Deepak Koirala

Contact Information
Office: MEYR 475D
Phone: 410-455-2512

Assistant Professor

Postdoc – The University of Chicago (2014 – 2020)
Ph.D. – Kent State University (2008 – 2014)
M.Sc. – Tribhuvan University, Nepal (2002 – 2004)
B.Sc. – Tribhuvan University, Nepal (1999 – 2002)

Professional Interests

RNA structures, functions and consequences

Research in our group focuses on understanding the structures and functions of RNA molecules involved in fundamental biological processes and exploring the opportunities for developing RNA-targeted therapeutics to treat both genetic and infectious diseases. Our laboratory interconnects biochemistry, biophysics and biology, providing the members of our laboratory an excellent opportunity to learn a wide array of both biochemical and biophysical techniques while pursuing cutting-edge research in the field of RNA structural biology. Followings are the current research directions in our laboratory.

Strategies of chaperone assisted RNA crystallography using synthetic antibodies

RNA structures associated with cap-independent viral translation 

In contrast to the 5ꞌ-cap-based canonical translation in most eukaryotes, many viral genomes and a subset of cellular mRNAs are translated via cap-independent mechanisms that involve structured RNA elements such as internal ribosome entry sites (IRESs) and 3ꞌ cap-independent translation elements (3ꞌ-CITEs). However, our understanding on how these RNA structures are organized and how they recognize translation initiation factors or the ribosome remains largely elusive. Our laboratory is focused on determining the 3-dimensional structures of RNA elements associated with the viral cap-independent translation and understanding how these structures hijack the canonical, cap-dependent translation machinery from the host cell to mediate and regulate the non-canonical, cap-independent viral translation.

RNA structure-based strategies of translation in cellular mRNAs and viral genomes

RNA structures associated with human repeat expansion disorders

Besides the mechanisms that involve mutant proteins expressed from the mRNAs with expanded nucleotide repeats, pathogenic pathways in human disorders such as huntington’s disease, myotonic dystrophy fragile-X syndrome and amyotrophic lateral sclerosis also involve RNA-related toxicity induced by the RNA structures of the corresponding mRNAs. However, our understanding on the structures formed by these mRNAs and their specific roles in pathogenesis remains elusive. Our laboratory is focused on developing the strategies to study the structural elements in both protein-coding and non-coding regions of these mRNAs and their contributions to the disease pathogenesis. We use synthetic antibodies that specifically bind the RNA structures formed by the expanded mRNAs to investigate their structures, cellular locations and life-cycles.

Outcomes of our research will not only provide insights into the mechanisms of fundamental biological processes but also unlock ample opportunities for developing targeted therapeutics to treat both genetic and infectious diseases. Moreover, structural understanding on the landscape of RNA structures combined with mechanistic insights into how particular structural features enable the biological function will be tremendously useful for developing algorithms to predict new RNA structures using bioinformatics and computational tools.

Selected Publications

Krochmal D., Shao Y., Li N.S., DasGupta S., Shelke S.A., Koirala D.*, Piccirilli J.A.*, Structural basis for substrate binding and catalysis by a self-alkylating ribozyme, Nat. Chem. Biol. (2022),

Roman C., Lewicka A., Koirala D., Li N.S., Piccirilli J.A., The SARS-CoV-2 programmed -1 ribosomal frameshifting element crystal structure solved to 2.09 Å using chaperone-assisted RNA crystallography, ACS Chem. Biol. 16, 1469-1481, 2021

Koirala D., Lewicka A., Koldobskaya Y., Huang H. & Piccirilli J.A., Synthetic antibody binding to a preorganized RNA domain of hepatitis C virus internal ribosome entry site inhibits translation, ACS Chem. Biol., 15, 1, 205-216, 2020

Koirala D., Shao Y., Koldobskaya Y., Fuller J. R., Watkins A.M., Shelke S.A., Pilipenko E.V., Das R., Rice P.A. & Piccirilli J. A., A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites, Nat. Commun., 10:3629, 2019

Koirala D., Shelke S.A., Dupont M., Ruiz S., Dasgupta S., Bailey L.J., Benner S.A. & Piccirilli J.A., Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography, Nucleic Acids Res., 46(5), 2624 – 2635, 2018

Koirala D., Shrestha P., Emura T., Hidaka K., Mandal S., Masayuki E., Sugiyama H. & Mao H., Single-molecule mechanochemical sensing using DNA origami nanostructures, Angew. Chem. Int. Ed. Engl., 2014, 53, 8137 – 8141 (Journal’s Cover Story)

Koirala D., Punnoose J.A., Shrestha P. & Mao H., Yoctoliter thermometry for single-molecule investigations: a generic bead-on-a-tip temperature-control module, Angew. Chem. Int. Ed. Engl., 2014, 53, 3470 – 3474 (Journal’s Cover Story & Highlights in Nat. Nanotechnology)

Koirala D., Ghimire C., Bohrer C., Sannohe Y., Sugiyama H. & Mao H., Long-loop G-quadruplexes are misfolded population minorities with fast transition kinetics in human telomeric sequences, J. Am. Chem. Soc., 2013,  135, 2235 − 2241

Koirala D, Dhakal S., Ashbridge B., Sannohe Y., Rodriguez R., Sugiyama S., Balasubramanian S. & Mao H.,  A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands, Nat. Chem., 2011, 3, 782-787 (Highlights in Nature News & Views)

Koirala D., Yu Z., Dhakal S. & Mao H., Detection of single nucleotide polymorphism using tension-dependent stochastic behavior of a single-molecule template, J. Am. Chem. Soc., 2011, 133, 9988-91

Honors and Awards

Jay and Taylor Graduate Research Award, Kent State University (2013)

Graduate Student Senate (GSS) Domestic Travel Grant, Kent State University (2013)

University Fellowship Award, Kent State University (2012)

Amrit and P.M. Singh Gold Medals, Tribhuvan University, Nepal (2005)

Harihar Raj Lohani Award, Nepal Chemical Society, Nepal (2003)

University Scholarship, Tribhuvan University, Nepal (1999 – 2004)

Courses Teaching

CHEM 437 Comprehensive Biochemistry I (Fall)
CHEM 490/CHEM 684 RNA Structure and Function (Spring)