Journal Articles

For an overview on PubMed of the most recent publications of the Li Lab and collaborators, click HERE.

2023

An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function

A Fluorogenic DNAzyme for A Thermally Stable Protein Biomarker from Fusobacterium nucleatum, a Human Bacterial Pathogen

Detecting Legionella pneumophila in Cooling Tower Water Samples with a DNAzyme/Bead-Based Fluorescence Assay

In Vitro Selection and Characterization of a DNAzyme Probe for Diverse Pathogenic Strains of Clostridium difficile

A Simple Colorimetric Au-on-Au Tip Sensor with a New Functional Nucleic Acid Probe for Food-borne Pathogen Salmonella typhimurium

Detection of Large Genomic RNA via DNAzyme-Mediated RNA Cleavage and Rolling Circle Amplification: SARS-CoV-2 as a Model

Comparative Characterization of Diverse DNA Aptamers for Recognition of Spike Proteins of Multiple SARS-CoV-2 Variants

2022

Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer

Discovery and translation of functional nucleic acids for clinically diagnosing infectious diseases: Opportunities and challenges

One Solution for All: Searching for Universal Aptamers for Constantly Mutating Spike Proteins of SARS-CoV-2

Aptamers for SARS-CoV-2: Isolation, Characterization, and Diagnostic and Therapeutic Developments

Development of Nucleic-Acid-Based Electrochemical Biosensors for Clinical Applications

A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern

Aptamers from random sequence space: Accomplishments, gaps and future considerations

2021

Facile Synthesis of Pd-Ir Nanocubes for Biosensing

LISzyme Biosensors: DNAzymes Embedded in an Anti-biofouling Platform for Hands-free Real-Time Detection of Bacterial Contamination in Milk

Target-Mediated 5’-Exonuclease Digestion of DNA Aptamers with RecJ to Modulate Rolling Circle Amplification for Biosensing

High-Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild-Type and B.1.1.7 SARS-CoV-2 in Unprocessed Saliva

DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective

A DNA Nanoflower-Assisted Separation-Free Nucleic Acid Detection Platform with a Commercial Pregnancy Test Strip

Functional Nucleic Acids for Pathogenic Bacteria Detection

Target-Dependent Protection of DNA Aptamers against Nucleolytic Digestion Enables Signal-On Biosensing with Toehold-Mediated Rolling Circle Amplification

Rapid and Specific Imaging of Extracellular Signaling Molecule Adenosine Triphosphate with a Self-Phosphorylating DNAzyme

Diverse high-affinity DNA aptamers for wild-type and B.1.1.7 SARS-CoV-2 spike proteins from a pre-structured DNA library

Biosensing with DNAzymes

Fast-responding functional DNA superstructures for stimuli-triggered protein release

Integrating programmable DNAzymes with electrical readout for rapid and culture-free bacterial detection using a handheld platform

Functional Nucleic Acids Under Unusual Conditions

A Syringe-Based DNAzyme Sensor for Bacterial Detection

One-pot high-yield synthesis of Pd nanocubes for Pd-Ir nanocube-based immunoassay of nucleocapsid protein from SARS-CoV-2

DNAzymes as key components of biosensing systems for the detection of biological targets

A Highly Specific DNA Aptamer for RNase H2 from Clostridium difficile

Selection and Characterization of an RNA-Cleaving DNAzyme Activated by Legionella pneumophila

2020

Evolution of a highly functional circular DNA aptamer in serum

Engineering Micrometer-Sized DNA Tracks for High-Speed DNA Synthesis and Biosensing

Aptamer-Based Biosensors for Environmental Monitoring

An Effective Method for Quantifying RNA Expression of IbsC-SibC, a Type I Toxin-Antitoxin System in Escherichia coli

Ribbon of DNA Lattice on Gold Nanoparticles for Selective Drug Delivery to Cancer Cells

In Vitro Selection of a DNA Aptamer Targeting Degraded Protein Fragments for Biosensing

A Multi-component All-DNA Biosensing System Controlled by a DNAzyme

In Vitro Selection of New DNA Aptamers for Human Vascular Endothelial Growth Factor 165

Protein-Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer-Containing DNA Primer

