The study of stacking energy for natural DNA sequences

The stacking energies between bases of DNA for both A and B conformation have been calculated by Aida & Nagata (1986, Int. J. Quantum Chem. 29, 1253-1261). For naturally occurring DNA sequences, by assuming that the average stacking energy of A conformation is completely identical with that of B, the lowest average stacking energy for double strand DNA has been calculated and found to be equal to -7.38 kcal M-1. This conclusion has been confirmed by the data of stacking energy of 112 promoter sequences of Escherichia coli and some other natural DNA sequences. Our result shows that the natural DNA sequences are bi-stable. One stable-state is the A conformation, the other is B. It is shown that the result is only applicable to the transcription processes that regulate the gene expression. Through the interaction with RNA polymerase in the processes of transcription, the conformation of DNA might undergo a transition of B----A----B.