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 who are 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 genetic and infectious diseases.

Please browse our website for more information on the latest news, events, research and publications. Should you have any questions or need additional information regarding me and our lab, please 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 437 – Comprehensive Biochemistry I, Fall 2021 – Present, Department of Chemistry & Biochemistry, UMBC

Instructor – Chem 490 & Chem 684 – RNA Structure & Function, Fall 2020 – Present, 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

2023                                         CAREER Award, National Science Foundation (NSF)

2023                                         Collaborative Development Award, CRNA

2021                                         Strategic Awards for Research Transitions (START), UMBC

2021                                         Summer Research Faculty Fellowship (SURFF), UMBC

2013                                         Taylor Scholarship for Graduate Research, Kent State University

2013                                         GSS Domestic Travel Grant, Kent State University

2012                                         University Fellowship, Kent State University

2008                                         Pandit Narayan Prasad Upadhaya Award, Nepal Chemical Society

2006                                         P.M. Singh Gold Medal, Tribhuvan University, Nepal

2006                                         Amrit Gold Medal, Tribhuvan University, Nepal

2005                                         Kirti-Sanu Gold Medal, Shesh-Hira Pratisthan, Nepal

2003                                         Harihar Raj Lohani Award, Nepal Chemical Society

1999 – 2004                            University Scholarship, Tribhuvan University, Nepal

RESEARCH SUPPORT & FELLOWSHIPS

2023 – present                         Structural studies of HIV-1 RRE and FSE using Fab-assisted RNA crystallography, NIAID (1U54AI170660), Sub-award SUBK00019302, Center for Structural Biology of HIV RNA                                                               (CRNA) Collaborative Development Award

2023 – present                         Structural and mechanistic studies of cap-independent genome translation in (+)-strand RNA viruses, NIH MIRA R35GM150869

2023 – present                         Structural and mechanistic studies of RNA-mediated enteroviral genome replication, NSF CAREER (MCB-2236996)

2021 – 2022                              Roles of structured RNA elements in viral cap-independent translation, UMBC START, P.I.

2021 – 2022                              Roles of structured RNA elements in viral cap-independent translation, UMBC SURFF, P.I.

2021 – 2022                              Understanding of the 3-Dimensional Structure of an RNA Aptamer RhoBAST, UMBC U-RISE, P.I.

2020 – 2025                             RNA structures, their functions, and therapeutic implications, UMBC Start-up, P.I.

PUBLICATIONS

Since 2020, after joining UMBC (* indicates undergraduates)

  1. Das N.K., Vogt J,* Patel A.,* Al Banna H., Koirala D., Structural basis for a highly conserved RNA-mediated enteroviral genome replication, Nucleic Acids Res., 2024, gkae627.
  2. Ojha M., Vogt J.,* Das N.K., Redmond E.,* Singh K., Al Banna H., Sadat T.,* Koirala D., Structure of saguaro cactus virus 3′ translational enhancer mimics 5′ cap for eIF4E binding, Proceedings of the National Academy of Sciences, 2024, 121 (4), e2313677121.
  3. Al Banna, H., Das, N. K., Ojha, M., Koirala D. Advances in chaperone-assisted RNA crystallography using synthetic antibodies. BBA advances, 2023, 100101.
  4. Das, N. K., Hollmann, N. M., Vogt, J.,* Sevdalis, S. E., Banna, H. A., Ojha, M., Koirala D., Crystal structure of a highly conserved enteroviral 5′ cloverleaf RNA replication element. Commun., 2023, 14(1), 1955.
  5. 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, Chem. Biol., 2022, 18, 376–384 (co-corresponding author).
  6. Rees H.C., Gogacz W., Li N.S., Koirala D., Piccirilli J.A., Structural basis for fluorescence activation by pepper RNA, ACS Chem. Biol. 2022, 17 (7) 1866–1875.
  7. Swain M., Ageeli A.A., Kasprzak W.K., Li M., Miller J.T., Sztuba-Solinska J., Schneekloth J.S., Koirala D., Piccirilli J.A., Fraboni A.J., Murelli R.P., Wlodawer A., Shapiro B.A., Baird N., Le Grice S.F.J., Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands, Nucleic Acids Res., 2021, 49(22):13179-13193.
  8. 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. , 2021, 16, 1469-1481

