Hello,

I am Deepak Koirala, principal investigator (PI) of the Koirala Lab at UMBC. Our group has a team of dedicated, dynamic and diligent researchers working 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.

Please browse through our website for more information on latest news, events, research and publications. Should you have any questions or need additional information regarding me and our lab, please feel free to email me at dkoirala@umbc.edu or stop by my office (Meyerhoff 475D) and the lab (Meyerhoff 456 & 460).

Curriculum Vitae

Deepak Koirala, Ph.D.

1000 Hilltop Circle, Baltimore, MD 21250

Department of Chemistry & Biochemistry, University of Maryland Baltimore Country (UMBC)

(+1) 410 455 2512 (office), dkoirala@umbc.edu

POSITIONS

Assistant Professor

University of Maryland Baltimore County (UMBC), Department of Chemistry & Biochemistry (August 2020 – Present)

Research – RNA structure and function, RNA structures associated with viral translation and human repeat expansion disorders

Postdoctoral Scholar

University of Chicago, Department of Biochemistry & Molecular Biology (April 2014 – August 2020)

Advisor – Prof. Joseph A. Piccirilli

Research – Chaperone-assisted RNA crystallography, RNA-antibody interaction, in vitro selection of RNA against synthetic antibody, phage display selection of antibody against RNA

EDUCATION

Doctor of Philosophy (Ph.D.)

Kent State University, Department of Chemistry & Biochemistry (August 2008 – March 2014)

Advisor – Prof. Hanbin Mao

Dissertation – Mechanochemistry, transition dynamics and ligand-induced stabilization of human telomeric G-quadruplexes at single-molecule level

Research – Single-molecule optical tweezers, biophysical analysis of unusual DNA & RNA structures, single-molecule biosensing, DNA nanotechnology, microfluidics

Master of Science (M.Sc.)

Tribhuvan University, Central Department of Chemistry, Kathmandu, Nepal (2002 – 2004)

Advisor – Prof. Raja Ram Pradhananga

Dissertation – Studies on the determination of fluoride using ion selective electrode

Bachelor of Science (B.Sc.)

Tribhuvan University, Patan Multiple Campus, Lalitpur, Nepal (1999 – 2001)

TEACHING

Instructor – Chem 490 & Chem 684 – RNA Structure & Function, Fall 2020, Department of Chemistry & Biochemistry, UMBC

Teaching Assistant – Undergraduate Labs, General Chemistry I & II, 2008 – 2014, Department of Chemistry & Biochemistry, Kent State University

Assistant Lecturer – M. Sc. Chemistry, 2006 – 2008, Central Department of Chemistry, Tribhuvan University, Kathmandu, Nepal

Chemistry Instructor – Grades 11 & 12, 2005 – 2008, United Academy, Lalitpur, Nepal

Assistant Lecturer – B. Sc. Chemistry, 2005 – 2006, Amrit Science Campus, Tribhuvan University, Kathmandu, Nepal

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)

PUBLICATIONS

Postdoctoral Research

Koirala D., Lewicka A., Koldobskaya , 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 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

Shelke S.A., Shao Y., Laski A., Koirala D., Weissman B.P., Fuller J.R., Tan X., Constantin T.P., Waggoner A.S., Bruchez M.P., Armitage B.A. & Piccirilli J.A., Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif, Commun., 9:4542, 2018

Ph.D. Research

Koirala D., Shrestha P., Emura T., Hidaka K., Mandal S., Masayuki E., Sugiyama H. & Mao H., Single-molecule mechanochemical sensing using DNA origami nanostructures, 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, Chem. Int. Ed. Engl., 2014, 53, 3470 – 3474 (Journal’s cover story & research 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., Mashimo T., Sannohe Y., Yu Z., Mao H. & Sugiyama H., Intramolecular folding in three tandem guanine repeats of human telomeric DNA, Commun., 2012, 48, 2006 – 2008

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, Chem., 2011, 3, 782-787 (highlighted 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, Am. Chem. Soc.,2011, 133, 9988-91

Shrestha P., Emura T., Koirala D., Cui Y., Hidaka K., Maximuk W.J., Endo M., Sugiyama H. & Mao H., Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores, Nucleic Acids Res., 2016, 44 (14), 6574-6582

Mandal S., Koirala D., Selvam S., Ghimire C. & Mao H., A molecular tuning fork in single-molecule mechanochemical sensing, Chem. Int. Ed. Engl., 2015, 54(26):7607 – 11

Jiang H.X., Cui Y., Zhao T., Fu H.W., Koirala D., Punnoose J.A., Kong D.M. & Mao H., Divalent cations and molecular crowding buffers stabilize G-triplex at physiologically relevant temperatures, Rep., 2015, 5:9255

Punnoose J.A., Cui Y.,Koirala D., Yangyuoru P.M., Ghimire C., Shrestha P. & Mao H., Interaction of G-quadruplexes in the full-length 3′ human telomeric overhang, Am. Chem. Soc., 2014, 136, 18062 – 18069

Selvam S.,Koirala D., Yu Z., & Mao H., Quantification of topological coupling between DNA superhelicity and G-quadruplex formation, Am. Chem. Soc., 2014, 136, 13967-13970

Cui Y., Koirala D., Kang H.J., Dhakal S., Yangyuoru P.M., Hurley L. H. & Mao H., Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL, Nucleic Acids Res., 2014, 42, 5755 – 5764 (featured story in Chemical & Engineering News)

