Journal Articles
110.
Carrasquilla, C., Yao, X., Xu, C.-Q., Li, Y. and Brennan, J. D. (2011). Enhancing Sensitivity and Selectivity of Long-Period Grating Sensors using Structure-Switching Aptamers Bound to Gold-Doped Macroporous Silica Coatings for Small Molecule Detection. Biosensors and Bioelectronics. Submitted.
109.
Ali, M. M., Aguirre, S. D., Mok, W. W. K, & Li, Y. (2011). Developing Fluorogenic RNA-cleaving DNAzymes for Biosensing Applications. Methods in Molecular Biology. Submitted.
108.
Lam, J. C. F., Kwan, S. O., & Li, Y. (2011). Characterization of Non-8-17 Sequences Uncovers Structurally Diverse RNA-cleaving Deoxyribozymes. Molecular BioSystems. In press. [link]
107.
Xu, Y., Pharand, L., Wen, Q., Gonzaga, F., Ali, M. M., Li, Y., Filipe, C. D. M., & Pelton, R. (2011). Controlling Biotinylation of Microgels and Modeling Streptavidin Uptake. Colloid and Polymer Science. 289, 659-666. [ink]
106.
Ali, M. M., Aguirre, S. D., Lazim, H., & Li, Y. (2011). Fluorogenic DNAzyme Probes as Bacterial Indicators. Angewandte Chemie International Edition. 50, 3751-4. [link]
Featured in:
[Science Daily]
[CTS TV News]
[McMaster Daily News]
[Internetchemistry.com]
[PhysOrg.com]
[Innovations Report]
105.
Carrasquilla, C., Li, Y., & Brennan, J. D. (2011). Surface Immobilization of Structure-Switching DNA Aptamers on Macroporous Sol-Gel-Derived Films for Solid-Phase Biosensing Applications. Analytical Chemistry. 83, 957-965. [link]
104.
Ali, M. M, Kanda, P., Aguirre, S. D., & Li, Y. (2011). Modulation of DNA-Modified Gold-Nanoparticle Stability in Salt with Concatemeric Single-Stranded DNAs for Colorimetric Bioassay Development. Chemistry – A European Journal. 17, 2052-2056. [link]
103.
Lau, P. S. & Li, Y. (2011). Functional nucleic acids as molecular recognition elements for small organic and biological molecules. Curr. Org. Chem. 15, 557-575. Invited review. [link]
102.
Mok, W. W. K., Patel, N., & Li, Y. (2010). Decoding Toxicity: Deducing the Sequence Requirements of IbsC, a Type I Toxin in Escherichia coli. Journal of Biological Chemistry. 285: 41627-36. [link]
101.
Lau, P. S., Coombes, B. K., & Li, Y. (2010). A General Approach to the Construction of Structure-Switching Reporters from RNA Aptamers. Angew. Chem. Int. Ed. 49, 7938-7942. [link]
100.
McManus, S. A., & Li, Y. (2010). The Structural Diversity of Deoxyribozymes. Molecules. 15, 6269-6284. Review. [link]
99.
Wang, B., Cao, L., Chiuman, W., Li, Y. & Xi, Z. (2010). Probing the function of nucleotides in the catalytic cores of the 8-17 and 10-23 DNAzymes by abasic nucleotide and C3 spacer substitutions. Biochemistry 49, 7553-7562. [link]
98.
Lam, J. & Li, Y. (2010). Influence of Cleavage Site on Global Folding of an RNA-Cleaving DNAzyme. ChemBioChem. 11, 1710 – 1719. [link]
97.
Fowler, C. C., Brown, E. D. & Li, Y. (2010). Using a riboswitch sensor to monitor coenzyme B12 metabolism and transport in E. coli. Chem. Biol. 17, 756-765. [link]
96.
Lam, J. C., Withers, J. B. & Li, Y. (2010). A complex RNA-cleaving DNAzyme that can efficiently cleave a pyrimidine-pyrimidine junction. J. Mol. Biol. 400, 689-701. [link]
95.
