We compare numerical calculations and experimental data showing that large, slow thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating a bacteriophage DNA gene promoter segment, we find that the large opening tends to occur at the transcription start site. Other probable large openings appear to be related to other regulatory sites. Sequence specificity, nonlinearity and entropy, are the basic elements for controlling coherent dynamics. To further characterize the dynamics related to the bubble formation we investigate the temperature dependence on the dynamic structure factor. A distinct feature in the dynamics structure factor
is identified and attributed to the denaturation bubbles.