Quadruplex recognition and discrimination by dynamic combinatorial chemistry

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 various alternative structural forms can exist. There is 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 known to exist is 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 the possibility of generating small molecule ligands that can specifically recognise such quadruplexes by targeting loop structures that appear to be unique for each quadruplex. This might in the longer term lead to a new class of therapeutic agents that function by selectively targeting DNA secondary 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. Small molecule ligands have been reported that bind to and therefore stabilise the quadruplex folded form of DNA. The focus of this proposal is to exploit the structural differences (loop size, loop sequences, strand polarity) between quadruplexes for developing original ligands specific for a given quadruplex by targeting its loops. We will employ a fragment-based approach that exploits the power of dynamic covalent chemistry (DCC) to identify fragments that recognise specifically each loop of the quadruplex. Highly specific ligands will be obtained by combining the selected loop-recognising building blocks to a quadruplex DNA binding platform. The proposal will expand on dynamic covalent methodology, provide fundamental insights into quadruplex recognition and generate new classes of quadruplex-specific ligands that will serve as valuable tools for biology.