Juewen Liu

University of Waterloo | UWaterloo · Department of Chemistry

Plastics are critical materials for modern technological applications, yet environmental contamination by microplastics has become a growing concern. In this study, DNA aptamers were isolated for two of the most abundant plastic materials: polyvinylchloride (PVC) and polystyrene (PS). These aptamers contain approximately 90 % cytosine and thymine b...

Kanamycin A is a widely used antibiotic, although it has a narrow therapeutic window demanding highly accurate monitoring. The sensing of kanamycin A using aptamers is of great interest since aptamers can be used for continuous monitoring with a rapid response. While kanamycin has been the target for at least four previous aptamer selections, the b...

Plastics are critical materials for modern technological applications, yet environmental contamination by microplastics has become a growing concern. In this study, DNA aptamers were isolated for two of the most abundant plastic materials: polyvinylchloride (PVC) and polystyrene (PS). These aptamers contain approximately 90% cytosine and thymine bu...

Measuring quinine is critical for the detection of its overdose, understanding its pharmacological and toxicological effects, and monitoring its pollution. While a previously reported aptamer named MN4 can bind quinine, it was not selected for it, leading to compromised binding affinity and specificity. In this work, a new quinine aptamer was isola...

Since 1990, numerous aptamers have been isolated and discovered for use in various analytical, biomedical, and environmental applications. This trend continues to date. A critical step in the characterization of aptamer binding is to measure its binding affinity toward both target and non‐target molecules. Dissociation constant (Kd) is the most com...

During an aptamer selection, using a lower target concentration may result in aptamers with a higher binding affinity. Consequently, this begs the question of whether there is a lower limit for target concentration. In this work, we conducted three aptamer selections using 5 μM, 500 nM and 50 nM guanine as the targets, respectively. Successful enri...

During a typical aptamer selection experiment, buffer molecules are used at 10 to 50 mM, whereas target molecules could be used at much lower concentrations even in low µM levels....

Effective monitoring of ocular drugs is crucial for personalized medicine and improving drug delivery efficacy. However, traditional methods face difficulties in detecting low drug concentrations in small volumes of ocular fluid, such as that found on the ocular surface. In this study, we used capture-SELEX to select aptamers for two commonly used...

The determination of kon and koff values through kinetic analysis is crucial for understanding the intricacies of aptamer‐target binding interactions. By employing kinetic ITC, we systematically analyzed a range of ITC data of various aptamers. Upon plotting their kon and koff values as a function of their Kd values, a notable trend emerged. Across...

Comprehensive Summary Interfacing DNA oligonucleotides and DNA aptamers with gold nanoparticles has generated numerous functional hybrid materials for sensing, self‐assembly and drug delivery applications. Our lab has been working in this area for 15 years. In this article, the current understanding of the adsorption of DNA to gold nanoparticles is...

Nanozymes, characterized by their nanoscale size and enzyme‐like catalytic activities, exhibit diverse therapeutic potentials, including anti‐oxidative, anti‐inflammatory, anti‐microbial, and anti‐angiogenic effects. These properties make them highly valuable in nanomedicine, particularly ocular therapy, bypassing the need for systemic delivery. Na...

Triplex DNA switches are attractive allosteric tools for engineering smart nanodevices, but their poor triplex‐forming capacity at physiological conditions limited the practical applications. To address this challenge, we proposed a low‐entropy barrier design to facilitate triplex formation by introducing a hairpin duplex linker into the triplex mo...

Triplex DNA switches are attractive allosteric tools for engineering smart nanodevices, but their poor triplex‐forming capacity at physiological conditions limited the practical applications. To address this challenge, we proposed a low‐entropy barrier design to facilitate triplex formation by introducing a hairpin duplex linker into the triplex mo...

Functionalized with the Au−S bond, gold nanoflares have emerged as promising candidates for theranostics. However, the presence of intracellular abundantly biothiols compromises the conventional Au−S bond, leading to the unintended release of cargoes and associated side‐effects on non‐target cells. Additionally, the hypoxic microenvironment in dise...

Functionalized with the Au‐S bond, gold nanoflares have emerged as promising candidates for theranostics. However, the presence of intracellular abundantly biothiols compromises the conventional Au‐S bond, leading to unintended release of cargoes and associated side‐effects on non‐target cells. Additionally, hypoxic microenvironment in diseased reg...

