There are currently several active projects in our laboratory. These projects are essentially focused on either on DNA/RNA structure or interaction of DNA with relevant proteins. We use single molecule fluorescence microscopy techniques as the main tool. In particular, single molecule Förster Resonance Energy Transfer (FRET) and high resolution particle tracking are the methods commonly used in our laboratory. Our methods take advantage of the high signal to noise ratio provided by total internal reflection to achieve single molecule resolution.
Most of our work is focused on interactions of various proteins with G-quadruplex (GQ) structures. GQ structures (GQs) are non-canonical DNA second structures that could form at chromosome ends (telomeres), within the genomic DNA, or in RNA. Depending on where they form, they perform different functions including protection and capping of telomeres, transcription or translation level gene expression regulation. As GQs are thermodynamically very stable, typically more stable than double stranded DNA formed by Watson-Crick pairing, they require protein action to be unfolded during replication, repair, or transcription. There are a number of single stranded DNA (ssDNA) binding proteins, such as Replication Protein A (RPA) and Protection of Telomere 1 (POT1), and helicases, such as Bloom and Werner helicases, that are capable of unfolding GQs with varying efficiency. The understanding the interactions of such physiologically significant proteins with GQs and deciphering the underlying principles of protein mediated GQ unfolding forms a significant aspect of our research efforts.
Of particular medical interest is the potential of GQs as specific drug target, due to their highly unusual planar structure that can be stabilized by small molecules. The underlying principle of these efforts is to deliver GQ stabilizing small molecules to cancer cells and stabilize the GQ structure such that they can not be efficiently unfolded by proteins interacting with them. How the complex formed by GQ and such small molecules interacts with proteins forms another aspect of our work.
Two sample figures are shown in the left panel that illustrate typical measurements and types of analysis performed in our work.