I am working with ~6000 bp plasmid DNA, which contains the promoter of my interest. This promoter has a cis-element, which forms non-canonical DNA structures in cells, which I have already proved. Now there is a equilibium of transcription inhibitory secondary structure and stimulatory duplex structure which allows the transcription to proceed. This interchange is mediated by transcription factors that I have shown in a couple of experiments. Now, my concern is to estimate (qualitatively or quantitatively) the negative superhelical density upon the evolution of different secondary structure isomers.