Time：10:00-11:30 AM, Monday, Jan. 13, 2020
Venue: Room 211, Building 4, Yunqi Campus, Westlake University
Host: Dr. Xiao Lin, PI of School of Science, Westlake University
Dr. Dong Zhang
Department of physics, University of Missouri
Dr. Dong Zhang is a Postdoc. in Physics, University of Missouri, working with Prof. Chen Shi-Jie. He received B.Sc. degree in 2010 and Ph.D. degree in 2015 from Zhejiang University, under supervision of Prof. Linxi Zhang. He has published papers in top journals, such as Annu. Rev. Biophys., Nat. Commun., PNAS.
RNA folding is one of important issues in biophysics. Through adopting specific three-dimensional structures and conformation transitions between distinct states, RNA molecules play broadly cellular functions from carrying genetic information to regulating gene expression and enzymatic activity. To understand the relationship between structure and function and to design RNAs with new functionalities, we have developed various computational approaches to model the folding dynamics, three-dimensional structure, and biological function of RNAs. First, to resolve the long-standing reference state challenge in statistical potentials, we developed an iterative simulated reference state approach to account for correlated interactions in RNA folding. Second, we proposed an accurate coarse-grained RNA model (IsRNA) for de novo prediction and blind screening of RNA three-dimensional structures based on molecular dynamics simulations. Third, combining coarse-grained molecular dynamics simulation in IsRNA model with nanopore snapshot experiment and theoretical analysis, the tertiary folding pathway of an RNA pseudoknot structure was elucidated. Fourth, we presented a physical framework with rigorous free-energy analysis to unravel SpCas9 cleavage activity for optimal guide RNA design in CRISPR/Cas9 genome-engineering technology. Finally, we computationally modeled the structures of RNA aptamers for potential RNA therapeutic applications.
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