Isaac Li - Single-Molecule Mechanobiology Lab

Publications

We specialize in quantitative single-molecule biophysics and mechanobiology, with a focus on developing cutting-edge methods to visualize and manipulate molecular forces in living cells. Our work includes creating innovative mechanosensitive DNA nanostructures to precisely control cellular motility and mechanosensitivity, as well as advancing high-throughput biophysical assays for drug screening and diagnostics. We are currently focusing on the following 3 areas:

#45

Engineering tunable catch bonds with DNA

M. Yang, D. Bakker, I.T.S. Li*

Nature Communications, 2024, 15, 8828.
#44

Altering cell junctional tension in spheroids through E-cadherin engagement modulation

S.H. Kim, I.T.S. Li*

ACS Applied Biomaterials, 2024, 7, 6, 3766–3776.
#43

Microbial diversity impacts non-protein amino acid production in cyanobacterial bloom cultures collected from Lake Winnipeg

S.L. Bishop, J.T. Solonenka, R.T. Giebelhaus, D. Bakker, I.T.S. Li, S.J. Murch*

Toxins 2024, 16(4), 169.
#42

A single strand: a simplified approach to DNA origami

M. Yang, D. Bakker, D. Raghu, I.T.S. Li*

Frontiers in Chemistry, 2023, 11:1126177.
#41

Super-resolution tension PAINT imaging with a molecular beacon

S.H. Kim, I.T.S. Li*

Angewandte Chemie, 2023, 62(7), e202217028.
#40

The effect of type-2 diabetes conditions on neutrophil rolling adhesion

K. Taverner, Y. Murad, A. Yasunaga, C. Furrer, J. Little, I.T.S. Li*

BMC Research Note, 2022, 15, 355.
#39

Targeting capabilities of native and bioengineered extracellular vesicles for drug delivery

L. Frolova, I.T.S. Li*

Bioengineering, 2022, 9(10), 496.
#38

Surveying life one molecule at a time: Single-molecule methods dig deeper into contemporary biology

S.H. Kim, S Ray, I.T.S. Li*

Frontiers in Molecular Biosciences, 2022, 9:967434.
#37

Mammalian melatonin agonist pharmaceuticals stimulate rhomboid proteins in plants

L.A.E Erland, C.R. Dumigan, J.L. Forsyth, L. Frolova, A.B. Yasunaga, W. Pun, I.T.S. Li, S.J. Murch*

Biomolecules, 2022, 12(7), 882.
#36

Nano-scale particle separation with tilted standing surface acoustic wave — experimental and numerical approaches

E. Taatizadeh, A. Dalili, H. Tahmooressi, N. Tasnim, I.T.S. Li*, M. Hoorfar*

Particle & Particle Systems Characterization, 2022, 39, 2200057.
#35

Neural network-based optimization of an acousto microfluidic system for submicron bioparticle separation

B. Talebjedi, M. Heydari, E. Taatizadeh, N. Tasnim, I.T.S. Li*, M. Hoorfar*

Frontiers in Bioengineering, 2022, 10, 878398.
#34

Imaging molecular adhesion in cell rolling by adhesion footprint assay

S.M. An, S.H. Kim, V.J. White, A.B. Yasunaga, K.M. McMahon, Y. Murad, I.T.S. Li*

JoVE, 2021, (175), e63013.
#33

Tunable metacrylated hyaluronic acid-based hybrid bioinks for stereolithography 3d bioprinting

R.H. Rakin, H. Kumar, F. Menard, I.T.S. Li, K. Kim

Biofabrication, 2021, 13 (4), 044109.
#32

Quantification of fast molecular adhesion by fluorescence footprinting

A. Yasunaga, I.T.S. Li*

Science Advances, 2021, 7 (34), eabe6984.
#31

Micron-sized particle separation with standing surface acoustic wave - experimental and numerical approaches

E. Taatizadeh, A. Dalili, P. Rellstab-Sánchez, H. Tahmooressi, A. Ravishankara, N. Tasnim, H. Najjaran, I.T.S. Li*, M. Hoorfar*

