Recent Advances on DNAzyme‐Based Sensing

Huang, Zhimei; Wang, Xiangnan; Wu, Zhenkun; Jiang, Jian‐Hui

doi:10.1002/asia.202101414

Cited by 26 publications

(9 citation statements)

References 116 publications

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“…DNAzymes are catalytically active oligonucleotides. , Among the DNAzymes, sequence-specific strands promote the site-specific cleavage of RNA or DNA substrates, often in the presence of metal ions , or amino acids (e.g., histidine) as cofactors. DNAzymes have demonstrated a number of applications in sensing technology, − as signal transducers in DNA-based networks, , the design of nucleic acid-based machineries, − and as tools to regulate biochemical processes. , The spatiotemporal control of DNAzyme activity is an attractive goal and, not surprisingly, strategies for the photocaging of DNAzyme activities have been actively pursued.…”

Section: Applications Of Photocleavable Dna Nanostructuresmentioning

confidence: 99%

Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

et al. 2023

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This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell–cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.

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Section: Applications Of Photocleavable Dna Nanostructuresmentioning

confidence: 99%

Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

et al. 2023

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“…Single-stranded DNA can fold into stable tertiary structures with binding affinities and catalytic activities. − These functional DNA molecules, including aptamers and catalysts (deoxyribozymes) have emerged as invaluable tools in various research fields, such as chemical biology and molecular medicine, − because their synthesis and modification process is straightforward and affordable. However, compared with their protein counterparts, functional DNAs often exhibit inferior performances.…”

Section: Introductionmentioning

confidence: 99%

Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity

Zhang,

Wei,

Chen

et al. 2024

J. Am. Chem. Soc.

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Functional DNAs are valuable molecular tools in chemical biology and analytical chemistry but suffer from low activities due to their limited chemical functionalities. Here, we present a chemoenzymatic method for site-specific installation of diverse functional groups on DNA, and showcase the application of this method to enhance the catalytic activity of a DNA catalyst. Through chemoenzymatic introduction of distinct chemical groups, such as hydroxyl, carboxyl, and benzyl, at specific positions, we achieve significant enhancements in the catalytic activity of the RNA-cleaving deoxyribozyme 10–23. A single carboxyl modification results in a 100-fold increase, while dual modifications (carboxyl and benzyl) yield an approximately 700-fold increase in activity when an RNA cleavage reaction is catalyzed on a DNA–RNA chimeric substrate. The resulting dually modified DNA catalyst, CaBn, exhibits a k obs of 3.76 min–1 in the presence of 1 mM Mg2+ and can be employed for fluorescent imaging of intracellular magnesium ions. Molecular dynamics simulations reveal the superior capability of CaBn to recruit magnesium ions to metal-ion-binding site 2 and adopt a catalytically competent conformation. Our work provides a broadly accessible strategy for DNA functionalization with diverse chemical modifications, and CaBn offers a highly active DNA catalyst with immense potential in chemistry and biotechnology.

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“…As a proof of concept, DNA units containing metal ion-responsive DNAzyme strands have been incorporated into the active layer of the bilayer hydrogel films to demonstrate the feasibility of the biosensing platform in detecting specific ions (Scheme B). Discovered through in vitro selection processes, DNAzymes capable of catalyzing reactions in the presence of specific cofactors offer many advantages for sensing applications, such as lower cost and higher stability than protein enzymes. − Specifically, Pb 2+ -responsive DNAzyme (GR5) and UO 2 2+ -responsive DNAzyme (39E), which can cleave RNA base-containing substrate strands in the presence of specific target ions, have been chosen as exemplary systems. − Thus, a DNA unit consisting of a DNAzyme strand and a DNA substrate strand was incorporated into the active layer of the bilayer hydrogel film. The introduction of negatively charged DNA units into the active layer imparts a nondiffusible net negative charge to the polymer network, and the internal electrostatic repulsive forces between DNA units and the high osmotic pressure induced by the rich counterions drive the swelling of the active layer to a relatively larger volume than the passive layer, resulting in the formation of a curved geometry of the bilayer film.…”

Section: Introductionmentioning

confidence: 99%

Smart Free-Standing Bilayer Polyacrylamide/DNA Hybrid Hydrogel Film-Based Sensing System Using Changes in Bending Angles as a Visual Signal Readout

Yin,

Zhang,

Liang

et al. 2024

Anal. Chem.

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Stimuli-responsive DNA hydrogels have shown great potential in sensing applications due to their attractive properties such as programmable target responsiveness, excellent biocompatibility, and biodegradability. In contrast to the extensively developed DNA hydrogel sensing systems based on the stimuli-responsive hydrogel-to-solution phase transition of the hydrogel matrix, the quantitative sensing application of DNA hydrogels exhibiting smart shape deformations has rarely been explored. Moreover, bulk DNA hydrogel-based sensing systems also suffer from high material cost and slow response. Herein, free-standing bilayer polyacrylamide/DNA hybrid hydrogel films with programmable responsive properties directed by the sequence of functional DNA units have been constructed. Compared with bulk DNA hydrogels, these DNA hydrogel films with a thickness at the micrometer scale not only greatly reduce the consumption of DNA materials but also facilitate the mass transfer of biomacromolecular substances within the hydrogel network, thus favoring their sensing applications. Therefore, a target-responsive smart DNA hydrogel film-based sensor system is further demonstrated based on the large amplitude macroscopic shape deformation of the film as a visual signal readout. As a proof of concept, Pb 2+ or UO 2 2+ ion-responsive DNA units were introduced into the active layer of the bilayer hydrogel films. In the presence of Pb 2+ or UO 2 2+ ions, the occurrence of a cleavage reaction within the DNA units leads to the release of DNA segments from the hydrogel film, inducing a dramatic shape deformation of the film, and thus sensing of Pb 2+ or UO 2 2+ ions with high specificity is achieved based on measuring the bending angle changes of these smart free-standing films. These smart DNA hydrogel film sensors with target-programmable responsiveness, simple operation, and ease of storage may hold promise for future rapid on-site testing applications.

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Recent Advances on DNAzyme‐Based Sensing

Cited by 26 publications

References 116 publications

Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity

Smart Free-Standing Bilayer Polyacrylamide/DNA Hybrid Hydrogel Film-Based Sensing System Using Changes in Bending Angles as a Visual Signal Readout

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