Triplex forming ability of a c-myc promoter element predicts promoter strength

Most transcription factors are believed to bind promoter elements in the B-DNA conformation, wherein linear sequence determines specificity. However, there are promoter elements that can form complex structures such as intramolecular triplexes, and these structures may participate in the activity of these promoter elements. We have previously shown that a c-myc promoter element, termed the nuclease-sensitive element or NSE, can form tandem intramolecular triplexes of the H-DNA type and has a repeating sequence motif (ACCCTCCCC)4. The NSE was mutated and examined for transcriptional activity and for intra- and intermolecular triplex forming ability. The transcriptional activity of mutant NSEs can be predicted by the element's ability to form H-DNA and not by repeat number, position, or the number of mutant base pairs. DNA may therefore be a dynamic participant in the transcription of the c-myc gene.