STATISTICAL-MECHANICAL TREATMENT OF VIOLATIONS OF THE DOUBLE HELIX IN SUPERCOILED DNA

We consider the problem of making allowance for superhelicity in the statistical‐mechanical calculations of fluctuational violations of the DNA double helix. A simple model is discussed, making it possible in the calculations to use an approach based on the theory of helix–coil transition in DNA. The proposed algorithms allow calculating the effect of superhelicity on the base‐pair fluctuational opening for any given sequence of nucleotides. An algorithm is also proposed allowing for the hairpin and cruciform structures in the palindromic regions of a sequence, as well as the open and helical states. The theory is used to calculate the melting curve for superhelical DNA at temperatures well below the melting point of the linear or nicked forms. The maps of opening probability are calculated for SV40 and ϕX174 DNA using their recently published complete nucleotide sequences. The data explain well the experimental results of probing the secondary structure of these DNA by single strand‐specific endonucleases. Copyright © 1979 John Wiley & Sons, Inc.