stress, even when the intrinsic shape is essentially straight. The biological functions of bending and flexibility include apposition of sites that would otherwise be far apart on the stiff DNA duplex, creation of a recognition site for other proteins, organization of supercoiling geometry, decreasing DNA duplex stability, and compaction of the DNA in chromatin.