Ultrasonics Sonochemistry, 2021, 76, 105651.
#30

Quantitative interpretation of cell rolling velocity distribution

A. Yasunaga, Y. Murad, V. Kapras, F. Menard, I.T.S. Li*

Biophysical Journal, 2021, 120(12), 2511-2520.
#29

Mechanical flexibility of DNA: a quintessential tool for DNA Nanotechnology

R. Saran, Y. Wang, I.T.S. Li*, Sensors

Sensors, 2020, 20(24), 7019.
#28

Quantifying molecular tension – classifications, interpretations and limitations of force sensors

A. Yasunaga, Y. Murad, I.T.S. Li*

Physical Biology, 2020, 17, 011001.
#27

Quantifying Molecular Forces with Serially Connected Force Sensors

Y. Murad, I.T.S. Li*

Biophysical Journal, 2019, 116 (7), 1282-1291.
#26

Challenges and opportunities in exosome research – perspectives from biology, engineering, and cancer therapy

X. Li, A.L. Corbett, E. Taatizadeh, N. Tasnim, J.P. Little, C. Garnis, M. Daugaard, E. Guns, M. Hoorfar, I.T.S. Li*

APL Bioengineering, 2019, 3, 011503. (Cover)
#25

Direct visualization of location and uptake of applied melatonin and serotonin in living tissues and their redistribution in plants in response to thermal stress

L.A.E. Erland, A. Yasunaga, I.T.S. Li, S.J. Murch, P.K. Saxena

Journal of Pineal Research, 2018, 66(1), 12527.
#24

Minimal Information for Studies of Extracellular Vesicles 2018 (MISEV2018)

C. Thery, et al.

Journal of Extracellular Vesicles, 2018, 7(1), 1535750.
#23

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

J. Fei, M. Jadaliha, T. Harmon, I.T.S. Li, B. Hua, Q. Hao, A.S. Holehouse, M. Reyer, Q. Sun, S.M. Freier, R.V. Pappu, K.V. Prasanth, T. Ha

Journal of Cell Science, 2017, 130, 4180-4192.
#22

Mapping cell surface adhesion by rotation tracking and adhesion footprinting

I.T.S. Li, T. Ha, Y.R. Chemla

Scientific Report, 2017, 44502.
#21

Defining single molecular forces required for notch activation using nano yoyo

F. Chowdhury, I.T.S. Li, T.T.M. Ngo, B.J. Leslie, B.C. Kim, J.E. Sokoloski, E. Weiland, X. Wang, Y.R. Chemla, T.M. Lohman, T. Ha

Nano Letter, 2016, 16(6), 3892-2897.
#20

Constructing modular and universal single molecule tension senor using protein G to study mechano-sensitive receptors

X. Wang, Z. Rahil, I.T.S. Li, F. Chowdhury, D. Leckband, Y. Chemla, T. Ha

Scientific Report, 2016, 6, 21584.
#19

Single molecular force across single integrins dictates cell spreading

F. Chowdhury, I.T.S. Li, B.J. Leslie, S. Doganay, R. Singh, X. Wang, J. Seong, S. Lee, S. Park, N. Wang, T. Ha

Integrative Biology, 2015, 7,1265-1271.
#18

How osmolytes influence hydrophobic polymer conformation: a unified view from experiment and theory

J. Mondal, D. Halverson, I.T.S. Li, G. Stirnemann, G.C. Walker, B.J. Berne

PNAS, 2015, 112(30), 9270-9275.
#17

Synthesis, self-assembly and photophysical properties of oligo(2,5-dihexyloxy-1,4-phenylene vi-nylene)-block-poly(ethylene glycol)

C. Feng, M. J. Gonzalez, Y. Song, I.T.S. Li, G. Zhao, G. Molev, G. Guerin, G.C. Walker, G.D. Scholes, I. Manners, W.A. Winnik

Soft Matter, 2014, 10(44), 8875-8887.
#16

Single polymer studies of hydrophobic hydration

I.T.S. Li, G.C. Walker

Accounts of Chemical Research, 2012, 45(11), 2011-2021.
#15

Polymer Nanomechanics

J.K. Li, I.T.S. Li, G.C. Walker, R.M.A. Sullan, S. Zou,Y. Sun

Polymer Science: A Comprehensive Reference, 2012, 7, 377-404.
#14

Signature of Hydrophobic Hydration in a Single Polymer

I.T.S. Li, G.C. Walker

PNAS, 2011, 108(40), 16527-16532.