Budz, H. A., Ali, M. M., Li, Y. & LaPierre, R. R. (2010). Photoluminescence Model for a Hybrid Aptamer-GaAs Optical Biosensor. J. Appl. Phys. 107, 104702 (1-9). [link]
94.
Schlosser, K. & Li, Y. (2010). A versatile endoribonuclease made of DNA: characteristics and applications of the 8-17 DNAzyme. ChemBioChem. 11, 866-879. Review. [link]
93.
Ali, M. M, Aguirre, S. D., Xu,Y., Filipe, C. D. M., Pelton, R. & Li, Y. (2009). Detection of
DNA Using Bioactive Paper Strips. Chem. Comm. 2009, 6640-2. [link]
92.
Kandadai, S. A., Mok, W. W. K., Ali, M. M., & Li, Y. (2009). Characterization and
Optimization of an RNA-Cleaving Deoxyribozyme Active at pH 5. Biochemistry 48, 7383-91. [link]
91.
Schlosser, K., Lam, J. & Li, Y. (2009). A genotype-to-phenotype map of in vitro selected RNA-
cleaving DNAzymes: Implications for accessing the target phenotype. Nucleic Acids Res. 37,
3545-57. [link]
90.
Ali, M. M., Imoto, S., Li, Y., Sasaki, S. & Nagatsugi. (2009). Incorporation of an inducible
nucleotide analog into DNA by DNA polymerases. Bioorg. Med. Chem. 17, 2859-63. [link]
89.
Nakamura, I., Shi, A., Nutiu, R., Yu, J. M. Y. & Li, Y. (2009). Kinetic modeling of designed
signaling DNA aptamers. Physical Review E. 79: 031906. [link]
88.
Ali, M. M. & Li, Y. (2009). Colorimetric sensing using allosteric DNAzyme-coupled rolling
circle amplification and a peptide nucleic acid-organic dye probe. Angew. Chem. Int. Ed. 48,
3512-3515. [link]
87.
Schlosser, K. & Li, Y. (2009). Biologically inspired synthetic enzymes made from DNA. Chem.
Biol. Invited review. 16, 311-22. [link]
86.
Schlosser, K. & Li, Y. (2009). DNAzyme-mediated catalysis with only guanosine and cytidine
nucleotides. Nucleic Acids Res. 37, 413-420. [link]
85.
Mok, W. W. K., Navani, N. K. Barker, C., Sawchyn, B. L., Gu, J., Pathania, R., Zhu, R. D.,
Brown, E. D. & Li, Y. (2009). Identification of a toxic peptide through bidirectional expression
of small RNAs. ChemBioChem. 10, 238-241. [link]
84.
Mok, W. W. K. & Li, Y. (2008). Recent Progress in Nucleic Acid Aptamer-Based Biosensors
and Bioassays. Sensors. 8, 7050-7084. Review. [link]
83.
Zhao, W., Ali, M. M., Aguirre, S., Brook, M. A. & Li, Y. (2008). Paper-based Bioassays Using
Gold Nanoparticle Colorimetric Probes. Anal. Chem. 80, 8431-8437. [link]
82.
Sun, G., Fan, J., Wang, Z., Li, Y. (2008). A DNA-Catalyzed Aldol Reaction in Water. SynLett.
2008, 16, 2491-2494. [link]
81.
Zhao, W., Brook, M. A. & Li, Y. (2008). Design of gold nanoparticle-based colorimetric
biosensing assays. ChemBioChem. 9, 2363-2371. Review. [link]
80.
Schlosser, K., Gu, J., Lam, J. C. F. & Li, Y. (2008). In vitro selection of small RNA-cleaving
deoxyribozymes that cleave pyrimidine-pyrimidine junctions. Nucleic Acids Res. 36, 4768-
4777. [link]
79.
Fan, J., Sun, G., Wan, C., Wang, Z. & Li, Y. (2008). Investigation of DNA as a Catalyst for
Henry Reaction in Water. Chem. Comm. 2008, 3792-3794. [link]
78.
