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Peter Z. Qin

Professor of Chemistry
Physical Chemistry / Biochemistry

B.S., 1991, Peking University, Beijing, China
Ph.D., 1999, Columbia University, New York, USA
Office: TRF 119
Phone: (213) 821-2461
Fax: (213) 740-0930
Email: pzq@usc.edu
 Group Homepage


Research Focus

 

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.

Selected publications

 

  1. Sowa, G.Z. and P.Z. Qin, Site-directed spin labeling studies on nucleic acid structure and dynamics., in Prog. Nucleic Acids Res. Mol. Biol. 2008. p. 147-197.
  2. Qin, P.Z., et al., Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nat. Protocols, 2007. 2: p. 2354-2365.
  3. Zhang, X., et al., Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling. J. Am. Chem. Soc., 2012. 134: p. 2644–2652.
  4. Grant, G.P.G., et al., Motions of the Substrate Recognition Duplex in a Group I Intron Assessed by Site-Directed Spin Labeling. J. Am. Chem. Soc., 2009. 131: p. 3136-3137.
  5. Zhang, X., et al., Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Nucleic Acids Research, 2014. 42: p. 2789-2797.
  6. Xu, C.-X., et al., A Nitroxide-Tagged Platinum(II) Complex Enables the Identification of a DNA G-Quadruplex Binding Mode. Chemistry – A European Journal, 2016. 22: p. 3405-3413.
  7. Tangprasertchai, N.S., et al., CRISPR–Cas9 Mediated DNA Unwinding Detected Using Site-Directed Spin Labeling. ACS Chem. Biol., 2017. 12: p. 1489-1493.
  8. Vazquez Reyes, C., et al., Nucleic Acid-Dependent Conformational Changes in CRISPR–Cas9 Revealed by Site-Directed Spin Labeling. Cell Biochem Biophys, 2017. 75: p. 203-210.
  9. Shi, F., et al., Single-DNA electron spin resonance spectroscopy in aqueous solutions. Nature Methods, 2018. 15: p. 697-699.

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