Circular Nucleic Acids: Discovery, Functions and Applications

Advances in functional nucleic acid based paper sensors

Selection and applications of synthetic functional DNAs for bacterial detection

Highly Sensitive RNA-Cleaving DNAzyme Sensors from Surface-to-Surface Product Enrichment

An Unintentional Discovery of a Fluorogenic DNA Probe for Ribonuclease I

A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

Biosensors Made of Synthetic Functional Nucleic Acids Toward Better Human Health

2019

Unraveling Determinants of Affinity Enhancement in Dimeric Aptamers for a Dimeric Protein

A DNAzyme-Based Colorimetric Paper Sensor for Helicobacter pylori

In Vitro Selection of Circular DNA Aptamers for Biosensing Applications

Investigation of RNA structure-switching aptamers in tunable sol–gel-derived materials

2018

Discovery of Butyrylcholinesterase-Activated Near-Infrared Fluorogenic Probe for Live-Cell and In Vivo Imaging

Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors

Colorimetric Detection of Uranyl Using a Litmus Test

Target-Induced Catalytic Assembly of Y-Shaped DNA and Its Application for In Situ Imaging of MicroRNAs

Graphene-DNAzyme-based fluorescent biosensor for Escherichia coli detection

A Paper Sensor Printed with Multifunctional Bio/Nano Materials

DNAzyme Feedback Amplification: Relaying Molecular Recognition to Exponential DNA Amplification

DNAzymes: Selected for Applications

Serendipitous Discovery of a Guanine-rich DNA Molecule with a Highly Stable Structure in Urea

Selection and characterization of DNA aptamers for detection of glutamate dehydrogenase from Clostridium difficile

2017

Selection and characterization of DNA aptamers for detection of glutamate dehydrogenase from Clostridium difficile

A Printed Multicomponent Paper Sensor for Bacterial Detection

Discovery and Biosensing Applications of Diverse RNA-Cleaving DNAzymes

Sol–Gel-Derived Biohybrid Materials Incorporating Long-Chain DNA Aptamers

Detection of DNA Amplicons of Polymerase Chain Reaction Using Litmus Test

Optical biosensors utilizing graphene and functional DNA molecules

A DNAzyme Feedback Amplification Strategy for Biosensing

In Vitro Selection of DNA Aptamers that Binds Geniposide

Automating multi-step paper-based assays using integrated layering of reagents

Electrophoretic Concentration and Electrical Lysis of Bacteria in a Microfluidic Device Using a Nanoporous Membrane

RNA Protection is Effectively Achieved by Pullulan Film Formation

2016

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Programming a topologically constrained DNA nanostructure into a sensor

Colorimetric Detection of Bacteria Using Litmus Test

In vitro selection of RNA-cleaving DNAzymes for bacterial detection

Topological DNA Assemblies Containing Identical or Fraternal Twins

Simple and ultrastable all-inclusive pullulan tablets for challenging bioassays

Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With Recurrent Clostridium difficile Infection

Target-Induced and Equipment-Free DNA Amplification with a Simple Paper Device

A Catalytic DNA Activated by a Specific Strain of Bacterial Pathogen

Integrating graphene oxide, functional DNA and nucleic-acid-manipulating strategies for amplified biosensing

2015

A Quarter Century of In Vitro Selection

Sequence Mutation and Structural Alteration Transform a Noncatalytic DNA Sequence into an Efficient RNA-Cleaving DNAzyme

Printed Paper Sensors for Serum Lactate Dehydrogenase using Pullulan-Based Inks to Immobilize Reagents

Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly

Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence

An Efficient Catalytic DNA that Cleaves L-RNA

Optimal DNA Templates for Rolling Circle Amplification Revealed by In Vitro Selection

Patterned Paper Sensors Printed with Long-Chain DNA Aptamers

Fluorescence Activation Imaging of Cytochrome c Released from Mitochondria Using Aptameric Nanosensor

Highly Specific Recognition of Breast Tumors by an RNA-Cleaving Fluorogenic DNAzyme Probe

2014

Examination of Bacterial Inhibition Using a Catalytic DNA

A Dual Reporter System for Detecting RNA Interactions in Bacterial Cells

Translating Bacterial Detection by DNAzymes into a Litmus Test

An inkjet-printed bioactive paper sensor that reports ATP through odour generation

