Targeting DNA Junctions with Small Molecules for Therapeutic Applications in Oncology

DNA junctions exist at the branch point of three or four DNA duplexes (dsDNA, or B DNA) in hairpin and cruciform structures. These structures occur when repeated dsDNA sequences open up to expose single-stranded DNA (ssDNA), which then folds upon itself to form an intramolecular hairpin. Junctions are thus formed during DNA transactions, i.e., when the dsDNA is being replicated, transcribed or repaired. Three-way junctions (TWJs) and four-way junctions (FWJs) can encapsulate small molecules, termed ligands, which stabilise the non-B DNA structural motif. In vitro assays employ this stabilisation effect to identify junction-binding small molecules. TWJ-binding molecules have C3 symmetry, are approximately 10 Å in diameter and contain aromatic and positively charged chemical groups; FWJ-binding ligands are often larger with similar chemical motifs and C2 symmetry. We describe here the discovery of junction-binding molecules, culminating in those which show exceptional in vitro binding and promising in cellulo properties. Ligands able to stabilise DNA junctions in cells hinder DNA transactions and thus induce a DNA damage response (DDR), leading to cytotoxicity. This approach is cancer-specific as cancer cells are particularly sensitive to DNA damage due to their impaired DDR mechanisms. Recently, these ligands were incorporated in synthetic lethality strategies, demonstrating the enormous progress that the field of junction targeting has made in only 30 years, which should inspire chemical biologists in the pursuit of more specific ligands and techniques to characterise their molecular mechanism