Citrate is a key metabolite and nutrient in humans. Its level is associated with many diseases from tumor growth to bone diseases. Detection of citrate has relied on its high negative charge, metal chelating properties and as an enzyme substrate. In this work, the capture‐selection method is used to isolate DNA aptamers for citrate. After 18 rounds...

Tetracyclines are a class of commonly used four‐ringed antibiotics. A series of DNA aptamers were recently obtained using the capture‐SELEX (systematic evolution of ligands by exponential enrichment) method to bind to oxytetracycline, and one of the aptamers can bind to a few other tetracycline antibiotics as well. Upon binding to the aptamers, the...

Previous aptamers for porphyrins and metalloporphyrins were all guanine‐rich sequences that can fold in G‐quadruplex structures. Due to stacking‐based binding, these aptamers can hardly tell different porphyrins apart, and they can also bind other planar molecules, hindering their practical applications. In this work, we used the capture selection...

Cytidine and uridine are two essential pyrimidine ribonucleotides, and accurate detection of these nucleosides holds significant biological importance. While many aptamers were reported to bind purines, little success was achieved for pyrimidine binding. This study employs the library‐immobilization capture‐SELEX technique to isolate aptamers capab...

Previous aptamers for porphyrins and metalloporphyrins were all guanine‐rich sequences that can fold in G‐quadruplex structures. Due to stacking‐based binding, these aptamers can hardly tell different porphyrins apart, and they can also bind other planar molecules, hindering their practical applications. In this work, we used the capture selection...

In recent years, there has been a surge in annual plastic production, which has contributed to growing environmental challenges, particularly in the form of microplastics. Effective management of plastic and microplastic waste has become a critical concern, necessitating innovative strategies to address its impact on ecosystems and human health. In...

While many dye binding aptamers have been reported, most of them were for light‐up aptamers that can significantly enhance the quantum yield of fluorophores. Sulforhodamine B (SRhB) was used as a target previously to select both DNA and RNA aptamers, and the DNA aptamer was a G‐quadruplex that can bind to a number of rhodamine analogs. In addition,...

Due to their programmable structures, many aptamers can be readily split into two halves while still retaining their target binding function. While split aptamers are prevalent in the biosensor field, fundamental studies of their binding are still lacking. In this work, we took advantage of the fluorescence enhancement property of a new aptamer nam...

We recently reported that some adenosine binding aptamers can also bind caffeine and theophylline with around 20‐fold lower affinities. This discovery led to the current work to examine the cross‐binding of adenosine to theophylline aptamers. For the DNA aptamer for theophylline, cross‐binding to adenosine was observed, and the affinity was 18 to 3...

Salicylic acid (SA) is a hydrolysis product and an active form of aspirin, and SA is found in a range of fruits and other food products. For food and drug and analysis there is a strong desire to detect SA. Since SA is a very small molecule, aptamers have advantages over antibodies for its detection. In this work, we used the library‐immobilization...

Nanodiamonds (NDs) have attracted considerable attention owing to their quantum properties and versatility in biological applications. In this study, we systematically investigated the adsorption of DNA oligonucleotides onto NDs with three types of surface groups: carboxylated (COOH-), hydroxylated (OH-), and hydrogenated (H-). Among them, only the...

The classical DNA aptamer for adenosine and ATP was selected twice using ATP as the target in 1995 and 2005, respectively. In 2022, this motif appeared four more times from selections using adenosine, ATP, theophylline, and caffeine as targets, suggesting that this aptamer can also bind methylxanthines. In this work, using thioflavin T fluorescence...

Electrochemiluminescence (ECL) is a widely used light output mechanism from electrochemical excitation. Understanding the intrinsic essence for ideal ECL generation remains a fundamental challenge. Here, based on the molecular orbital theory, we reported an energy level engineering strategy to regulate the ECL performance by using ligand-protected...

Rapid, accurate and high throughput measurement of infectious viruses is an urgent need to prevent viral transmission. Loop-mediated isothermal amplification (LAMP) is an attractive isothermal amplification method for nucleic acid detection, especially for point-of-care (POC) testing, but it needs at least four primers and its sensitivity is also l...

The detection of insulin is an important analytical task. Previously, guanine-rich DNA was believed to bind insulin, and an insulin aptamer was selected based on a few guanine-rich libraries. Insulin is a unique analyte, and it forms different aggregation states as a function of its concentration and buffer conditions, which may affect the detectio...

