Solution structure of the ATF-2 recognition site and its interaction with the ATF-2 peptide

The effect of leucine zipper proteins binding to the DNA recognition site is controversial. Results from crystallography, gel and solution methods have led to opposite conclusions about the conformation of the DNA in the complex. The role of the DNA binding site in the recognition process and in the gene induction mediated by transcription factors needs to be investigated further. In this article the self-complementary 16 bp oligodeoxynucleotide (CATGTGACGTCACATG)2, which contains the cAMP response element recognised by numerous transcription factors of the leucine zipper family, has been examined free from proteins and in its interaction with the mammalian activating transcription factor 2. The recognition process has been investigated by circular dichroism analysis, which has revealed conformational changes in both DNA and protein upon binding. The solution structure of the 16mer, important in order to define the effects induced by binding of leucine zipper proteins and the intrisic bending properties of DNA, has been determined from NMR data using direct refinement against NOE intensities, analysis of scalar coupling constants and restrained molecular dynamics calculations. Final structures starting from the A and B forms of DNA agreed to a pairwise root mean square deviation (r.m.s.d.) of 1.04 +/- 0.3 A (0.7 +/- 0.2 A to the average) for all atoms. The terminal base pairs were less well determined, and the pairwise deviation of the 12 core bp was 0.83 +/- 0.27 A (0.55 +/- 0.19 A to the average). The final structures are within the B-family with an average helical twist of 36+/-2 degrees. No significant intrinsic DNA bend is shown in the activating transcription factor regulatory site. However, there are substantial deviations from the canonical B-DNA (r.m.s.d. = 3.6 A) in the core of the molecule, associated with relatively large base inclinations.