Li, Y. (2008). Chemical Biology meets Systems Biology. Biochem. Cell Biol. 86, vii-viii. [link]
77.
Fowler, C. C., Brown, E. D. & Li, Y. (2008). A FACS-Based Approach to Engineering
Artificial Riboswitches. ChemBioChem. 9, 1906-1911. [link]
76.
Zhao, W., Ali, M. M., Brook, M. A., & Li, Y. (2008). Rolling Circle Amplification: New
Applications in Nanotechnology and Functional Nucleic Acid-Based Biodetection. Angew. Chem. Int. Ed. 47, 6330-6337. Review. [link]
75.
Zhao, W., Lam, J. C. F, Chiuman, W., Brook, M. A. & Li, Y. (2008). Enzymatic cleavage of
nucleic acid on gold nanoparticle: a generic platform for facile colorimetric biosensors. Small.
4, 810-816. [link]
74.
Zhao, W., Chiuman W., Lam, J. C. F, McManus, S. A., Chen, W., Cui, Y., Pelton, R., Brook,
M. A. & Li, Y. (2008). DNA Aptamer Folding on Gold Nanoparticle: from Colloid Chemistry
to Biosensors. J. Am. Chem. Soc. 130, 3610-3618. [link]
73.
Su, S., Ali, M. M., Filipe, C. D. M., Li, Y. & Pelton, R. (2008). Microgel-based Inks for Paper-
supported Biosensing Applications. Biomacromolecules. 9, 935-941. [link]
72.
Schlosser, K., & Li, Y. (2008). Sequence-function relationships provide new insight into the
cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme. Nucleic Acids Res. 36,
1472-1481. [link]
71.
McManus, S. A. & Li, Y. (2008). A Deoxyribozyme with a Novel Guanine Quartet-Helix
Pseudoknot Structure. J. Mol. Biol. 375: 960-968. [link]
70.
Yang, J., Sandhu, P., Liang, W, Xu, C.-Q.,. & Li, Y. (2007). Label-Free Fiber Optic Biosensors
with Enhanced Sensitivity. IEEE J. Selected Topics in Quantum Electronics. 13, 1691-1696. [link]
69.
Schlosser K. & Li, Y. (2007). Understanding DNA-based catalysis one molecule at a time. Nat.
Chem. Biol. 3, 753-754. News & Views. [link]
68.
Chiuman, W. & Li, Y. (2007). Simple fluorescent sensors engineered with catalytic DNA MgZ
based on a non-allosteric design. PloS ONE. 2, e1224. [link]
67.
Allali-Hassani, A., Pereira, M. P., Navani, N. K., Brown, E. D. & Li, Y. (2007). Isolation of
DNA aptamers for CDP-ribitol synthase and characterization of their inhibitory and structural
properties. ChemBioChem. 8, 2052-2057. [link]
66.
Ali, M. M., Su, S., Filipe, C. D. M., Pelton, R. & Li, Y. (2007). Enzymatic Manipulations of
DNA Oligonucleotides on Microgel: Towards Development of DNA-Microgel Biosensors.
Chem. Comm. 2007, 4459-4461. [link]
(Highlighted in the chemical biology news of Royal Chemical Society, 2007, 2, B83).
65.
Fowler, C. C. & Li, Y. (2007). Aptamers and small Molecules play tug of war. Chem. Biol. 14,
736-738. Preview. [link]
64.
Zhao, W., Chiuman, W., Lam, J. C. F, Brook, M. A. & Li, Y. (2007). Simple and rapid
colorimetric enzyme sensing assays using non-crosslinling gold nanoparticle aggregation. Chem. Comm. 2007, 3729 – 3731. [link]
63.
Zhao, W., Gonzaga, F., Li, Y. & Brook, M. A. (2007). Highly Stabilized Nucleotide-capped
Small Gold Nanoparticles with Tunable Size. Adv. Mater. 19, 1766-1771. [link]
62.