Chloramphenicol (CAP) is a potent antibiotic. Due to its side effects, CAP is currently banned in most countries, but it is still found in many food products and in the environment. Developing aptamer-based biosensors for the detection of CAP has interested many researchers. While both RNA and DNA aptamers were previously reported for CAP, they wer...

ATP, a small molecule with high intracellular concentration (mM level), provides a fuel to power signal amplification, which is meaningful for biosensing. However, traditional ATP-powered amplification is based on ATP/aptamer recognition, which is susceptible to the complex biological microenvironment (e.g., nuclease). In this work, we communicate...

Peroxidase-based assays are the most extensively used in bioanalytical sensors because of their simple colorimetric readout and high sensitivity owing to enzymatic signal amplification. To improve the stability, modification, and cost of protein-based enzymes, such as horseradish peroxidase (HRP), various enzyme mimics, such as DNAzymes and nanozym...

Wettability of microplastics may change due to chemical or physical transformations at their surface. In this work, we studied the adsorption of spherical nucleic acids (SNAs) with a gold nanoparticle core and linear DNA of the same sequence to probe the wettability of microplastics. Soaking microplastics in water at room temperature for 3 months r...

The classical DNA aptamer for adenosine and ATP has been the most used small molecule binding aptamer for biosensing, imaging, and DNA nanotechnology. This sequence has recurred multiple times in previous aptamer selections, and all previous selections used a high concentration of ATP as the target. Herein, two separate selections were performed us...

Tetracyclines are a class of antibiotics with a similar four-ringed structure. Due to this structural similarity, they are not easily differentiated from each other. We recently selected aptamers using oxytetracycline as a target and focused on an aptamer named OTC5, which has similar affinities for oxytetracycline (OTC), tetracycline (TC), and dox...

Microplastics can adsorb and spread a variety of pollutants in the ecosystem posing a threat to human health. One of the common pollution sources of environmental waters is metal ions, which not only adsorb on microplastics but can also promote the adsorption of other invasive species such as environmental DNA. Recently, we showed that environmenta...

“Nanozyme” is used to describe various catalysts from immobilized inorganic metal complexes, immobilized enzymes to inorganic nanoparticles. Here, the history of nanozymes is dvescribed in detail, and they can be largely separated into two types. Type 1 nanozymes refer to immobilized catalysts or enzymes on nanomaterials, which were dominant in the...

L‐lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need additional oxidants. In this work, DNA aptamers for L‐lactate were obtained using a library‐immobilization selection...

L‐lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need other substrates. In this work, DNA aptamers for L‐lactate were obtained using a library‐immobilization selection met...

L-lactate is a key metabolite indicative of physiological state, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need other substrates. In this work, DNA aptamers for L-lactate were obtained using a library-immobilization selection meth...

The accurate, simple, and efficient measurement of the concentration of single-stranded DNA (ssDNA) is important for many analytical applications, such as DNA adsorption, biosensor design, and disease diagnosis, but it is still a challenge. Herein, we studied a cationic conjugated polymer (CCP)-based ssDNA assay taking advantage of the obvious fluo...

Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such secondary structure information into consideration, a new algorithm combining conserved primary sequences and...

Gold nanoparticles (AuNPs) are one of the most commonly used reagents in colloidal science and biosensor technology. In this work, we first compared AuNPs prepared using four different reducing agents including citrate, glucose, ascorbate, and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES). At the same absorbance at the surface plasmon...

Uric acid is the end‐product of purine metabolism in humans and an important biomarker for many diseases. To achieve the detection of uric acid without using enzymes, we previously selected a DNA aptamer for uric acid with a Kd of 1 μM but the aptamer required multiple Na⁺ ions for binding. Saturated binding was achieved with around 700 mM Na⁺ and...

The reliable, readily accessible and label-free measurement of aptamer binding remains a challenge in the field. Recent reports have shown large changes in the intrinsic fluorescence of DNA upon the formation of G-quadruplex and i-motif structures. In this work, we examined whether DNA intrinsic fluorescence can be used for studying aptamer binding...

Removal and degradation of microplastics are often carried out separately. In this work, hydrophilic bare Fe3O4 nanoaggregates allowed efficient removal of the most common microplastics including high‐density polyethylene, polypropylene, polyvinyl chloride, polystyrene, and polyethylene terephthalate. Full extraction was achieved using Fe3O4 at 1 %...

