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Deepak Koirala

TitlePost Doctoral Scholar
InstitutionUniversity of Chicago
DepartmentBiochem/Mol Bio
AddressChicago IL 60637
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    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA. Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation. ACS Chem Biol. 2020 01 17; 15(1):205-216. PMID: 31765566.
      View in: PubMed
    2. Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun. 2019 08 09; 10(1):3629. PMID: 31399592.
      View in: PubMed
    3. Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun. 2018 10 31; 9(1):4542. PMID: 30382099.
      View in: PubMed
    4. Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA. Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography. Nucleic Acids Res. 2018 03 16; 46(5):2624-2635. PMID: 29309709.
      View in: PubMed
    5. Shrestha P, Emura T, Koirala D, Cui Y, Hidaka K, Maximuck WJ, Endo M, Sugiyama H, Mao H. Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores. Nucleic Acids Res. 2016 08 19; 44(14):6574-82. PMID: 27387283.
      View in: PubMed
    6. Mandal S, Koirala D, Selvam S, Ghimire C, Mao H. A molecular tuning fork in single-molecule mechanochemical sensing. Angew Chem Int Ed Engl. 2015 Jun 22; 54(26):7607-11. PMID: 25960021.
      View in: PubMed
    7. Jiang HX, Cui Y, Zhao T, Fu HW, Koirala D, Punnoose JA, Kong DM, Mao H. Divalent cations and molecular crowding buffers stabilize G-triplex at physiologically relevant temperatures. Sci Rep. 2015 Mar 19; 5:9255. PMID: 25787838.
      View in: PubMed
    8. Abraham Punnoose J, Cui Y, Koirala D, Yangyuoru PM, Ghimire C, Shrestha P, Mao H. Interaction of G-quadruplexes in the full-length 3' human telomeric overhang. J Am Chem Soc. 2014 Dec 31; 136(52):18062-9. PMID: 25438191.
      View in: PubMed
    9. Selvam S, Koirala D, Yu Z, Mao H. Quantification of topological coupling between DNA superhelicity and G-quadruplex formation. J Am Chem Soc. 2014 Oct 08; 136(40):13967-70. PMID: 25216033.
      View in: PubMed
    10. Koirala D, Shrestha P, Emura T, Hidaka K, Mandal S, Endo M, Sugiyama H, Mao H. Single-molecule mechanochemical sensing using DNA origami nanostructures. Angew Chem Int Ed Engl. 2014 Jul 28; 53(31):8137-41. PMID: 24931175.
      View in: PubMed
    11. Cui Y, Koirala D, Kang H, Dhakal S, Yangyuoru P, Hurley LH, 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 May; 42(9):5755-64. PMID: 24609386.
      View in: PubMed
    12. Koirala D, Punnoose JA, 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 Mar 24; 53(13):3470-4. PMID: 24596309.
      View in: PubMed
    13. Ghimire C, Koirala D, Mathis MB, Kooijman EE, Mao H. Controlled particle collision leads to direct observation of docking and fusion of lipid droplets in an optical trap. Langmuir. 2014 Feb 11; 30(5):1370-5. PMID: 24447288.
      View in: PubMed
    14. Yangyuoru PM, Zhang AY, Shi Z, Koirala D, Balasubramanian S, Mao H. Mechanochemical properties of individual human telomeric RNA (TERRA) G-quadruplexes. Chembiochem. 2013 Oct 11; 14(15):1931-5. PMID: 24038851.
      View in: PubMed
    15. Adhikari S, Sathian B, Koirala DP, Rao KS. Profile of children admitted with seizures in a tertiary care hospital of Western Nepal. BMC Pediatr. 2013 Mar 27; 13:43. PMID: 23536998.
      View in: PubMed
    16. Dhakal S, Cui Y, Koirala D, Ghimire C, Kushwaha S, Yu Z, Yangyuoru PM, Mao H. Structural and mechanical properties of individual human telomeric G-quadruplexes in molecularly crowded solutions. Nucleic Acids Res. 2013 Apr 01; 41(6):3915-23. PMID: 23396442.
      View in: PubMed
    17. 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 Feb 13; 135(6):2235-41. PMID: 23327686.
      View in: PubMed
    18. Yu Z, Koirala D, Cui Y, Easterling LF, Zhao Y, Mao H. Click chemistry assisted single-molecule fingerprinting reveals a 3D biomolecular folding funnel. J Am Chem Soc. 2012 Aug 01; 134(30):12338-41. PMID: 22799529.
      View in: PubMed
    19. Dhakal S, Lafontaine JL, Yu Z, Koirala D, Mao H. Intramolecular folding in human ILPR fragment with three C-rich repeats. PLoS One. 2012; 7(6):e39271. PMID: 22761750.
      View in: PubMed
    20. Dhakal S, Yu Z, Konik R, Cui Y, Koirala D, Mao H. G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA. Biophys J. 2012 Jun 06; 102(11):2575-84. PMID: 22713573.
      View in: PubMed
    21. Yangyuoru PM, Dhakal S, Yu Z, Koirala D, Mwongela SM, Mao H. Single-molecule measurements of the binding between small molecules and DNA aptamers. Anal Chem. 2012 Jun 19; 84(12):5298-303. PMID: 22702719.
      View in: PubMed
    22. Koirala D, Mashimo T, Sannohe Y, Yu Z, Mao H, Sugiyama H. Intramolecular folding in three tandem guanine repeats of human telomeric DNA. Chem Commun (Camb). 2012 Feb 14; 48(14):2006-8. PMID: 22234724.
      View in: PubMed
    23. Koirala D, Dhakal S, Ashbridge B, Sannohe Y, Rodriguez R, Sugiyama H, Balasubramanian S, Mao H. A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands. Nat Chem. 2011 Aug 28; 3(10):782-7. PMID: 21941250.
      View in: PubMed
    24. 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 Jul 06; 133(26):9988-91. PMID: 21639132.
      View in: PubMed
    25. Dhakal S, Schonhoft JD, 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. J Am Chem Soc. 2010 Jul 07; 132(26):8991-7. PMID: 20545340.
      View in: PubMed
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