A General Strategy to Create RNA Aptamer Sensors Using “Regulated” Graphene Oxide Adsorption

Engineering interlocking DNA rings with weak physical interactions

A Graphene-Based Biosensing Platform Based on the Release of DNA Probes and Rolling Circle Amplification

Pullulan Encapsulation of Labile Biomolecules to Give Stable Bioassay Tablets

Fluorescence Analysis of the Properties of Structure-Switching DNA Aptamers Entrapped in Sol–Gel-Derived Silica Materials

Therapeutic Peptides: New Arsenal Against Drug Resistant Pathogens

Arrest of Rolling Circle Amplification by Protein-Binding DNA Aptamers

Turning Tryptophanase into Odor-Generating Biosensors

Artificial Riboswitch Selection: A FACS-Based Approach

Construction and Application of Riboswitch-Based Sensors That Detect Metabolites Within Bacterial Cells

Lysozyme-stabilized gold nanoclusters as a novel fluorescence probe for cyanide recognition

Exploration of Structure-Switching in the Design of Aptamer Biosensors

2013

Evolving Wonder-RNAs in a Test Tube

Phosphorescence detection of L-ascorbic acid with surface-attached N-acetyl-L-cysteine and L-cysteine Mn doped ZnS quantum dots

Exploring Intermolecular Interactions of a Substrate Binding Protein Using a Riboswitch-Based Sensor

A Sensitive DNA Enzyme-Based Fluorescent Assay for Bacterial Detection

Assessing the Amount of Quadruplex Structures Present within G2-Tract Synthetic Random-Sequence DNA Libraries

A novel phosphorescence sensor for Co2+ ion based on Mn-doped ZnS quantum dots

Turning a Kinase Deoxyribozyme into a Sensor

Quality Control Certification of RNA Aptamer-Based Detection

A Highly Efficient Molecular Cloning Platform that Utilizes a Small Bacterial Toxin GeneMost accessed paper in 2013

Artificially Created Nucleic Acids and Peptides/Proteins in Chemical Biology

2012

Lighting Up RNA-Cleaving DNAzymes for Biosensing

Synthesis and evaluation of glucosamine-6-phosphate analogues as activators of glmS riboswitch

Stabilizing Structure-Switching Signaling RNA Aptamers by Entrapment in Sol–Gel Derived Materials for Solid-Phase Assays

Detection of Bacteria Using Fluorogenic DNAzymes

Multiplexed paper test strip for quantitative bacterial detection

Developing Fluorogenic RNA-Cleaving DNAzymes for Biosensing Applications

2011

Enhancing Sensitivity and Selectivity of Long-Period Grating Sensors using Structure-Switching Aptamers Bound to Gold-Doped Macroporous Silica Coatings

Characterization of non-8–17 sequences uncovers structurally diverse RNA-cleaving deoxyribozymes

Controlling biotinylation of microgels and modeling streptavidin uptake

Fluorogenic DNAzyme Probes as Bacterial IndicatorsFeatured in: [Science Daily] [CTS TV News] [McMaster Daily News] [Internetchemistry.com] [PhysOrg.com] [Innovations Report]

Surface Immobilization of Structure-Switching DNA Aptamers on Macroporous Sol−Gel-Derived Films for Solid-Phase Biosensing Applications

Modulation of DNA-Modified Gold-Nanoparticle Stability in Salt with Concatemeric Single-Stranded DNAs for Colorimetric Bioassay Development

Functional Nucleic Acids as Molecular Recognition Elements for Small Organic and Biological Molecules

2010

Decoding Toxicity: DEDUCING THE SEQUENCE REQUIREMENTS OF IbsC, A TYPE I TOXIN IN ESCHERICHIA COLI

A General Approach to the Construction of Structure-Switching Reporters from RNA Aptamers

The Structural Diversity of Deoxyribozymes

Probing the Function of Nucleotides in the Catalytic Cores of the 8−17 and 10−23 DNAzymes by Abasic Nucleotide and C3 Spacer Substitutions

Influence of Cleavage Site on Global Folding of an RNA-Cleaving DNAzyme

A Complex RNA-Cleaving DNAzyme That Can Efficiently Cleave a Pyrimidine–Pyrimidine Junction