Highlights:
www.sciencedebate.com - "Interaction Of Hydrophobic Molecules With Water – New Insights"
PNAS - "Unraveling the hydrophobic effect, one molecule at a time"
Nature - "Biophysics: More than a bystander"
F1000 - Schuler B: 2011. F1000.com/13361033
Virtual Journals - Virtual Journal of Biological Physics Research, 2011, 22 (8)
Water in Biology - "Lum-Chandler-Weeks under the microscope"
C&EN news - "Water Shell Undergoes Structural Changes"
ChemistryViews - "Folding Solution"
Superamolecular Space - "Honing in on hydrophobicity's autograph"
#13

FRep: a fluorescent protein-based bioprobe for in vivo detection of protein:dna interactions

S.H. Shahravan, I.T.S. Li, K. Truong, J.A. Shin

Analytical Chemistry, 2011, 83(24), 9643-9650.
#12

Microdomain orientation of diblock copolymer ultrathin films solvent annealed at low temperatures

C.M. Grozea, I.T.S. Li, D. Grozea, G.C. Walker

Macromolecules, 2011, 44, 3901-3909.
#11

Imaging secondary structure of individual amyloid fibrils of a ß2-microglobulin fragment using near-field infrared spectroscopy

M. Paulite, Z. Fakhaari, I.T.S. Li, N. Gunari, A.E. Tanur, G.C. Walker

JACS, 2011, 133, 7376-7383.
#10

Interfacial free energy governs single polystyrene chain collapse in water and aqueous solutions

I.T.S. Li, G.C. Walker

JACS, 2010, 132(18), 6530-6540.
#9

A computational tool for Monte Carlo simulations of biomolecular reaction networks modeled on physical principles

I.T.S. Li, E. Mills, K. Truong

IEEE Trans. Nanobioscience, 2010, 9(1), 24-30.
#8

FRET evidence that an isoform of caspase-7 binds but does not cleave its substrate

I.T.S. Li, E. Pham, J.Chiang, K.Truong

Biochem. Biophys. Res. Comm., 2008, 373(2), 325-329.
#7

Computational modeling approaches for studying of synthetic biological networks

E. Pham, I.T.S. Li, K. Truong

Current Bioinformatics, 2008, 3(2), 130-141.
#6

Sequence reversed peptide from CaMKK binds to calmodulin in reversible Ca2+-dependent manner

I.T.S. Li, K.R. Ranjith, K. Truong

Biochem. Biophys. Res. Comm., 2007, 352(4), 932-935.
#5

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

I.T.S. Li, W. Shum, K. Truong

BMC Bioinformatics, 2007, 8, 185.
#4

A computational tool for designing FRET protein biosensors by rigid-body sampling of their conformational space

E. Pham, J. Chiang, I.T.S. Li, W. Shum, K. Truong

Structure, 2007, 15(5), 515-523.
#3

Current approaches for engineering proteins with diverse biological properties

I.T.S. Li, E. Pham, K. Truong

Bio-Applications of Nanoparticles, 2007, 620, 18-33.
#2

Protein biosensors based on the principle of fluorescence resonance energy transfer for monitoring cellular dynamics

I.T.S. Li, E. Pham, K. Truong

Biotechnology Letters, 2006, 28(24), 1971-1982.
#1

Creation of circularly permutated yellow fluorescent proteins using fluorescence screening and a tandem fusion template

J. Chiang, I.T.S. Li, K. Truong

Biotechnology Letters, 2006, 28(7), 471-475.

