because the formation of the complex does not involve extensive Watson/Crick base pairing but is sensitive to RNase H, which cleaves RNA in an RNA-DNA hybrid and the complex binds to an antibody specific to RNA-DNA hybrids. Supercoiling Because of its helical structure, a double-stranded DNA molecule becomes topologically constrained in the covalently closed circular form which eliminates the rotation of the free ends. The number of times the two strands cross each other in a topologically constrained DNA is called the linking number (Lk), which is equivalent to the number of helical turns or twists in a circular molecule. The Lk of a topological DNA remains invariant, no matter how the DNA molecule is deformed, as long as neither strand is broken. The Lk of DNA in the relaxed form is defined as Lk0. For any DNA, Lk0 can be calculated by dividing the length (in bp) of the DNA by the number of bp per helical turn. This is equal to 10.4 bp for the relaxed B-form DNA. Any deviation from Lk0 causes supercoiling in DNA. A decrease in the linking number (Lk<Lk0) creates negative supercoiling whereas an increase in the linking number (Lk>Lk0) creates positive supercoiling. The supercoiled state (when Lk is not equal to Lk0) results in a transition in DNA structure that can manifest as a change in the number of twists (negative <10.4 bp/turn, positive >10.4 bp per turn) and/or in the formation of writhes, called supercoils. Thus, Lk is mathematically defined as a sign dependent sum of the two geometric parameters, twist and writhe. A quantitative measure of supercoiling that is independent of the size of DNA molecules is the supercoiling density (σ) where σ =∆Lk/Lk0. Writhes can adopt two structures; plectoneme and solenoid or toroid. A plectonemic structure arises from the interwinding of the helical axis. Toroidal supercoils originate when DNA forms several spirals, around an axis and not intersecting with each other, like those in a telephone cord. The writhes in the plectonemes form are right- and left-handed in positively or negatively supercoiled DNA, respectively. The handedness of the toroidal supercoils is opposite to those of plectonemes. Both plectonemes and toroidal supercoils can be either in a free form or restrained in a bound form with proteins. The best example of the bound toroidal supercoiling in biology is the eukaryotic nucleosome in which DNA wraps around histones. Plectonemic supercoils in E.