Before joining UMBC

  1. 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., 2020, 15 (1), 205-216.
  2. 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., 2019, 10:3629.
  3. 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., 2018, 46(5), 2624 – 2635.
  4. 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., 2018, 9:4542.
  5. 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).
  6. 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).
  7. Koirala D., Ghimire C., Bohrer C., Sannohe Y., Sugiyama H. & Mao, Long-loop G-quadruplexes are misfolded population minorities with fast transition kinetics in human telomeric sequences, J. Am. Chem. Soc.,2013,  135, 2235 – 2241.
  8. 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.
  9. 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).
  10. 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.
  11. Shrestha P., Emura T., Koirala D., Cui Y., Hidaka K., Maximuck 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.
  12. 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 – 1.
  13. 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.
  14. 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.
  15. 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.
  16. 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).
  17. 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).
  18. 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.
  19. 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
  20. 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
  21. Yangyuoru 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.
  22. 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.
  23. 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
  24. 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 the single-molecule level, Am. Chem. Soc., 2010, 132, 8991 – 8997
  25. Koirala D., Yangyuoru P.M. & Mao H., Mechanical affinity as a new metric to evaluate binding events, Anal. Chem., 2013, 32, 197 – 208 (invited, peer-reviewed)

Conference Proceedings

  1. Das N.K., Hollmann N., Koirala D., The crystal structure of coxsackievirus 5′ RNA replication platform, Acta Crystallographica A – foundation and advances, 79, A330-A330, 2023.
  2. Ojha M., Redmond E., Koirala D., The crystal structure of a PTE RNA element from a cactus virus that binds human eIF4E, Journal of Biological Chemistry, 299 (3), 104050, 2023.
  3. Al Banna H., Sadat T., Koirala D., Synthetic anti-RNA antibody derivatives for RNA visualization in cells, Journal of Biological Chemistry, 299 (3), 104217, 2023.
  4. Koirala D., Crystal structures of replication-linked RNAs from enteroviral genomes, Acta Crystallographica Section A: Foundations of Crystallography, 79, a156-a156, 2022.
  5. Al Banna H, Das N.K, Koirala D. Structural studies of domain IV RNA from type I picornaviral internal ribosome entry sites, Acta Crystallographica Section A: Foundations of Crystallography, 79, a344-a344, 2022.
  6. Roman C.A., Koirala D. & Piccirilli J.A., Crystalizing Structured RNAs Using a Surface-Entropy-Reduced Fab as a Crystallization Chaperone, Experimental Biology 2020 Meeting Abstracts, The FASEB Journal, 2020.
  7. Dhakal S., Yu Z., Konik R., Koirala D. & Mao H., Formation of human ILPR G-quadruplex in dsDNA, Re. Bi. C., 2, 191 – 192, 2011.

Patents

  1. Mao H., Koirala D., Sugiyama H., & Endo M., Mechanochemical sensing methods using DNA origami nanostructures, U.S. Patent Application No. 15/315, 856, 2015.
  2. Mao H., & Koirala D., Devices and methods for detecting single nucleotide polymorphisms, S. Patent Application No. 13/485, 201, 2012.

PRESENTATIONS

Conference Presentations

  1. Fab-assisted RNA Structure Determination by X-ray Crystallography and CryoEM, American Crystallographic Association 74th Annual Meeting, Denver, July 2024
  2. Understanding RNA Structure-based strategies of viral genome translation and replication, The 2024 FCBIS, UMBC, May 2024
  3. Structural basis for RNA-mediated enteroviral genome replication, 4th conference on Biomotors, Virus assembly and Nanotechnology, Columbus, December 2023
  4. Crystal Structures of replication-linked RNAs from enteroviral genomes, American Crystallographic Association 73rd Annual Meeting, Baltimore, July 2023
  5. Structural basis for RNA-based strategy of enteroviral genome replication, Gordon Research Conference on RNA Nanotechnology, Ventura, January 2023
  6. The crystal structures of replication-linked 5′ cloverleaf RNAs from enteroviral genomes, Pittcon Conference, Philadelphia, March 2022
  7. Structural basis of RNA self-alkylation, 4th International Webinar on Nucleic Acids and CRISPR, February 18-19, 2022
  8. Applications of anti-RNA antibodies for the crystallography of viral RNA domains and beyond, Biomotors, Virus Assembly and Nanotechnology, Columbus, July 2019
  9. Applications of anti-RNA antibodies for RNA crystallography and beyond, Nucleosides, Nucleotides, and Nucleic Acids Gordon Research Conference, Rhode Island, June 2019
  10. Crystal structure of an essential RNA domain from IRES of hepatitis A virus in complex with a synthetic antibody fragment, 23rd Annual Meeting of RNA Society, Berkeley, June 2018
  11. New RNA structures using Fabs as crystallization chaperones, Chicagoland RNA Club Meeting, University of Chicago, March 2018
  12. Single-molecule measurements of the binding between small molecules and DNA aptamers, Pittcon Conference, Philadelphia, March 2013
  13. Dynamics of the structures formed in human telomeric DNA oligomers revealed by single-molecule optical-tweezers measurements, Nucleosides, Nucleotides, and Nucleic Acids Gordon Research Conference, Rhode Island, July 2013
  14. Studies on the determination of fluoride using ion selective electrode, General assembly, Nepal Chemical Society, Nepal, 2005

