CLICK-17, a DNA enzyme that harnesses ultra-low concentrations of either Cu+ or Cu2+ to catalyze the azide-alkyne 'click' reaction in water

Ultrasensitive and Specific Phage@DNAzyme Probe-Triggered Fluorescent Click Chemistry for On-Site Detection of Foodborne Pathogens Using a Smartphone

Rapid, specific, and on-site detection of virulent foodborne pathogenic strains plays a key role in controlling food safety. In this work, an ultrasensitive and specific Phage@DNAzyme signal probe was designed to detect foodborne pathogens. The proposed sensing probe was composed of the selected phage and functionalized DNAzyme, which realized the specific recognition of target foodborne pathogens at the strain level and the efficient catalysis of copper(II) based azide-alkyne cycloaddition (CuAAC) click reaction with fluorescent signal, respectively. As a proof of concept, the virulent Escherichia coli O157:H7 (E. coli O157:H7) as the representative analyte was first enriched and purified from the complex food samples by a 4-mercaptophenylboronic acid-modified gold slide. Following, the Phage@DNAzyme probes were specifically combined with the captured E. coli O157: H7 and catalyzed the click reaction between 3-azido-7-hydroxycoumarin and 3-butyn-1-ol with the assistance of Cu(II) to generate a visual fluorescent signal. Finally, the corresponding fluorescent signals were measured by a smartphone to quantify the target concentrations. Under optimized conditions, the bioassay exhibited a wide linear range from 10² to 10⁸ CFU/mL and the detection limit was 50 CFU/mL (S/N = 3). It was further extended to the detection of another foodborne pathogen Salmonella typhimurium with satisfying sensing performances. This work gives a new path for developing rapid, specific, and on-site detection methods for trace levels of pathogenic strains in foods.

Biomolecular sensors for advanced physiological monitoring

Body-based biomolecular sensing systems, including wearable, implantable and consumable sensors allow comprehensive health-related monitoring. Glucose sensors have long dominated wearable bioanalysis applications owing to their robust continuous detection of glucose, which has not yet been achieved for other biomarkers. However, access to diverse biological fluids and the development of reagentless sensing approaches may enable the design of body-based sensing systems for various analytes. Importantly, enhancing the selectivity and sensitivity of biomolecular sensors is essential for biomarker detection in complex physiological conditions. In this Review, we discuss approaches for the signal amplification of biomolecular sensors, including techniques to overcome Debye and mass transport limitations, and selectivity improvement, such as the integration of artificial affinity recognition elements. We highlight reagentless sensing approaches that can enable sequential real-time measurements, for example, the implementation of thin-film transistors in wearable devices. In addition to sensor construction, careful consideration of physical, psychological and security concerns related to body-based sensor integration is required to ensure that the transition from the laboratory to the human body is as seamless as possible.

Preparation, applications, and challenges of functional DNA nanomaterials

As a carrier of genetic information, DNA is a versatile module for fabricating nanostructures and nanodevices. Functional molecules could be integrated into DNA by precise base complementary pairing, greatly expanding the functions of DNA nanomaterials. These functions endow DNA nanomaterials with great potential in the application of biomedical field. In recent years, functional DNA nanomaterials have been rapidly investigated and perfected. There have been reviews that classified DNA nanomaterials from the perspective of functions, while this review primarily focuses on the preparation methods of functional DNA nanomaterials. This review comprehensively introduces the preparation methods of DNA nanomaterials with functions such as molecular recognition, nanozyme catalysis, drug delivery, and biomedical material templates. Then, the latest application progress of functional DNA nanomaterials is systematically reviewed. Finally, current challenges and future prospects for functional DNA nanomaterials are discussed.

DNA-based platform for efficient and precisely targeted bioorthogonal catalysis in living systems

As one of the typical bioorthogonal reactions, copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction holds great potential in organic synthesis, bioconjugation, and surface functionalization. However, the toxicity of Cu(I), inefficient catalytic activity, and the lack of cell specific targeting of the existing catalysts hampered their practical applications in living systems. Herein, we design and construct a DNA-based platform as a biocompatible, highly efficient, and precisely targeted bioorthogonal nanocatalyst. The nanocatalyst presents excellent catalytic efficiency in vitro, which is one order of magnitude higher than the commonly used catalyst CuSO₄/sodium ascorbate. The theoretical calculation further supports the contribution of DNA structure and its interaction with substrates to the superior catalytic activity. More importantly, the system can achieve efficient prodrug activation in cancer cells through cell type-specific recognition and produce a 40-fold enhancement of transformation compared to the non-targeting nanocatalyst, resulting in enhanced antitumor efficacy and reduced adverse effects. In vivo tumor therapy demonstrates the safety and efficacy of the system in mammals.

Copper-click reaction has been used for a wide range of bio-conjugations but does suffer from toxicity issues. Here, the authors report on the growth of copper nanoparticles on DNA with linked aptamer targeting and demonstrate high catalytic effect and improved application due to targeting and biocompatibility.