Photoluminescence model for a hybrid aptamer-GaAs optical biosensor

A Versatile Endoribonuclease Mimic Made of DNA: Characteristics and Applications of the 8–17 RNA-Cleaving DNAzyme

2009

Detection of DNA using bioactive paper strips

Characterization of an RNA-cleaving deoxyribozyme with optimal activity at pH 5

A genotype-to-phenotype map of in vitro selected RNA- cleaving DNAzymes: Implications for accessing the target phenotype

Incorporation of an inducible nucleotide analog into DNA by DNA polymerases

Kinetics of signaling-DNA-aptamer–ATP binding

Colorimetric Sensing by Using Allosteric-DNAzyme-Coupled Rolling Circle Amplification and a Peptide Nucleic Acid–Organic Dye Probe

Biologically Inspired Synthetic Enzymes Made from DNA

Identification of a Toxic Peptide through Bidirectional Expression of Small RNAs

2008

DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides

Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays

Paper-Based Bioassays Using Gold Nanoparticle Colorimetric Probes

A Novel DNA-Catalyzed Aldol Reaction

Design of Gold Nanoparticle-Based Colorimetric Biosensing Assays

In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine–pyrimidine junctions

Investigation of DNA as a catalyst for Henry reaction in water

Chemical Biology meets Systems Biology

A FACS-Based Approach to Engineering Artificial Riboswitches

Rolling Circle Amplification: Applications in Nanotechnology and Biodetection with Functional Nucleic Acids

Enzymatic Cleavage of Nucleic Acids on Gold Nanoparticles: A Generic Platform for Facile Colorimetric Biosensors

DNA Aptamer Folding on Gold Nanoparticles:  From Colloid Chemistry to Biosensors

Microgel-Based Inks for Paper-Supported Biosensing Applications

Sequence-function relationships provide new insight into the cleavage site selectivity of the 8–17 RNA-cleaving deoxyribozyme

A Deoxyribozyme with a Novel Guanine Quartet-Helix Pseudoknot Structure

2007

Label-Free Fiber Optic Biosensors With Enhanced Sensitivity

Understanding DNA-based catalysis one molecule at a time

Simple Fluorescent Sensors Engineered with Catalytic DNA ‘MgZ’ Based on a Non-Classic Allosteric Design

Isolation of DNA Aptamers for CDP-Ribitol Synthase, and Characterization of Their Inhibitory and Structural Properties

Enzymatic manipulations of DNA oligonucleotides on microgel: towards development of DNA–microgel bioassays

Aptamers and Small Molecules Play Tug of War

Simple and rapid colorimetric enzyme sensing assays using non-crosslinking gold nanoparticle aggregation

Highly Stabilized Nucleotide-Capped Small Gold Nanoparticles with Tunable Size

Simple and Rapid Colorimetric Biosensors Based on DNA Aptamer and Noncrosslinking Gold Nanoparticle Aggregation

Characterization of pH3DZ1 — An RNA-cleaving deoxyribozyme with optimal activity at pH 3

A synthetic luxCDABE gene cluster optimized for expression in high-GC bacteria

Entrapment of Fluorescence Signaling DNA Enzymes in Sol−Gel-Derived Materials for Metal Ion Sensing

Optimization of Cladding-Structure-Modified Long-Period-Grating Refractive-Index Sensors

Multiple Occurrences of an Efficient Self-Phosphorylating Deoxyribozyme Motif

Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates

Adsorption and Covalent Coupling of ATP-Binding DNA Aptamers onto Cellulose

2006

Catalysis and Rational Engineering of trans-Acting pH6DZ1, an RNA-Cleaving and Fluorescence-Signaling Deoxyribozyme with a Four-Way Junction Structure

Evolution of High-Branching Deoxyribozymes from a Catalytic DNA with a Three-Way Junction

Long-period grating refractive index sensor with a modified cladding structure for large operational range and high sensitivity

Small-Molecule Screening Made Simple for a Difficult Target with a Signaling Nucleic Acid Aptamer that Reports on Deaminase Activity

Wrapping single-walled carbon nanotubes with long single-stranded DNA molecules produced by rolling circle amplification

DNA Polymerization on Gold Nanoparticles through Rolling Circle Amplification: Towards Novel Scaffolds for Three-Dimensional Periodic Nanoassemblies