Ghimire C., Koirala D., Mathis M.B., Kooijman E.E. & Mao H., Controlled particle collision leads to direct observation of docking and fusion of lipid droplets in an optical trap, Langmuir, 2014, 30, 1370−1375 (key scientific article in Global Medical Discovery)

Yangyuoru P.M., Zhang A.Y., Shi Z., Koirala D., Balasubramanian S. & Mao H., Mechanochemical properties of individual human telomeric RNA (TERRA) G-quadruplexes, ChemBioChem, 2013, 14, 1931 – 1935

Dhakal S., Cui Y., Koirala D., Ghimire C., Kushwaha S., Yu Z., Yangyuoru P.M. & Mao H., Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions, Nucleic Acids Res., 2013, 41, 3915 – 3923

Yu Z., Koirala D., Cui Y., Easterling L.F., Zhao Y. & Mao H., Click-chemistry assisted single-molecule fingerprinting reveals a 3D biomolecular folding funnel, Am. Chem. Soc.,2012, 134, 12338 – 12341

Yangoru P.M., Dhakal S., Yu Z., Koirala D., Mwongela S.M. & Mao H., Single-molecule measurements of the binding between small molecules and DNA aptamers, Chem., 2012, 84, 5298 – 5303

Dhakal S., Yu Z., Konik R., Cui Y., Koirala D. & Mao H, G-quadruplex and i-motif are mutually exclusive in double stranded ILPR DNA, Biophys J., 2012, 102, 2575 – 2584

Dhakal S., Lafontaine J.L., Yu Z., Koirala D. & Mao H., Intramolecular folding in human ILPR fragment with three C-rich repeats, PLoS ONE, 2012, 7(6): e39271

Dhakal S., Schonhoft J.D., Koirala D., Yu Z., Basu S. & Mao H., Coexistence of an ILPR i-motif and a partially folded structure with comparable mechanical stability revealed at single-molecule level, Am. Chem. Soc., 2010, 132, 8991 – 8997

Reviews, Conference Proceedings & Patents

Koirala D., Yangyuoru P.M. & Mao H., Mechanical affinity as a new metrics to evaluate binding events, Anal. Chem., 2013, 32, 197 – 208 (invited, peer-reviewed)

Dhakal S., Yu Z., Konik R., Koirala D. and Mao H., Formation of human ILPR G-quadruplex in dsDNA, Re. Bi. C., 2011, 2,191 – 192

Mao H., Koirala D., Sugiyama H., & Endo M., Mechanochemical sensing methods using DNA origami nanostructures, U.S. Patent 10690685

Mao H., & Koirala D., Devices and methods for detecting single nucleotide polymorphisms, U.S. Patent Application No. 13/485, 201, 2012

PRESENTATIONS

Biomotors, Virus Assembly and Nanotechnology, Columbus Ohio, July 2019: 20-minute talk on “Applications of anti-RNA antibodies for crystallography of viral RNA domains and beyond”

Nucleosides, Nucleotides and Nucleic Acids Gordon Research Conference, Salve Regina University, Rhode Island, June 2019: 15-minute talk on “Applications of anti-RNA antibodies for RNA crystallography and beyond”

23rd Annual Meeting of RNA Society, University of California, Berkeley, June 2018: 10-minute talk on “Crystal structure of an essential RNA domain from IRES of hepatitis A virus in complex with a synthetic antibody fragment”

Chicagoland RNA Club meeting, University of Chicago, March 2018: 30-minute talk on “New RNA structures using Fabs as crystallization chaperones”

Chemistry-Biology Interface Training Program, University of Chicago, October 2015: 30-minute talk on “Maturation of Fab-RNA binding affinity for chaperone-assisted RNA crystallization (CARC)”

Nucleosides, Nucleotides and Nucleic Acids Gordon Research Conference, Salve Regina University, Rhode Island, July 2013: 15-minute talk on “Dynamics of the structures formed in human telomeric DNA oligomers revealed by single-molecule optical-tweezers measurements

General assembly, Nepal Chemical Society, Kathmandu, Nepal, 2005

30-minute talk on “Studies on the determination of fluoride using ion selective electrode”

Department of Biochemistry & Molecular Biology, University of Chicago, Annual Retreat, Galena IL, October 2017: Poster presentation on “Optimization of a portable Fab – RNA module for chaperone-assisted RNA crystallography”

American Chemical Society – Student Chapter, Kent State University and Stark State College, Second Annual Honors Week Poster Session, Kent, OH, April 2014: Poster presentation on “Controlled particle collision leads to direct observation of docking, hemifusion, and full fusion of lipid droplets in an optical trap”

Pittcon Conference, Philadelphia, PA, March 2013: Poster presentation on “Single-molecule measurements of the binding between small molecules and DNA aptamers”

LEADERSHIP AND SERVICE

President, Nepalese Students Association at Kent State University, 2012 – 2013

Vice-President, Nepalese Students Association at Kent State University, 2008 – 2009

Chief Election Commissioner, Chemistry Students Association, Tribhuvan University, Nepal, 2003 – 2004

Coordinator, Spectrum – Annual Science Magazine, Tribhuvan University, Nepal, 2003 – 2004

PROFESSIONAL MEMBERSHIPS

RNA Society, Nepal Chemical Society