Zhao, W., Chiuman, W., Brook, M. A. & Li, Y. (2007). Simple and Rapid Colorimetric
Biosensors Based on DNA Aptamer and Non-crosslinking Gold Nanoparticle Aggregation".
ChemBioChem. 8, 727-731. [link]
61.
Ali, M. M., Kandadai, S. & Li, Y. (2007). Characterization of pH3DZ1—an RNA-Cleaving
Deoxyribozyme with Optimal Activity at pH 3. Can. J. Chem. 85, 261-273. [link]
60.
Craney, Ar., Hohenauer, T., Xu, Y., Kumar, N., Li, Y. & Nodwell, J. (2007). A synthetic
luxCDABE gene cluster optimized for expression in high-GC bacteria. Nucleic Acids Research.
35, e46. [link]
59.
Shen, Y., Mackey, G., Rupcich, N., Gloster, D., Chiuman, W., Li, Y. and Brennan, J. D. (2007).
Entrapment of Fluorescence-Signaling DNA Enzymes in Sol-Gel Derived Materials for Metal
Ion Sensing. Anal. Chem. 79, 3494-3503. [link]
58.
Yang, J., Yang, L., Xu, C-Q., Huang, W. and Li, Y. (2007). Optimization of cladding structure
modified long-period grating refractive index sensors. Journal of Lightwave Technology. 25,
372-380. [link]
57.
McManus, S., Li, Y. (2007). Multiple Occurrences of an Efficient Self-Phosphorylating
Deoxyribozyme Motif. Biochemistry 46, 2198-2204. [link]
56.
Chiuman, W. & Li, Y. (2007). Efficient Signaling Platforms Built from a Small Catalytic DNA
and Doubly Labeled Fluorogenic Substrates. Nucleic Acids Research. 35, 401-405. [link]
55.
Su, S., Nutiu, N., Filipe, C. D. M., Li, Y. & Pelton, R. (2007). Adsorption and Covalent
Coupling of ATP-Binding DNA Aptamers onto Cellulose. Langmuir. 23, 1300-1302. [link]
54.
Shen, Y., Chiuman, W., Brennan, J. D. & Li, Y. (2006). Catalytic and signaling properties of trans-acting
pH6DZ1, an RNA-cleaving and fluorescence-signaling deoxyribozyme with a four-way
junction structure. ChemBioChem. 7, 1343-1348. [link]
53.
Chiuman, W. & Li, Y. (2006). Evolution of high-branching deoxyribozymes from a catalytic
DNA with a three-way junction. Chem. Biol. 13, 1061-1069. [link]
52.
Yang, J., Yang, L., Xu, C.-Q., Xu, C., Huang, W. & Li, Y. (2006) Long-period grating
refractive index sensor with a modified cladding structure for large operational range and high
sensitivity. Applied Optics. 45, 6142-6147. [link]
51.
Elowe, N. H., Nutiu, R., Allali-Hassani, A., Cechetto, J. D., Hughes, D. W., Li, Y. & Brown, E.
D. (2006). Screening made simple for a difficult target with a signaling aptamer for deaminase
activity. Angew. Chem. Int. Ed. 45, 5648-5652. [link]
50.
Zhao, W., Gao, Y., Brook, M. A. & Li, Y. (2006) Wrapping Single-Walled Carbon Nanotubes
with Long Single-Stranded DNA Molecules Produced by Rolling Circle Amplification. Chem.
Comm. 2006, 3582 –3584. 45. [link]
49.
Zhao, W., Gao, Y., Kandadai, S. A., Brook, M. A. & Li, Y. (2006) DNA Polymerization on
Gold Nanoparticles via Rolling Circle Amplification: Towards Novel Scaffold for Three-
Dimensional Periodical Nanoassembly. Angew. Chem. Int. Ed. 45, 2409-2413. [link]
48.
Navani, N. K. & Li, Y. (2006) Nucleic acid aptamers and enzymes as sensors. Curr. Opin.