A Novel Truncated DNAzyme Modified Paper Analytical Device for Point-of-Care Test of Copper Ions in Natural Waters

On-site determination of trace copper ions in natural waters is of great significance to environmental monitoring, and how to develop accurate and specific point-of-care test methods is one critical issue. In the study, a paper-based analytical device (PAD) being modified with a new truncated DNAzyme (CLICK-T, which was derived from a reported DNAzyme-CLICK-17) was developed for Cu ions detection. The detection mechanism was based on Cu(II)-catalyzed azide-alkyne cycloaddition (Cu(II)AAC) reaction. It can directly conduct on-site analysis of Cu(II) ions based on fluorescent signals detected using a mobile phone. In the assay, the CLICK-T was firstly modified on the PADs. Then, water samples containing Cu ions mixed with 3-azido-7-hydroxycoumarin and 3-butyn-1-ol were instantly dripped on PADs and incubated for 20 min. Finally, the PADs were excited at 365 nm and emitted fluorescence which could be analyzed on site using smart phones. The Cu(II) concentration could be quantified through RGB analysis with the aid of iPhone APP software. The limit of detection is 0.1 µM by the naked eye due to the fact that CLICK-T exhibited a good catalytic effect on Cu(II)AAC. The Cu(II) concentration could also be directly detected without using reductant, such as ascorbic acid, which is prone to be oxidized in air. This simplifies the PDA detection process improves its efficiency. The PAD is convenient for the on-site analysis of Cu ions in natural waters.

Highly sensitive colorimetric sensing of copper(ii) ions based on "CLICK-17" DNAzyme-catalyzed azide modified gold nanoparticles and alkyne capped dsDNA cycloaddition

A click chemistry assay based on a newly discovered DNAzyme, CLICK-17, with azide modified gold nanoparticles (azide-AuNPs) and alkyne capped dsDNA (alkyne-linker DNA) was employed for novel and selective detection of Cu²⁺ visually. The strategy involved using CLICK-17 to mediate a catalytic reaction for triazole formation between azide-AuNPs and alkyne-linker DNA under the help of Cu²⁺ (without sodium ascorbate) or Cu⁺, which eventually led to the aggregation of AuNPs. The obvious color change from ruby red to bluish purple was then observed by the naked eye and the absorbance peak shifted from 525 to 570 nm. Interestingly, CLICK-17 and Cu⁺-catalyzed click reaction had the best performance compared to either Cu⁺ alone or CLICK-17 and Cu²⁺-mediated reaction in terms of the reaction time and sensitivity. This system has been demonstrated to allow quantitative measurement of Cu²⁺ with a detection limit as low as 26.8 nM and also has high specificity that can distinguish Cu²⁺ from other metal ions. Further, the method was tested with a real mineral water sample for Cu²⁺ concentration determination. Satisfactory recoveries of 90.8% and 99.8% were achieved.

We report selective and visual detection of Cu²⁺ based on aggregation of azide modified gold nanoparticles induced by CLICK-17 DNAzyme and Cu²⁺ or Cu⁺ catalyzed click reaction between azide-AuNPs and alkyne-dsDNA.

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD+-capped transcripts

Nicotinamide adenine diphosphate (NAD⁺) is a novel messenger RNA 5' cap in Escherichia coli, yeast, mammals, and Arabidopsis Transcriptome-wide identification of NAD⁺-capped RNAs (NAD-RNAs) was accomplished through NAD captureSeq, which combines chemoenzymatic RNA enrichment with high-throughput sequencing. NAD-RNAs are enzymatically converted to alkyne-RNAs that are then biotinylated using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Originally applied to E. coli RNA, which lacks the m⁷G cap, NAD captureSeq was then applied to eukaryotes without extensive verification of its specificity for NAD-RNAs vs. m⁷G-capped RNAs (m⁷G-RNAs). In addition, the Cu²⁺ ion in the CuAAC reaction causes RNA fragmentation, leading to greatly reduced yield and loss of full-length sequence information. We developed an NAD-RNA capture scheme utilizing the copper-free, strain-promoted azide-alkyne cycloaddition reaction (SPAAC). We examined the specificity of CuAAC and SPAAC reactions toward NAD-RNAs and m⁷G-RNAs and found that both prefer the former, but also act on the latter. We demonstrated that SPAAC-NAD sequencing (SPAAC-NAD-seq), when combined with immunodepletion of m⁷G-RNAs, enables NAD-RNA identification with accuracy and sensitivity, leading to the discovery of new NAD-RNA profiles in Arabidopsis Furthermore, SPAAC-NAD-seq retained full-length sequence information. Therefore, SPAAC-NAD-seq would enable specific and efficient discovery of NAD-RNAs in prokaryotes and, when combined with m⁷G-RNA depletion, in eukaryotes.

DNAmoreDB, a database of DNAzymes

Deoxyribozymes, DNA enzymes or simply DNAzymes are single-stranded oligo-deoxyribonucleotide molecules that, like proteins and ribozymes, possess the ability to perform catalysis. Although DNAzymes have not yet been found in living organisms, they have been isolated in the laboratory through in vitro selection. The selected DNAzyme sequences have the ability to catalyze a broad range of chemical reactions, utilizing DNA, RNA, peptides or small organic compounds as substrates. DNAmoreDB is a comprehensive database resource for DNAzymes that collects and organizes the following types of information: sequences, conditions of the selection procedure, catalyzed reactions, kinetic parameters, substrates, cofactors, structural information whenever available, and literature references. Currently, DNAmoreDB contains information about DNAzymes that catalyze 20 different reactions. We included a submission form for new data, a REST-based API system that allows users to retrieve the database contents in a machine-readable format, and keyword and BLASTN search features. The database is publicly available at https://www.genesilico.pl/DNAmoreDB/.