Periodic interactions of heat shock transcriptional elements

The activity of some genes is known to be a periodic function of the amount of DNA between the binding sites of its regulatory proteins. The period observed is close to 10.5 base pairs (bp), that is, one turn of the B form of the DNA helix. Such periodicity is also seen in the cooperative binding of phage lambda and lac repressors. These periodic phenomena have been attributed to a requirement for a unique rotational alignment in forming essential contacts between the bound proteins. Here we report a strong periodic dependence of the transcription of a cloned Drosophila melanogaster heat shock gene on the amount of DNA inserted between its two heat shock consensus elements. In addition, we find a similar periodicity for insertions just 3' to the proximal heat shock element. Consistent with the torsional flexibility of DNA, these periodic effects are seen for short insertions, up to approximately 80 bp, but not for much longer ones. We conclude that maximal transcription requires rotationally unique contacts between proteins bound to the two heat shock elements and also requires correct alignment of additional sites of DNA-protein binding downstream of the proximal element.