Theses

PhD

Hydrophobic hydration of a single polymer

I.T.S. Li, 2012, PhD Thesis.
MSc

Monte Carlo simulations of biomolecular reaction networks modeled on physical principles

I.T.S. Li, 2007, MSc Thesis.

Random bits

NextGen's tools for the future - Sleep Paper Reader

Science. 2015, 348(6230), 32-35.

Li Lab in single-molecule mechanobiology

Li Lab in single-molecule mechanobiology

Publications

Engineering tunable catch bonds with DNA

Altering cell junctional tension in spheroids through E-cadherin engagement modulation

Microbial diversity impacts non-protein amino acid production in cyanobacterial bloom cultures collected from Lake Winnipeg

A single strand: a simplified approach to DNA origami

Super-resolution tension PAINT imaging with a molecular beacon

The effect of type-2 diabetes conditions on neutrophil rolling adhesion

Targeting capabilities of native and bioengineered extracellular vesicles for drug delivery

Surveying life one molecule at a time: Single-molecule methods dig deeper into contemporary biology

Mammalian melatonin agonist pharmaceuticals stimulate rhomboid proteins in plants

Nano-scale particle separation with tilted standing surface acoustic wave — experimental and numerical approaches

Neural network-based optimization of an acousto microfluidic system for submicron bioparticle separation

Imaging molecular adhesion in cell rolling by adhesion footprint assay

Tunable metacrylated hyaluronic acid-based hybrid bioinks for stereolithography 3d bioprinting

Quantification of fast molecular adhesion by fluorescence footprinting

Micron-sized particle separation with standing surface acoustic wave - experimental and numerical approaches

Quantitative interpretation of cell rolling velocity distribution

Mechanical flexibility of DNA: a quintessential tool for DNA Nanotechnology

Quantifying molecular tension – classifications, interpretations and limitations of force sensors

Quantifying Molecular Forces with Serially Connected Force Sensors

Challenges and opportunities in exosome research – perspectives from biology, engineering, and cancer therapy

Direct visualization of location and uptake of applied melatonin and serotonin in living tissues and their redistribution in plants in response to thermal stress

Minimal Information for Studies of Extracellular Vesicles 2018 (MISEV2018)

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

Mapping cell surface adhesion by rotation tracking and adhesion footprinting

Defining single molecular forces required for notch activation using nano yoyo

Constructing modular and universal single molecule tension senor using protein G to study mechano-sensitive receptors

Single molecular force across single integrins dictates cell spreading

How osmolytes influence hydrophobic polymer conformation: a unified view from experiment and theory

Synthesis, self-assembly and photophysical properties of oligo(2,5-dihexyloxy-1,4-phenylene vi-nylene)-block-poly(ethylene glycol)

Single polymer studies of hydrophobic hydration

Polymer Nanomechanics

Signature of Hydrophobic Hydration in a Single Polymer

FRep: a fluorescent protein-based bioprobe for in vivo detection of protein:dna interactions

Microdomain orientation of diblock copolymer ultrathin films solvent annealed at low temperatures

Imaging secondary structure of individual amyloid fibrils of a ß2-microglobulin fragment using near-field infrared spectroscopy

Interfacial free energy governs single polystyrene chain collapse in water and aqueous solutions

A computational tool for Monte Carlo simulations of biomolecular reaction networks modeled on physical principles

FRET evidence that an isoform of caspase-7 binds but does not cleave its substrate

Computational modeling approaches for studying of synthetic biological networks

Sequence reversed peptide from CaMKK binds to calmodulin in reversible Ca2+-dependent manner

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

A computational tool for designing FRET protein biosensors by rigid-body sampling of their conformational space

Current approaches for engineering proteins with diverse biological properties

Protein biosensors based on the principle of fluorescence resonance energy transfer for monitoring cellular dynamics

Creation of circularly permutated yellow fluorescent proteins using fluorescence screening and a tandem fusion template

Theses

Hydrophobic hydration of a single polymer

Monte Carlo simulations of biomolecular reaction networks modeled on physical principles

Random bits

NextGen's tools for the future - Sleep Paper Reader