Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

Abstract

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.

Light-controlled growth of DNA organelles in synthetic cells

“…Our results build on previous studies highlighting the potential of light irradiation to control condensation [27,28]. Reversible coacervation and shuttling of molecules upon sequential exposure to UV-visible light were demonstrated in mixtures of double-stranded DNA and a light-responsive azobenzene cation [29].…”

Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids

“…132 In respect of this problem, the incorporation of a photoresponsive linker into the assembled DNA probes can provide an effective solution. 133–135 Thus, polyA-mediated SNAs can be activated by remote light for intracellular target detection with high temporal and spatial control. In addition, the binding affinity of the photoresponsive SNAs also can be tuned by light, which can be used to tune the dynamic range of the biosensors.…”

Controlling differentiation of stem cells via bioactive disordered cues

“…47–49 This homogeneous coat is then precisely etched with a UV light source and a photomask to allow specific immobilization of the protein of interest. 50–53 While being broadly adopted, this method has the inconvenient feature that each time one wants to make a novel micropattern, a new mask has to be manufactured by adding cost and time to the scientific process. In addition, only flat materials can be used.…”