Group Members - Research: Biosensing - Research: Single-Molecules

Selected Publications


  • "Duplex DNA is Weakened in Nanoconfinement". Sagun Jonchhe, Shankar Pandey, Deepak Karna, Pravin Pokhrel, Yunxi Cui, Shubham Mishra, Hiroshi Sugiyama, Masayuki Endo and Hanbin Mao. JACS. 2020. DOI: 10.1021/jacs.0c01978. see PDF
  • "Detecting the COVID-19". Pravin Pokhrel, Changpeng Hu, Hanbin Mao. Preprints. 2020, 2020040201, doi: 10.20944/preprints202004.0201.v1. see PDF
  • "Chiral Interaction Is a Decisive Factor To Replace D-DNA with L-DNA Aptamers". Xue-Nan Feng, Yun-Xi Cui, Jing Zhang, An-Na Tang, Hanbin Mao and De-Ming Kong. Analytical Chemistry. 2020, 92, 9, 6470-6477, doi: 10.1021/acs.analchem.9b05676. see PDF


  • "Chaperone Assisted Host-Guest Interactions Revealed by Single-Molecule Force Spectroscopy". Shankar Pandey, Dilanka Kankanamalage, Xiao Zhou, Changpeng Hu, Lyle Isaacs, Janarthanan Jayawickramarajah, Hanbin Mao. Journal of the American Chemical Society. 2019, 141, 46, 18385-18389. ja-2019-09019n. see PDF.

  • "Single-Molecule Topochemical Analyses for Large-Scale Multiplexing Tasks". Shankar Mandal, Xiaoqing Zhang, Shankar Pandey, Hanbin Mao. Analytical Chemistry. 2019, 91, 21, 13485-13493. see .PDF

  • "Submolecular dissection reveals strong and specific binding of polyamide-pyridostatin conjugates to human telomere interface". Mandal, Shankar; Kawamoto, Yusuke; Yue, Zhizhou; Hashiya, Kaori; Cui, Yunxi; Bando, Toshikazu; Pandey, Shankar; Mohammed Enamul Hoque, Mohammad Akter Hossain, Sugiyama, Hiroshi; Mao, Hanbin; Nucleic Acid Research, 2019, 47, 3295-3305. see PDF.

  • "Binding of a Telomestatin Derivative Changes Mechanical Anisotropy of Human Telomeric G-quadruplex". Sagun Jonchhe, Chiran Ghimire, Yunxi Cui, Shogo Sasaki, Mason McCool, Soyoung Park, Keisuke Iida, Kazuo Nagasawa, Hiroshi Sugiyama and Hanbin Mao; Angewandte Chemie International Edition, 2019, 58, 877-881, Accepted. DOI: 10.1002/anie.201811046. see PDF.


  • "Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures". Sagun Jonchhe, Shankar Pandey, Tomoko Emura, Kumi Hidaka, Mohammad Akter Hossain, Prakash Shrestha, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao; Proceedings of National Academy of Sciences of USA, 2018, 115 (38), 9539-9544. see PDF.

  • "Random formation of G-quadruplexes in human telomere overhangs leads to a kinetic folding pattern with targetable vacant G-tracts", Jibin Abraham Punnoose; Yue Ma; Mohammed Enamul Hoque; Yunxi Cui; Shogo Sasaki; Athena Huixin Guo; Kazuo Nagasawa; Hanbin Mao; Biochemistry, 2018, 57, 6946-6955. DOI: 10.1021/acs.biochem.8b00957. see PDF.

  • "Mechanical Cooperativity in DNA Cruciform Structures", Shankar Mandal, Sangeetha Selvam, Yunxi Cui, Mohammed Enamul Hoque, and Hanbin Mao; ChemPhysChem 2018, 19, 2627-2634. see PDF.

#See Cover Feature ,

  • "A new concentration jump strategy reveals the lifetime of i-motif at physiological pH without force". Sagun Jonchhe, Prakash Shrestha, Katia Ascencio, Hanbin Mao; Analytical Chemistry, 2018, 90 (5), 3205-3210. see PDF: 10.1021/acs.analchem.7b04661.

  • "Single-molecule mechanochemical pH sensing revealing the proximity effect of hydroniums generated by an alkaline phosphatase". Prakash Shrestha, Yunxi Cui, Jia Wei, Sagun Jonchhe, Hanbin Mao; Analytical Chemistry, 2018, 90, 1718-1724. see PDF.


