Two mutant binding sites of the activating transcription factor region within the E2A promoter of adenovirus exist in a novel conformation

The solution conformations of two mutants of the ATF (activating transcription factor) binding site within the E2A promoter of adenovirus have been determined in vitro by NMR and CD methods. Both sequences have conformations which incorporate north-like sugar puckers in helices which are stacked in a B-like manner as seen with the parent binding site (Borden, K.L.B. (1993) Biochemistry 32, 6506-6514). The PATFm sequence has similar binding affinities and specificities to ATF while the PM2 oligonucleotide is recognized by a different subset of proteins within the ATF family. Both sequences contain unusual amounts of sugar puckers in north-like conformations but the specific distribution of north-like and south-like structures differs between them. These data indicate that the existence of this novel conformation is not characteristic of only the parent sequence. Further, there is a sequence dependent component as illustrated by the variation of the distribution of the north-like sugar puckers within the two mutant oligonucleotides. Differences in sugar pucker conformation can cause bending of the helix and will alter the phosphate backbone surface of the oligonucleotide. Both factors are important to the protein nucleic acid recognition process and thus to cellular control of transcription.