Nucleic acid aptamers and enzymes as sensors

Phosphoester-transfer mechanism of an RNA-cleaving acidic deoxyribozyme revealed by radioactivity tracking and enzymatic digestion

Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection

Solid-Phase Enzyme Activity Assay Utilizing an Entrapped Fluorescence-Signaling DNA Aptamer

Revitalization of Six Abandoned Catalytic DNA Species Reveals a Common Three-way Junction Framework and Diverse Catalytic Cores

Quenching of Fluorophore-Labeled DNA Oligonucleotides by Divalent Metal Ions:  Implications for Selection, Design, and Applications of Signaling Aptamers and Signaling Deoxyribozymes

Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozyme

2005

Complexation of well-controlled low-molecular weight polyelectrolytes with antisense oligonucleotides

Aptamers with fluorescence-signaling properties

Diverse Evolutionary Trajectories Characterize a Community of RNA-Cleaving Deoxyribozymes: A Case Study into the Population Dynamics of In VitroSelection

Characterizing the Secondary Structure and Identifying Functionally Essential Nucleotides of pH6DZ1, a Fluorescence-Signaling and RNA-Cleaving Deoxyribozyme

A DNA–Protein Nanoengine for “On-Demand” Release and Precise Delivery of Molecules

Entrapment of Fluorescent Signaling DNA Aptamers in Sol−Gel-Derived Silica

Structure-switching allosteric deoxyribozymes

Secondary-Structure Characterization of Two Proficient Kinase Deoxyribozymes

Tau protein binds single-stranded DNA sequence specifically – the proof obtained in vitro with non-equilibrium capillary electrophoresis of equilibrium mixtures

In Vitro Selection of Structure-Switching Signaling Aptamers

2004

Synthesis and characterization of topologically linked single-stranded DNA rings

Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties

DNAzymes: From Creation In Vitro to Application In Vivo

Signaling Aptamers for Monitoring Enzymatic Activity and for Inhibitor Screening

Tracing Sequence Diversity Change of RNA-Cleaving Deoxyribozymes under Increasing Selection Pressure during in Vitro Selection

Ligating DNA with DNA

Structure-Switching Signaling Aptamers: Transducing Molecular Recognition into Fluorescence Signaling

Dinucleotide Junction Cleavage Versatility of 8-17 Deoxyribozyme

2003

Catalytic DNAs as reporter molecules

Assemblage of Signaling DNA Enzymes with Intriguing Metal-Ion Specificities and pH Dependences

Structure-Switching Signaling Aptamers

Affinity Analysis of a Protein−Aptamer Complex Using Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures

An Efficient RNA-Cleaving DNA Enzyme that Synchronizes Catalysis with Fluorescence Signaling

2002

Making AppDNA using T4 DNA ligase

Tripartite molecular beacons

Sequence Diversity, Metal Specificity, and Catalytic Proficiency of Metal-Dependent Phosphorylating DNA Enzymes

2001

In Vitro Selection of Kinase and Ligase Deoxyribozymes

2000

Capping DNA with DNA

1999

Deoxyribozymes: New players in the ancient game of biocatalysis

Phosphorylating DNA with DNA

Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group

1998

DNA-enhanced peroxidase activity of a DNA aptamer-hemin complex

The modus operandi of a DNA enzyme: enhancement of substrate basicity

1997

Toward an Efficient DNAzyme

1996

A catalytic DNA for porphyrin metallation

Recognition of Anionic Porphyrins by DNA Aptamers

1992

Li, Y. & Wang, H. (1992). Studies on bromination of phenol by dioxane-dibromide. Journal of Chemical Reagents 14, 50-51.

1991

Li, Y. & Zhou, C. (1991). Synthesis and Bioactivity of Some Novel Non-Ester Pyrethroids (I). Chemical Journal of Chinese Universities 12, 479-481.

Li, Y. & Zhou, C. (1991). Synthesis and bioactivity of some novel non-ester pyrethroids (II). Journal of Applied Chemistry 8, 63-66.

1990

Li, Y. & Zhou, C. (1990). A new synthetic route for alkane pyrethroids. Journal of Pesticide Science 187, 39-43.

Li, Y. & Zhou, C. (1990). Synthesis of p-fluoro-m-phenoxytoluene. Journal of Pesticide Science 183, 17-20.