  • "Quantification of Chemical and Mechanical Effects on the Formation of the G-Quadruplex and i-Motif in Duplex DNA", Sangeetha Selvam, Shankar Mandal, and Hanbin Mao; Biochemistry, 2017, 56, 4616-4625. see PDF here.

# See Cover Story ,

  • "Adaptive and Specific Recognition of Telomeric G-quadruplexes via Polyvalency Induced Unstacking of Binding Units". Jibin Abraham Punnoose, Yue Ma, Yuanyuan Li, Mai Sakuma, Shankar Mandal, Kazuo Nagasawa, Hanbin Mao; Journal of the American Chemical Society, 2017, 139, 7476-7484. PDF here.

  • "Confined Space Facilitates G-quadruplex Formation", Prakash Shrestha, Sagun Jonchhe, Tomoko Emura, Kumi Hidaka, Masayuki Endo, Hiroshi Sugiyama, and Hanbin Mao, Nature Nanotechnology, 2017, 12, 582-588. doi:10.1038/nnano.2017.29. see PDF here.

# See highlighted story from Science Daily

# See another highlighted sotry from Eurekalert


  • "A Mechanosensor Mechanism Controls the G-Quadruplex/i-Motif Molecular Switch in the MYC Promoter NHE III", Caleb Sutherland, Yunxi Cui, Hanbin Mao, Laurence Hurley; Journal of the American Chemical Society, 2016, 138 (42), 14138-14151.see PDF here.

  • "A Pharmacological Chaperone Molecule Induces Cancer Cell Death by Restoring Tertiary DNA Structures in Mutant hTERT Promoters", Hyun-Jin Kang, Yunxi Cui, Holly Yin, Amy Scheid, William Hendricks, Jessica Schmidt, Aleksandar Sekulic, Deming Kong, Jeffrey Trent, Vijay Gokhale, Hanbin Mao, Laurence Hurley; Journal of the American Chemical Society, 2016,138 (41), 13673-13692. see PDF here.

  • "Mechanochemical Sensing of Single and Few Hg (II) Ions Using Polyvalent Principles", Shankar Mandal, Sangeetha Selvam, Prakash Shrestha, Hanbin Mao; Analytical Chemistry, 2016, 88 (19), 9479-9485. see PDF here.

  • "Mechanical Properties of DNA Origami Nanoassemblies are Determined by Holliday Junction Mechanophores." P. Shrestha, T. Emura, K. Deepak, Y. Cui, H. Kumi, William J Maximuck, M. Endo, H. Sugiyama, H. Mao; Nucleic Acids Research (2016), 44, 6574-6582. see PDF here.

  • "Mutually Exclusive Formation of G-quadruplex and i-Motif is a General Phenomenon Governed by Steric Hindrance in Duplex DNA", Yunxi Cui; Deming Kong; Chiran Ghimire; Cuixia Xu; Hanbin Mao. Biochemistry, 2016, 55(15): 2291-9. see PDF here.

  • "Exploded View of Higher Order G-quadruplex Structures through Click-Chemistry Assisted Single-Molecule Mechanical Unfolding", Sangeetha Selvam, Zhongbo Yu, Hanbin Mao; Nucleic Acids Research. 2016, 44: 45-55. see PDF here.


  • "A Molecular Tuning Fork in Single-Molecule Mechanochemical Sensing", Shankar Mandal, Deepak Koirala, Sangeetha Selvam, Chiran Ghimire and Hanbin Mao, Angewandte Chemie International Edition. 2015, 54: 7607-11. see PDF here.

  • "Mechanochemical Sensing: A Biomimetic Sensing Strategy", Prakash Shrestha, Shankar Mandal, and Hanbin Mao, (Invited Review, peer reviewed) ChemPhysChem, 2015, 16:1829-37. see PDF here.

  • "Dual Binding of an Antibody and a Small Molecule Increases the Stability of TERRA G-Quadruplex", Philip M. Yangyuoru, Marco Di Antonio, Chiran Ghimire, Giulia Biffi, Shankar Balasubramanian, Hanbin Mao. Angewandte Chemie International Edition. 2015, 54, 910-913. DOI: 10.1002/anie.201408113, see PDF here.

  • "Dissecting Cooperative Communications in Protein with a High-Throughput Single-Molecular Scalpel", Zhongbo Yu, Yunxi Cui, Sangeetha Selvam, Chiran Ghimire, and Hanbin Mao. ChemPhysChem, 2015, 16, 223-232. see PDF: DOI: 10.1002/cphc.

