After Joining UMBC (Undergraduate* & High-School** Student Researchers)

Manju Ojha, Jeff Vogt*, Naba K. Das, Emily Redmond*, Karndeep Singh, Hasan Al Banna, Tasnia Sadat* & Deepak Koirala. “Structure of saguaro cactus virus 3′ translational enhancer mimics 5′ cap for eIF4E binding.” Proceedings of the National Academy of Sciences 121, no. 4 (2024): e2313677121.

Naba K. Das, Nele M. Hollmann, Jeff Vogt*, Spiridon E. Sevdalis, Hasan A. Banna, Manju Ojha & Deepak Koirala, Crystal structure of a highly conserved enteroviral 5′ cloverleaf RNA replication element. Nat Commun 14, 1955 (2023).

Huw C. Rees, Wojciech Gogacz, Nan-Sheng Li, Deepak Koirala, and Joseph A. Piccirilli, Structural Basis for Fluorescence Activation by Pepper RNA, ACS Chemical Biology 2022 17 (7), 1866-1875
DOI: 10.1021/acschembio.2c00290

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, (co-corresponding author).

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., 49(22):13179-13193, 2021

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

Before Joining UMBC (Undergraduate* & High-School** Student Researchers)

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 (Recommended in Faculty Opinions)

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

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

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

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., Yangyuoru P.M. & Mao H., Mechanical affinity as a new metrics to evaluate binding events, Anal. Chem., 2013, 32, 197 – 208

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, Nat. 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.,2012134, 12338 – 12341

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, Anal. 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 the single-molecule level, Am. Chem. Soc., 2010, 132, 8991 – 8997

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