Chem. Biol. 10, 272-281. Review. [link]
47.
Kandadai, S. A., Chiuman, W. & Li, Y. (2006). Phosphoester-transfer mechanism of an RNA-
cleaving acidic deoxyribozyme revealed by radioactivity tracking and enzymatic digestion.
Chem. Comm. 2006, 2359-2361. [link]
46.
Schlosser, K., Lam, J. & Li, Y. (2006). Characterization of long RNA-cleaving deoxyribozymes
with short catalytic cores: The effect of excess sequence elements on the outcome of in vitro
selection. Nucleic acids Res. 34, 2445-2454. [link]
45.
Rupcich, N., Nutiu, R., Li, Y. & Brennan, J. D. (2006). Solid-Phase Enzyme Activity Assay
Utilizing an Entrapped Fluorescence-Signaling DNA Aptamer. Angew. Chem. Int. Ed. 45,
3295-3299. [link]
44.
Chiuman, W. & Li, Y. (2006). Revitalization of six abandoned catalytic DNA species reveals a
common three-way junction framework and diverse catalytic cores. J. Mol. Biol. 357, 748–754. [link]
43.
Rupcich, N., Chiuman, W., Nutiu, R., Mei, S., Flora, K. K., Li, Y. & Brennan, J. D. (2006).
Quenching of Fluorophore-labeled DNA Oligonucleotides by Divalent Metal Ions:
Implications for Selection, Design and Applications of Signaling Aptamers and Signaling
Deoxyribozymes. J. Am. Chem. Soc. 2006, 128, 780-790. [link]
42.
Kandadai, S. & Li, Y. (2006). Characterization of a catalytically efficient acidic RNA-cleaving
deoxyribozyme. Nucleic Acids Res. 33, 7164–7175. [link]
41.
Jin, J., Achenbach, J. C., Zhu, S. & Li, Y. (2005). Complexation of Well-Controlled Low-
Molecular-Weight Polyelectrolytes with Antisense Oligonucleotides. Colloid and Polymer
Science. 283, 1197 - 1205. [link]
40.
Nutiu, R. & Li, Y. (2005). Aptamers with fluorescence-signaling properties. Methods. 37, 16-
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39.
Schlosser, K. & Li, Y. (2005). Diverse evolutionary trajectories characterize a community of
RNA-cleaving deoxyribozymes: A case study into population dynamics of in vitro selection. J.
Mol. Evol. 61, 192-206. [link]
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Shen, Y., Brennan, J. D. & Li, Y. (2005). Characterizing the secondary structure and identifying
functionally essential nucleotides of pH6DZ1, a fluorescence-signaling and RNA-cleaving
deoxyribozyme. Biochemistry 44, 12066-12076. [link]
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Nutiu, R. & Li, Y. (2005). A DNA-Protein Nanoengine for 'On-Demand' Release and Precise
Delivery of Molecules. Angew. Chem. Int. Ed. 44, 5464-5467. [link]
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Rupcich, N., Nutiu, R. & Li, Y., Brennan, J. D. (2005). Entrapment of Fluorescent signaling
aptamers in Sol-Gel Derived Silica. Anal. Chem. 77, 4300-4307. [link]
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Achenbach, J. C., Nutiu, R & Li, Y. (2005). Structure-switching allosteric deoxyribozymes.
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Achenbach, J. C., Jeffries, G., McManus, S., Billen, L. P. & Li, Y. (2005). Secondary-structure
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Krylova, S. M., Musheeva. M., Nutiu, R., Li, Y., Lee, G. & Krylov, S. N. (2005). Tau protein
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Nutiu, R. & Li, Y. (2005). In vitro selection of structure-switching signaling aptamers. Angew.
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Nutiu, R., Mei, S. H. J., Liu, Z. & Li, Y. (2004). Engineering DNA aptamers and DNA
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Schlosser, K. & Li, Y. (2004). Tracing sequence diversity change of RNA-cleaving
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