A recurrent DNA sequence at sites of protein interaction

Abstract

Variation in the observed spin lattice relaxation rate (Robs) interpreted as proton exchange dominated in sequences corresponding to part of promoters where RNA polymerase initiates mRNA synthesis has been observed by both Patel et al. and Reid and co-workers. A higher Robs was also seen in the TA pair of the GTG/CAC in the sequence corresponding to the lambda phage cro repressor binding site by Kyogoku et al. As we pointed out in the introduction, the one case where a three-dimensional structure for a turn of a helix is known shows clear structural heterogeneity which has led to detailed consideration of geometry of regulatory regions. Nussinov and collaborators have generalized the details of the Dickerson dodecomer to note potential similarities in operators including the lac system and the enhancer sequences described above. Like the steric considerations of Calladine and Dickerson and nearest neighbor structure analysis of Bubienko et al., the focus is on the geometry of a sequence leading to base tilt angles and potential overlap since they are measurable parameters. With the observation that the DNA molecule is both structurally and dynamically flexible, there will no doubt be many new variables that can be made as a function of DNA sequence. Biophysical chemists in some ways are like the intoxicated person searching for a lost key at a site different from where it was lost because that is where the light is best. Thus, each physical method has its most convenient observable. It is hoped that the above discussion illustrates that a very large and diverse set of biochemical results are awaiting detailed explanation in molecular terms using the illumination of high resolution physical techniques.