With more and more new aptamers being reported, a general, cost-effective yet reliable aptamer binding assay is still needed. Herein, we studied cationic conjugated polymer (CCP)-based binding assays taking advantage of the conformational change of aptamer after binding with a target, which is reflected by the fluorescence change of the CCP. Poly(3...

Removal and degradation of microplastics are often carried out separately. In this work, hydrophilic bare Fe3O4 nanoaggregates allowed efficient removal of the most common microplastics including high‐density polyethylene, polypropylene, polyvinyl chloride, polystyrene, and polyethylene terephthalate. Full extraction was achieved using Fe3O4 at 1%...

While polyvalent metal ions and heating can both degrade nucleic acids, we herein report that a combination of them leads to stabilization. After incubating 4 mM various metal ions and DNA oligonucleotides at 95 °C for 3 h at pH 6 or 8, metal ions were divided into four groups based on gel electrophoresis results. Mg2+ can stabilize DNA at pH 6 wit...

Tetracyclines are a widely used group of antibiotics, many of which are currently only used in veterinary medicine and animal husbandry due to their adverse side effects. For the detection of tetracyclines, we previously reported a DNA aptamer named OTC5 that binds to tetracycline, oxytetracycline, and doxycycline with similar KD’s of ~100 nM. Tetr...

Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such a secondary structure information into consideration, a new algorithm combining conserved primary sequences a...

K+ enhanced the intrinsic fluorescence of a series of G-quadruplex DNA, while Pb2+ quenched the fluorescence. The metals showed interesting quadruplex binding kinetics with various DNA sequences.

DNA‐directed seeded growth of gold nanoparticles has been used for the development of aptamer‐based biosensors with the assumption that target analytes can modulate the adsorption of aptamers to the gold seeds and thus affect the growth reaction. To understand the reaction, the effect of single‐ and double‐stranded DNA is first examined, and it is...

Since the report of the RNA aptamer for theophylline, theophylline has become a key molecule in chemical biology for designing RNA switches and riboswitches. In addition, theophylline is an important drug for treating airway diseases including asthma. The classic RNA aptamer with excellent selectivity for theophylline has been used to design biosen...

Tetracyclines are a group of important antibiotics with a common four-ring scaffold. While most tetracyclines are currently used only in animals, their leaching into the environment and residues in food have caused health concerns. Aptamers are an attractive way to detect tetracyclines, and all previously reported aptamers for tetracyclines were ob...

The cover image shows a fluorescent biosensor based on a DNA aptamer for uric acid generated by SELEX. Uric acid is a biomarker linked to many common diseases including gout and chronic kidney diseases. In the initial state of the sensor, the fluorescence is quenched. In the presence of uric acid, target binding to the aptamer induces dissociation...

Glucose is the most important analyte for biosensors. Recently a DNA aptamer was reported allowing binding‐based detection. However, due to a relatively weak binding affinity, it is difficult to perform binding assays to understand the property of this aptamer. In this work, we replaced the only adenine base in the aptamer binding pocket with a 2‐a...

Uric acid is a biomarker for a range of diseases and hyperuricemia is the cause of many diseases including gout. While most biosensors for detecting uric acid relied on enzymatic reactions, in this work a library‐immobilization method was used to obtain DNA aptamers for uric acid. After 18 rounds of selection, two representative aptamers were obtai...

Imidazole-based metal-organic frameworks (MOFs) are easy to prepare as well-dispersed nanoparticles, which have attracted a lot of interest in cation/anion sensing. Metal substitution is an effective way to regulate the composition and performance of MOFs. Herein, by tuning the contents of Co and Zn, a series of homobimetallic CoxZn100-x-ZIF (x = 0...

Various functional DNA molecules have been developed for the detection of environmental contaminants in water, but their practical applications have been limited. To address this gap, this review highlights the efforts to develop field-deployable water quality biosensors. The biosensor devices include microfluidic, lateral flow and paper-based devi...

Phosphorothioate (PS) modification refers to replacing one of the nonbridging oxygen atoms in nucleic acids with sulfur. PS modifications can be easily introduced during solid-phase DNA synthesis. It has been extensively used in ribozyme and DNAzyme research to achieve a bioinorganic understanding of metal binding, bioanalytical applications of met...

Fertilization and early embryonic development as the beginning of a new life are key biological events. Hydrogen polysulfide (H2Sn) plays important roles during physiological regulation, such as antioxidation‐protection. However, no report has studied in situ H2Sn fluctuation during early embryonic development because of the low abundance of H2Sn a...