  • "Divalent cations and molecular crowding buffers stabilize G-triplex at physiologically relevant temperatures", Hong-Xin Jiang, Yunxi Cui, Ting Zhao, Hai-Wei Fu, Deepak Koirala, Jibin Abraham Punnoose, De-Ming Kong, and Hanbin Mao. Scientific Reports. 2015, 5:9255. see PDF.


  • "Interaction of G-quadruplexes in the Full-length 3' Human Telomeric Overhang", Jibin Abraham Punnoose, Yunxi Cui, Deepak Koirala, Philip M. Yangyuoru, Chiran Ghimire, Prakash Shrestha, and Hanbin Mao. Journal of the American Chemical Society, 2014,136 (52), 18062-18069. DOI 10.1021/ja510079u.
  • "Direct Quantification of Loop Interaction and pi-pi Stacking for G-quadruplex Stability at the Sub-molecular Level". Chiran Ghimire, Soyoung Park, Keisuke Iida, Philip M. Yangyuoru, Haruka Otomo, Zhongbo Yu, Kazuo Nagasawa, Hiroshi Sugiyama, and Hanbin Mao. Journal of the American Chemical Society, 2014, 136 (44), 15537-15544. DOI: 10.1021/ja503585h.

  • "Quantification of Topological Coupling between DNA Superhelicity and G-quadruplex Formation". Sangeetha Selvam, Deepak Koirala, Zhongbo Yu, and Hanbin Mao. Journal of the American Chemical Society, 2014, 136, 13967-13970. DOI: See Sangeetha's perspective for this paper soon.

  • "Intermediates Stabilized by Tryptophan Pairs Exist in Trpzip Beta-Hairpins". Zhongbo Yu, Sangeetha Selvam, and Hanbin Mao, Biochemistry, 2014, 53, 5978-5986. DOI:

# Highlighted on the Biochemistry website!

  • "Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures". Deepak Koirala, Prakash Shrestha, Tomoko Emura, Kumi Hidaka, Shankar Mandal, Masayuki Endo, Hiroshi Sugiyama, and Hanbin Mao, Angewandte Chemie International Edition. 2014, 53, 8137-8141. see pdf here.

# See Cover Story from the Journal!

  • "Nascent RNA Transcripts Facilitate the Formation of G-quadruplexes". Prakash Shrestha, Shan Xiao, Soma Dhakal, Zheng Tan, Hanbin Mao, Nucleic Acids Research, 2014;42(11):7236-46. DOI: 10.1093/nar/gku416. See Abstract.
  • "Molecular Population Dynamics of DNA Structures in a Bcl-2 Promoter Sequence is Regulated by Small-molecules and the Transcription Factor hnRNP LL". Yunxi Cui, Deepak Koirala, HyunJin Kang, Soma Dhakal, Philip Yangyuoru, Laurence H. Hurley, and Hanbin Mao. Nucleic Acids Research, 2014, 42, 5755-5764. DOI: 10.1093/nar/gku185.

# See Featured story from Chemical and Engineering News!

  • "Yoctoliter Thermometry for Single-Molecule Investigations: A Generic Bead-on-a-Tip Temperature-Control Module", Deepak Koirala, Jibin Abraham Punnoose, Prakash Shrestha and Hanbin Mao. Angewandte Chemie International Edition. 2014, 53, 3470-3474.

# See Research Highlights from Nature Nanotechnology: SINGLE-MOLECULE THERMOMETRY: A controlled jump

# See Cover Story from the Journal See Personal Account from Deepak soon!

  • "Controlled Particle Collision Leads to Direct Observation of Docking and Fusion of Lipid Droplets in an Optical Trap", Chiran Ghimire, Deepak Koirala, Malcom B. Mathis, Edgar E. Kooijman, and Hanbin Mao. Langmuir, 2014, 30, 1370-1375. see PDF here.

# See Key Scientific Article from Global Medical Discovery.


  • "Mechanochemical Properties of Individual Human Telomeric RNA G-quadruplexes", Philip Yangyuoru, Amy Y.Q. Zhang, Zhe Shi, Deepak Koirala, Shankar Balasubramanian, Hanbin Mao. ChemBioChem, 2013, 14, 1931-1935.

  • "Mechanical Affinity as a New Metrics to Evaluate Binding Events", Deepak Koirala, Philip Yangyuoru, Hanbin Mao (Invited Reveiw, peer reviewed). Reviews in Analytical Chemistry, 2013, 32, 197-208.