Other Professional Presentations

  1. Structural plasticity of HIV-1 RRE stem-loop II modulates Rev binding cooperativity and oligomerization, Center for Structural Biology of HIV RNA (CRNA) Science Monthly, July 2024
  2. Non-coding RNA structures associated with viral genome translation and replication, National Institute of Health (NIH), Bethesda, invited seminar, June 2024
  3. Structural Biology of RNA-mediated Viral Genome Replication and Translation, University of California Davis, Department of Biochemistry and Molecular Medicine, invited seminar, June 2024
  4. Structural Studies of HIV-1 RRE Using Fab-assisted RNA Crystallography, Center for Structural Biology of HIV RNA (CRNA) Annual Retreat, University of Michigan, October 2023
  5. Structural basis for RNA-based strategy of enteroviral genome replication, Biochemistry & Molecular Biology Retreat, UMB/UMBC GPLIS, invited seminar, January 2023
  6. Crystal structures of RNA domains that promote viral genome replication and translation, The George Washington University, Department of Chemistry, invited seminar, November 2022
  7. Understanding functional RNA structures using chaperone-assisted X-ray crystallography, Department of Biochemistry and Molecular Biology, UMB, invited seminar, April 2022
  8. RNA crystallography using synthetic antibodies as chaperones, Department of Biophysics, Johns Hopkins University, invited seminar, March 2021
  9. Optimization of a portable Fab – RNA module for chaperone-assisted RNA crystallography, Department of Biochemistry & Molecular Biology, University of Chicago, Annual Retreat, Galena, IL, October 2017
  10. Maturation of Fab-RNA binding affinity for chaperone-assisted RNA crystallization (CARC), Chemistry-Biology Interface (CBI) Training Program, University of Chicago, October 2015
  11. Controlled particle collision leads to direct observation of docking, hemifusion, and full fusion of lipid droplets in an optical trap, American Chemical Society – Student Chapter, Kent State University & Stark State College, Second Annual Honors Week, Kent, OH, April 2014

LEADERSHIP AND SERVICE

2022 – 2024                                Co-chair, Seminar Committee

Fall 2020 – present                      Member, Graduate Recruitment Committee

2022 – present                            Nepalese Students Association at UMBC, Faculty Advisor

Summer 2022 – present            Member, UMB/UMBC Biochemistry Graduate Education Committee

Spring 2024                                Member of Organizing Committee, The FCBIS 2024

Spring 2023                                Member of Organizing Committee at UMBC, Science Olympiad 2023

Fall 2022 – present                    Member, American Crystallographic Association (ACA)

June 2015 – present                  Member, RNA Society

Fall 2022 – present                    Reviewer, NSF Grant Proposals

Fall 2020 – Fall 2022                 Academic Guest Editor, Genes (ISSN 2073-4425), MDPI

Fall 2020 – Present                   Reviewer of the following peer-reviewed journals (since 2020): Nature Communications, Nature Structural & Molecular Biology, Proceedings of National Academy of Science, ACS                                                          Nano, ACS Omega, ACS Biochemistry, MDPI Cells, Frontiers in Molecular Biosciences, Royal Society Open Science, Elsevier Computational and Structural Biotechnology,                                                                          ChemMedChem, The Journal of Visualized Experiments, PLoS One, and Microscopy Research and Technique

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

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

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

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