Publications
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2024 # represents Undergrad Students
G-Quadruplex Structure in the ATP-Binding DNA Aptamer Strongly Modulates Ligand Binding Activity, Aleah N. Edwards, Alexandria N. Iannucci, Jacob VanDenBerg, Tommie Rice, Srishty Sethi, Soma Dhakal, and Philip M. Yangyuoru, ACS Omega, 2024, Link
2023
Roaa Mahmoud, Jagan Kalivarathan, Abdul J. Castillo, #Sasha Wang, Brian Fuglestad, Mazhar A. Kanak & Soma Dhakal, Aptabinding of tumor necrosis factor-α (TNFα) inhibits its proinflammatory effects and alleviates islet inflammation, Biotechnology Journal, 2023 Accepted, (link)
Godfred O. Sabbih, Kalani M. Wijesinghe, Chamika Harshani Algama, Soma Dhakal & Michael K. Danquah, Computational generation and characterization of IsdA-binding aptamers, Biotechnology Journal, 2023, (link)
Kalani M. Wijesinghe, Godfred Sabbih, Chamika Harshani Algama, #Rida Syed, Michael K. Danquah, & Soma Dhakal, FRET-based single-molecule detection of pathogen-protein IsdA using computationally selected aptamers, Anal. Chem., 2023, 95, 26, 9839–9846 (link)
†Kaur, A., †Mahmoud, R., Megalathan, A., #Pettit, S. & Dhakal, S. Multiplexed smFRET nucleic acid sensing using DNA nanotweezers, Biosensors, 2023, 13, 119 (link) † Co-first author
2022
Multiplexed and recyclable single-molecule sensors for quantitative analysis of nucleic-acid biomarkers, US Patent, 2022, US11441182B2, Status: Patent Granted (link)
Mahmoud, R. & Dhakal, S. Single-molecule analysis of DNA branch migration under biomimetic environments, J. Phys. Chem. B, 2022, 126, 38, 7252–7261 (link)
Ghimire, M., Gibbs, D., Mahmoud, R., Dhakal, S. & Reiner, J. Nanopore analysis as a tool for studying rapid Holliday junction dynamics and analyte binding, Analytical Chemistry, 2022, 94, 28, 10027–10034 (link)
Wijesinghe, K.M., Kanak, M. A., Chuck Harrell, J. & Dhakal, S. Single-molecule sensor for high-confidence detection of miRNA, ACS Sensors, 2022, 7, 4, 1086–1094 (link)
2021
Kaur, A., #Ellison, M. & Dhakal, S. MASH FRET: A simplified approach for single-molecule multiplexing using FRET, Anal. Chem. 2021, 93, 25, 8856–8863 (link)
Gibbs, D.R., Mahmoud, R., Kaur, A. & Dhakal, S. Direct unfolding of RuvA-HJ complex [using optical tweezers] at the single-molecule level, Biophysical Journal, 2021, 120, 10, 1894-1902 (link)
†Megalathan, A., †Wijesinghe, K. M., & Dhakal, S. Single-molecule FRET-based dynamic DNA sensor, ACS Sensors, 2021,6, 3, 1367–1374 (link) † Co-first author
Megalathan, A., Wijesinghe, K. M., #Ranson, L. & Dhakal, S. Single-molecule analysis of nanocircle-embedded i-motif under crowding, J. Phys. Chem. B, 2021, 125, 9, 2193–2201 (link)
2020
Sapkota, K. & Dhakal S. FRET-Based Aptasensor for the Selective and Sensitive Detection of Lysozyme, Sensors., 2020, 20, 914 (link)
Kaur, A. & Dhakal S. Recent applications of FRET-based multiplexed techniques, Trends Anal. Chem., 2020, 123, 115777 (link)
2019
Gibbs, D.R. & Dhakal, S. Homologous Recombination under the Single Molecule Fluorescence Microscope, Int. J. Mol. Sci., 2019, 20, 6102 (link)
Sapkota, K., Kaur, A., Megalathan, A., #Donkoh-Moore, C. & Dhakal, S. Single-step FRET-based detection of femtomoles DNA, Sensors, 2019, 19, 3495 (link)
Megalathan, A., Cox, B.D., Wilkerson, P.D., Kaur, A., Sapkota K., Reiner, J.E. & Dhakal, S. Single molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles, Nucleic Acids Research, 2019, 47, 7199–7212 (link)
Kaur, A., Sapkota K. & Dhakal, S. Multiplexed nucleic acid sensing with single-molecule FRET, ACS Sensors, 2019, 4, 623 – 633 (link)