  • "Long-Loop G-Quadruplexes are Misfolded Population Minorities with Fast Transition Kinetics in Human Telomeric Sequences". Deepak Koirala, Chiran Ghimire, Christopher Bohrer, Yuta Sannohe, Hiroshi Sugiyama, and Hanbin Mao. Journal of the American Chemical Society, 2013, 135(6): 2235-41. DOI: 10.1021/ja309668t. See pdf.

  • "Structural and Mechanical Properties of Individual Human Telomeric G-quadruplexes in Molecularly Crowded Solutions". Soma Dhakal, Yunxi Cui, Deepak Koirala, Chiran Ghimire, Saurabh Kushwaha, Zhongbo Yu, Philip M. Yangyuoru, and Hanbin Mao. Nucleic Acids Research, 2013, 41, 3915-3923. See pdf and Story for this paper.

  • "Non-B DNA Structures Show Diverse Conformations and Complex Transition Kinetics Comparable to RNA or Proteins - a Perspective from Mechanical Unfolding and Refolding Experiments". Zhongbo Yu and Hanbin Mao. (Invited Review, peer reviewed). Chemical Record, 2013, 13(1):102-16


  • "Click-Chemistry Assisted Single-Molecule Fingerprinting Reveals a 3D Biomolecular Folding Funnel". Zhongbo Yu, Deepak Koirala, Yunxi Cui, Leah F. Easterling, Yuan Zhao, and Hanbin Mao. Journal of the American Chemical Society, 2012, 134, 12338-12341. See pdf.and Story for this paper.

  • "Intramolecular Folding in Human ILPR Fragment with Three C-Rich Repeats". Soma Dhakal, Javonne L Lafontaine, Zhongbo Yu, Deepak Koirala, Hanbin Mao. PLoS ONE. 06/2012; 7(6):e39271. See pdf.
  • "Single-Molecule Measurements of the Binding between Small Molecules and DNA Aptamers." Philip M Yangyuoru, Soma Dhakal, Zhongbo Yu, Deepak Koirala, Simon M Mwongela, Hanbin Mao. Analytical Chemistry, 2012, 84, 5298-5303. See pdf.
  • "G-quadruplex and i-motif are mutually exclusive in double-stranded ILPR DNA", Soma Dhakal, Zhongbo Yu, Ryan Konik, Yunxi Cui, Deepak Koirala, and Hanbin Mao. Biophysical Journal, 2012, 2575-2584. See pdf.
  • "The Tertiary DNA Structure in the Single-Stranded hTERT Promoter Fragment Unfolds and Refolds by Parallel Pathways via Cooperative or Sequential Events", Zhongbo Yu; Vanessa Gaerig; Yunxi Cui; HyunJin Kang; Vijay Gokhale; Yuan Zhao; Laurence Hurley; Hanbin Mao. Journal of the American Chemical Society, 2012, 134, 5157-5164 See pdf and Story for this paper.

  • "Intramolecular folding in three tandem guanine repeats of human telomeric DNA", Deepak Koirala, Tomoko Mashimo, Yuta Sannohe, Zhongbo Yu, Hanbin Mao* and Hiroshi Sugiyama*, Chemical Communications, 2012, 48, 2006-2008. See pdf.


  • "A Single-Molecule Platform for Investigation of Interactions between G-quadruplexes and Small-Molecule Ligands". Deepak Koirala, Soma Dhakal, Beth Ashbridge, Yuta Sannohe, Raphine Rodriguez, Hiroshi Sugiyama, Shankar Balasubramanian, Hanbin Mao*, Nature Chemistry, 2011, 3, 782-787. See story for this paper and pdf.

# See News and Views by Professor Mark Williams, Nature Chemistry, 2011, 3, 754.

  • "Detection of Single Nucleotide Polymorphism Using Tension-Dependent Stochastic Behavior of a Single-Molecule Template". Deepak Koirala, Zhongbo Yu, Soma Dhakal, Hanbin Mao*, Journal of the American Chemical Society, 2011, 133, 9988-91. See Personal Account from Deepak and Story for this paper. See pdf.


  • "Coexistence of an ILPR i-motif and a partially folded structure with comparable mechanical stability revealed at the single molecular level", Soma Dhakal, Joseph Schonhoft, Deepak Koirala, Zhongbo Yu, Soumitra Basu, Hanbin Mao*, Journal of the American Chemical Society, 2010, 132, 8991-8997. See Story for this paper. See pdf.


