Photochemical Probes for Non-B DNA

There has been recent evidence to suggest that G-quadruplexes play an important role in vivo in regulating gene expression and other transactions of DNA. Analysis of the human genome sequence has shown that there are many sequences containing runs of G which could fold into G-quadruplexes. There is also evidence from fluorescent G-quadruplex binding drugs and from anti-G quadruplex antibodies that these structures exist in vivo. Unfortunately what these probes are actually binding to, or whether or not they may be inducing formation of G-quadruplexes that wouldn't otherwise be present is unknown. We recently discovered that certain G-quadruplexes undergo photochemical crosslinking which suggests that the stable crosslinked product could be used as evidence for the existence of the G-quadruplex. We are therefore developing post-labeling, isotope dilution mass spectrometry, and Next-Gen sequencing protocols for determining if these photoproducts are present and where in the genome.