|PhD||Physics||University of California, San Diego||San Diego, Calif.|
Prediction of RNA structure and functions and computational design of RNA-based therapeutic strategies.
We develop computer models for biomolecular structure and function with focus on RNA molecules. Biological molecules are large organic molecules composed of hundreds or thousands of atoms bound together by covalent bonds into a chain-like structure. One of the best known challenges in biology is to understand how biomolecules fold properly into compact structures to perform biological functions and how they misfold to cause disease. We develop computational methods to study RNA folding, predict RNA 3D structures, and model RNA-small molecule and RNA-metal ion interactions, RNA in vivo folding kinetics, and cellular functions at the level of gene expression and regulation. Furthermore, through collaborations with experimental labs, we design RNA-based therapeutic strategies involving aptamer binding and CRISPR-Cas9 gene editing.
Notable Honors and Service
- Fellow, American Association for the Advancement of Science, 2018
- Curators Distinguished Professor, University of Missouri System, 2018
- Founding Council Member: International Society of RNA Nanotechnology and Nanomedicine (ISRNN), 2017
- Fellow, American Physical Society, 2013
Zhang D, Hurst T, Duan D, Chen SJ. (2019). Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. Proc Natl Acad Sci U S A. 116(18):8693-8698. doi: 10.1073/pnas.1820523116. [PubMed]
Hurst T, Xu X, Zhao P, Chen SJ. (2018). Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. J Phys Chem B. 122(18):4771-4783. doi: 10.1021/acs.jpcb.8b00575. [PubMed]
Zhang D, Chen SJ. (2018). IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding. J Chem Theory Comput. 14(4):2230-2239. doi: 10.1021/acs.jctc.7b01228. [PubMed]
Sun LZ, Heng X, Chen SJ. (2017). Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation. Front Mol Biosci. 4:92. doi: 10.3389/fmolb.2017.00092. eCollection 2017. Review. [PubMed]
Kranawetter C, Brady S, Sun L, Schroeder M, Chen SJ, Heng X. (2017). Nuclear Magnetic Resonance Study of RNA Structures at the 3′-End of the Hepatitis C Virus Genome. Biochemistry. 56(37):4972-4984. doi: 10.1021/acs.biochem.7b00573. [PubMed]