Analysis of Quadruplex Function in the Genome

DNA is presumed to exist largely as the Watson-Crick double helix in living cells. There is growing evidence to suggest that the folded structure of DNA is dynamic and that alternative structural forms can exist and have function. A four-stranded form of DNA / a quadruplex helix called a G-quadruplex / that is known to form in certain G-rich sequences of DNA is likely to exist in many different places in our chromosomes. There is evidence to support that the formation of the quadruple helix can switch 'off' certain genes. This proposal aims to explore this hypothesis along with the chemical possibility of designing molecules that selectively stabilise such quadruple helix structures, and by doing so affect the function of certain genes. This would represent a new and exciting way to alter biological function by directly controlling genes. Given that genes form the basis for normal function and also for disease, the overall aims of this programme has the potential to inspire new therapeutic approaches to address human diseases and conditions by selectively targeting DNA structures, rather than proteins.

DNA sequence motifs with four or more stretches of Gs are predisposed to the formation of four stranded G-quadruplexes. Recent evidence points to the existence and function of such motifs in telomeres and also in gene promoters. A number of quadruplex forming sequences have been reported in the promoters of genes, leading to the hypothesis that quadruplex formation in gene promoters is mechanistically linked to the regulation of expression of that gene. We have identified a set of 20 genes in the human genome that have strong associations with properties that support this promoter-quadruplex hypothesis. We have also validated design principles for small molecules and engineered proteins that bind and stabilise the quadruplex folded form of DNA. In this programme we propose a large scale, genome-wide analysis on the effects of ligand induced quadruplex stabilisation on the expression of a) our 20 selected genes; b) all genes in the human genome. By doing so we will rigorously address the hypothesis and elucidate whether it represents a widespread mechanism for the control of genes. The programme will generate ligands that induce changes in the expression of selected genes by acting at the level of DNA recognition.