An associative memory Hamiltonian model for DNA and nucleosomes
Fig 3
Supercoiling behavior of DNA minicircles.
(a) Commonly observed shapes of DNA minicircles (b) Writhe analysis of DNA topoisomers -4 to 4. Positively supercoiled minicircles relax torsional stress forming plectonemes, which manifest in increasing writhe and are visible in the DNA conformations in (a). Moderately negatively supercoiled minicircles also form plectonemes, this time resulting in negative writhe. Strongly negatively supercoiled minicircles do not appear to form plectonemes. (c) Negatively supercoiled DNA relaxes torsional strain through local melting of the DNA double helix. The figure shows an example structure of a topoisomer -2, defects are indicated by the black and red arrows. (d) Bending angle along DNA for the minicircle structure in (c). Local defects are clearly visible at index 304 and 193, once again indicated by the black and red arrows.