Extracting details of the mechanism of promoter function in transcription has been widely studied. We have chosen to look at one of the simplest aspects of this process, namely, the strength of strand pairing in the promoter region. Specifically, the stability of the DNA double helix was determined in the vicinity of the promoter by computing the free energy for strand separation as a function of dinucleotide free energy values taken from the calorimetric measurements of Breslauer et al. The stability of 224 prokaryotic promoter regions was studied within a window of +/- 250 nucleotides on either side of the mRNA start sites. We found that for this set of promoters the -10 region was significantly the least stable. We also compared the free energies of 121 promoter mutations within the -35 and -10 regions with the free energies of their corresponding wild type sequences and found a correlation between the free energy change and the mutation type in the -10 region. 80% of the mutations in this region with increased/decreased promoter activity were observed to be less/more stable than the wild types.