2018
Gibbs, D.R., Kaur, A., Megalathan, A., Sapkota K. & Dhakal, S. Build your own microscope: Step-by-step guide for building a prism-based TIRF microscope, Methods & Protocols, 2018, 1, 40 (link)
Gibbs, D.R. & Dhakal, S. Single-molecule imaging reveals conformational manipulation of Holliday junction DNA by the junction processing protein RuvA. Biochemistry, 2018, 57, 3616-3624 (link)
Valero, J., Pal, N., Dhakal, S., Walter N.G., & Famulok, M. A bio-hybrid DNA rotor/stator nanoengine that moves along predefined tracks. Nature Nanotechnology, 2018, 13, 496–503 (link) See highlight in ScienceDaily
Before Joining VCU
Fu, J., Yang, YR, Dhakal, S. Zhao, Z., Liu, M., Zhang, T., Walter N.G., and Yan, H. Assembly of multienzyme complexes on DNA nanostructures. Nature Protocols, 2016, 11, 2243-2273
Dhakal, S. Adendorff, M., Liu, M., Yan, H., Bathe, M. & Walter N.G. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. Nanoscale, 2016, 8, 3125-3137.
Zhao, Z., Fu, J., Dhakal, S., Johnson-Buck, A., Liu, M., Zhang, T., Woodbury, N., Liu, Y., Walter, N.G. & Yan, H. Nano-caged enzymes with enhanced activity and stability. Nature Commun., 2016, 7, 10619. See highlight of this publication in phys.org.
Mallik, L.┴, Dhakal, S.┴, Nichols, J., Mahoney, J., Dosey, A. M., Jiang, S., Sunahara, R. K., Skiniotis, G. & Walter, N. G. Electron microscopic visualization of protein assemblies on flattened DNA origami. ACS Nano, 2015, 9, 7133-7141.┴Co-first author
Widom. JR., Dhakal, S., Heinicke, LA., Walter, N. G. Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Archives of toxicology, 2014, 88, 1965-1985.
Shrestha, P., Xiao, S., Dhakal, S., Tan, Z. & Mao, H. Nascent RNA transcripts facilitate the formation of G-quadruplexes, Nucleic acids research, 2014, 42, 7236-7246
Cui, Y., Koirala, D., Kang, H., Dhakal, S., Yangyuoru, P., Hurley, LH. and 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 Research, 2014, 42, 5755-5764. See highlight of this publication in Chemical & Engineering News.
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 Research, 2013, 41, 3915–3923.
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. doi:10.1371/journal.pone.0039271.
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. Biophysical Journal, 2012, 102, 2575–2584.
Dhakal, S., Mao, H., Rajendran, A., Endo, M., Sugiyama, H., Eds: Spindler L, Spada G. P, Haider S, Silva M. W. D, Fritzsche W. “G-quadruplex nanostructures probed at the single molecular level by force-based methods” in guanine quartets: structure and application. Royal Society of Chemistry Publishing, 2012, UK.
Koirala, D., Dhakal, S., Ashbridge, B., Sannohe, Y., Rodriguez, R., Sugiyama, H., Balasubramanian, S. & Mao. H. Single-Molecule Platform for Investigation of G-quadruplex and Ligand Interactions. Nature Chemistry, 2011, 3, 782-787. See highlight of this publication in Nature News & Views.
Dhakal, S., Yu, Z., Konik, R., Koirala, D. & Mao, H. Formation of human ILPR G-quadruplex in dsDNA. International Review of Biophysical Chemistry, 2011, 2, N. 6.
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 molecular level. J. Am. Chem. Soc., 2010, 132, 8991–8997.
Yu, Z., Schonhoft, JD., Dhakal, S., Bajracharya, R., Hegde, R., Basu S. & Mao, H. ILPR G-quadruplexes formed in seconds demonstrate high mechanical stabilities. J. Am. Chem. Soc., 2009, 131, 1876–1882.
Schonhoft, JD., Bajracharya, R., Dhakal, S., Yu, Z., Mao, H. & Basu S. Direct experimental evidence for quadruplex-quadruplex interaction within the human ILPR. Nucleic Acids Research, 2009, 37, 3310–3320.