Research in the Qin group focuses on understanding mechanisms of nucleic acid recognition using a combination of biophysical and biochemical techniques. The Qin group has spearheaded the development of a biophysical technique, Site-Directed Spin Labeling (SDSL), to study nucleic acids and protein-nucleic acid complexes in bulk solution and at the single-molecule level. SDSL monitors site-specifically attached stable radicals (e.g., nitroxide spin labels) using Electron Paramagnetic Resonance (EPR) spectroscopy, and provides unique structural (e.g., distance constraints) and dynamic (e.g., motions at the labeling site) information on high-molecular-weight complexes under physiological conditions (1). The Qin group has developed a R5-family of nucleotide-independent nitroxide labels that can be efficiently attached at any desired site within a strand of DNA or RNA (2), and used the R5-family of labels to investigate global structure of a non-coding RNA (3); nano- to micro-second dynamics in a folded ribozyme (4); relationship between sequence-dependent DNA shape and recognition by the p53 tumor suppressor (5); interaction between DNA G-quadruplexes and metal-based small molecules (6); and DNA recognition by CRISPR-Cas9 (7, 8). Furthermore, collaboration between the Qin group and Professor Jiangfeng Du yielded the first single-molecule EPR spectrum of R5-labeled DNA at ambient temperature in aqueous buffer (9), paving the way for single-molecule SDSL investigation of biomolecules in native-like environments.
Current projects in the Qin group centers on investigating mechanisms of DNA target recognition by the programmable CRISPR-Cas nucleases that have led to a still rapidly evolving revolution in genome engineering. The CRISPR studies utilize a combination of spin-labeling, fluorescence spectroscopy, enzyme kinetics assays, and structural characterization; and are intimately connected to further development of SDSL techniques in bulk solutions and at the single-molecule level. Please visit the Qin group page for details and recent progresses.