  • "Direct Experimental Evidence for Quadruplex-Quadruplex Interaction within the Human ILPR", Joseph Schonhoft, Rabindra Bajracharya, Soma Dhakal, Zhongbo Yu, Hanbin Mao*, Soumitra Basu*, Nucleic Acids Research, 2009, 37, 3310-3320. pdf.

  • "ILPR G-quadruplexes Formed in Seconds Demonstrate High Mechanical Stabilities", Zhongbo Yu, Joseph D Schonhoft, Soma Dhakal, Rabindra Bajracharya, Ravi Hegde, Soumitra Basu*, and Hanbin Mao*, Journal of the American Chemical Society, 2009, 131,1876-1882. See Story for this paper. See pdf.

# See comments by Professor Stephen Neidle: Faculty of 1000 Biology J Am Chem Soc.evaluations for Yu Z et al 2009 Feb 11 131 (5):1876-82.

2008 and before

  • "Thermal Probing of E. coli RNA Polymerase Off-Pathway Mechanisms", Yara X Mejia, Hanbin Mao, Nancy R Forde, Carlos Bustamante, Journal of Molecular Biology, 2008. 382, 628-637. pdf.

  • "An Integrated Laser Tweezers Instrument for Microanalysis of Individual Protein Aggregates", Hanbin Mao and Paul Luchette, Sensors and Actuators B, 2008, 129,764-771. pdf.

  • "Microanalysis of Clouding Process at the Single Droplet Level", Paul Luchette, Nebiyu Abiy and Hanbin Mao, Sensors and Actuators B, 2007, 128, 154-160. pdf. Related Patent.


  • "Temperature Control Methods in a Laser Tweezers System", Hanbin Mao, J. Ricardo Arias-Gonzalez, Steve Smith, Ignacio Tinoco Jr. & Carlos Bustamante, Biophysical Journal, 2005, 89:1308-1316. pdf.

  • "High-Throughput Studies of the Effects of Polymer Structure and Solution Components on the Phase Separation of Thermoresponsive Polymers", Hanbin Mao, Chunmei Li, Yanjie Zhang, Steven Furyk, Paul S Cremer, David E Bergbreiter, Macromolecules, 2004, 37, 1031-1036.
  • "Probing the Mechanism of Aqueous Two-Phase System Formation for a-Elastin On-Chip", Yanjie Zhang, Hanbin Mao, Paul S Cremer, Journal of the American Chemical Society, 2003, 125, 15630-15635.
  • "Measuring LCSTs by Novel Temperature Gradient Methods: Evidence for Intermolecular Interactions in Mixed Polymer Solutions", Hanbin Mao, Chunmei Li, Yanjie Zhang, David Bergbreiter, Paul S Cremer, Journal of the American Chemical Society, 2003, 125, 2850-2851.
  • "Investigation of Bivalent Antibody Binding on Fluid Supported Phospholipid Membranes: The Effect of Hapten Density", Tinglu Yang, Olga K. Baryshnikova, Hanbin Mao, Matthew A. Holden, Paul S Cremer, Journal of the American Chemical Society, 2003, 125, 4779-4784.
  • "A Versatile, Sensitive Microfluidic Assay for Bacterial Chemotaxis", Hanbin Mao, Paul Cremer and Michael Manson, Proceedings of National Academy of Sciences of USA, 2003, 100, 5449-5454.
  • "Reusable Platforms for High-Throughput On-Chip Temperature Gradient Assays", Hanbin Mao, Matthew A. Holden, Min You, and Paul S. Cremer, Analytical Chemistry, 2002, 74, 5071-5075.
  • "A Microfluidic Device with a Linear Temperature Gradient for Parallel and Combinatorial Measurements", Hanbin Mao, Tinglu Yang, Paul Cremer, Journal of the American Chemical Society, 2002, 124, 4432-4435.
  • "Design and Characterization of Immobilized Enzymes in Microfluidic Systems", Hanbin Mao, Tinglu Yang, Paul Cremer, Analytical Chemistry, 2002, 74, 379-385.
  • "Fabrication of Phospholipid Bilayer Coated Microchannels for On-Chip Multivalent Immunoassays", Tinglu Yang, Seung-Yong Jung, Hanbin Mao and Paul S. Cremer, Analytical Chemistry, 2001, 73, 165-169.