A four-strand parallel G-quadruplex with 3 guanine tetrads (yellow squares)

Because of our familiarity with the Watson–Crick form of DNA, we often overlook the fact that DNA can adopt other biologically relevant structures. Differences in the DNA structure in the promoter region of the oncogene MYC have previously been shown to affect its transcription. Analysis of the structure of this DNA region, in combination with a small-molecule inhibitor of MYC transcription, provides new insights into the development of transcription-based anticancer drugs.

Within the promoter region of MYC is a nuclease-hypersensitive element known as NHE III1, which controls up to 90% of MYC transcription. This region contains a pyrimidine-rich and a purine-rich strand, and is thought to be able to form alternative DNA structures. In particular, a purine-rich 27-nucleotide stretch that contains six guanine tracts is thought to form multiple guanine (G)-quadruplex structures. G-quadruplexes consist of successive layers of two or more G-tetrads to form a box-like structure with a central cavity. The G-tetrad consists of four guanines arranged in a cyclic, hydrogen-bonded square planar alignment (see accompanying picture). Substitution of these guanines with adenines disrupts this structure and increases MYC transcription, whereas stabilization of the G-quadruplexes by the small molecule ligand TMPyP4 represses MYC transcription.

Anh Tuân Phan and colleagues have resolved the structure of a 24-nucleotide, 5 guanine tract sequence (Pu24) from the MYC NHE III1 element in a potassium-ion solution. The use of five guanine tracts has revealed new structural motifs not seen in previous structures that were resolved using four guanine tracts. By making a series of mutations based on this structure, the authors have identified novel motifs that are important for the folding and formation of this G-quadruplex. Importantly, the structural analysis of the interaction between the G-quadruplex and four different ligands has shown that all four bind on top of the G-tetrad core, but that subtleties occur in the effect that these ligands have on the stability of the G-quadruplex. Indeed, the kinetically slow binding of the TMPyP4 ligand to the G-quadruplex particularly enhances the stability of the complex, explaining its capacity to reduce MYC transcription.

The authors conclude that the new structural motifs and folding principles described for Pu24 will aid the understanding of other G-quadruplex structures. Such structures are evident in potential anticancer targets, such as the promoters of other oncogenes, and in telomeres.