Toolkit Items

Here, the latest research progresses in AAV-mediated gene editing and silencing strategies to modify that the genetic ocular diseases are systematically outlined, especially by base editing and prime editing.

CRISPR/Cas9 is a bacterial type II genome editing system repurposed as a programmable nuclease for target DNA cleavage and site-specific genome modification. The supplied evidence states that it was engineered for gene editing in mammalian cells by 2013 and is used to interrupt gene expression through cleavage of target DNA.

Prime editing is mentioned in the cited review as part of the broader set of genome-editing approaches considered in bacterial genome engineering. The supplied evidence does not describe its molecular architecture, target scope, or editing outcomes.

Transcription activator-like effector nucleases (TALENs) are programmable site-specific nucleases used for genome editing. The supplied evidence describes them as artificial systems with customizable DNA-binding motifs that can be designed to target specific genomic loci, bind practically anywhere in the genome, and cleave double-stranded DNA.

Chemogenetics is an engineering method in which target proteins are genetically engineered to interact with a designed chemical partner with high selectivity. It is used as a chemical-input strategy to manipulate protein or receptor function in cells and has also been used alongside optogenetics to perturb cellular structures such as specific microtubule subtypes.

Light-harvesting complex II (LHCII) is the major chlorophyll a/b-binding photosynthetic antenna complex of plants that has been studied in isolated native and recombinant forms. The cited literature indicates that light induces reversible conformational changes in LHCII that expose its N-terminal phosphorylation site and can also promote formation of dimeric LHCII states with distinct chlorophyll excitation-quenching properties.

SpCas9 is the Streptococcus pyogenes Cas9 CRISPR effector protein used for programmable genome editing and gene regulation. In the cited study, its activity was controlled indirectly by microRNA-dependent expression of the anti-CRISPR protein AcrIIA4, enabling cell-type-restricted activation of full-length Cas9, split-Cas9, and dCas9-VP64 variants.

AsLOV2-Jα is the light-oxygen-voltage-2/Jα photoswitch domain from Avena sativa phototropin1. In the reported LOV-TAP fusion, ligation of AsLOV2-Jα to TrpR enables light-dependent control of DNA binding through photoinduced structural and electrostatic changes.

NP-cIPTG, or 6-nitropiperonyl-caged IPTG, is a photocaged small-molecule inducer for light-regulated control of LacI-dependent bacterial gene expression. Illumination releases IPTG activity and enables optochemical induction, including in Rhodobacter capsulatus.

Opto-Casp8-V1 is a blue light-responsive caspase-8 optogenetic construct built in the context of Arabidopsis cryptochrome 2/CIB1N-based apoptosis control. Under blue light, related GFP-PHR-caspase8 and Flag-CIB1N-caspase8 fusion components show light-dependent interaction and cleavage, and Opto-Casp8-V1 is reported to undergo less efficient self-cleavage and consumption than Opto-Casp8-V2.

Opto-Casp8-V2 is a blue light-responsive optogenetic caspase-8 construct built from the Arabidopsis cryptochrome 2 system. Under blue light, it shows more efficient self-cleavage and consumption than Opto-Casp8-V1 and more strongly promotes caspase-associated cell death outputs.

Light-controlled crRNA is a chemically modified CRISPR guide RNA in which vitamin E is attached to the 5' terminus through a photolabile linker, creating a caged crRNA that inactivates CRISPR/Cas9 until light exposure. Upon irradiation, this design restores CRISPR/Cas9 activity and supports genome editing of VEGFA and knockdown of EGFP expression in human cells.

The photoactivatable CRISPR/Cas12a system is a light-gated nucleic acid sensing platform that integrates photoactivation with CRISPR/Cas12a for DNA and RNA detection. It has been used in visual assay formats, including HPV16 detection and biomarker imaging, to provide spatiotemporal control over Cas12a-based sensing.

BMP-2_pc is a recombinant BMP-2 construct linked through a coumarin-based 405 nm-photocleavable linker and covalently incorporated into an enzymatically crosslinked collagen-containing hydrogel composite. Blue-light stimulation triggers stepwise release of BMP-2 from the material.

Through the integration of computational structural biology and enzyme channel engineering, this study successfully elucidated the key intermediates in the stepwise hydroxylation-cleavage catalytic process of Digitalis purpurea-derived DlCYP87A enzyme. Building on this foundation, we implemented structure-guided rational design to precisely engineer the substrate channel and catalytic pocket.

We substituted its native proteolytic activation motif with a customized protease recognition sequence.

eSpCas9 is an increased-fidelity Streptococcus pyogenes Cas9 nuclease variant used in the optimization of CRISPR-Cas9 cleavage specificity. In comparative analyses of high-fidelity SpCas9 enzymes, eSpCas9 served as one of the variants whose mutations were combined to generate hybrid HeFSpCas9 nucleases.

HeFSpCas9 denotes engineered Streptococcus pyogenes Cas9 high-fidelity nuclease variants that combine mutations from eSpCas9 and SpCas9-HF1. These variants were developed to optimize the balance between on-target cleavage activity and genome-editing specificity across different target sites.

By engineering inducible protease variants whose activity is tightly regulated by an orally bioavailable, clinically approved small molecule, we achieved precise temporal control of pyroptosis.

Methylated guide RNA for CRISPR-Cas12a is a chemically modified crRNA bearing m6A or m1A marks that suppresses Cas12a activity. The methylated guide inhibits both cis- and trans-DNA cleavage, and activity can be reactivated through guide RNA demethylation.

SpCas9-HF1 is an engineered high-fidelity Streptococcus pyogenes Cas9 nuclease variant evaluated in comparative studies of increased-specificity SpCas9 enzymes. It is used for genome cleavage applications in which target-dependent optimization of specificity is required.

SpCas9 nucleases in this context are increased-fidelity CRISPR-Cas9 variants generated by combining mutations from eSpCas9 and SpCas9-HF1 into HeFSpCas9 forms. They are designed to preserve RNA-guided DNA cleavage while improving genome-editing specificity in a target-dependent manner.

The three-stranded DNAzyme probe (TSDP) is a CRISPR/Cas9-inducible DNA construct engineered with a 20-bp Cas9 recognition site that suppresses DNAzyme activity until cleavage. It was developed for in situ imaging of nuclear Zn2+ in living cells and was further combined with photoactivation and Boolean logic control for spatiotemporal imaging.

Anion channelrhodopsins (ACRs) are natural light-gated anion-conducting microbial rhodopsins from cryptophyte algae used as optogenetic actuators. In cultured neonatal rat ventricular cardiomyocytes, their expression enables light-evoked inhibitory currents, suppression of electrical activity, and shortening of action potential duration when illumination is applied during repolarization.

Photocaged carbohydrates are synthetic light-responsive small molecules generated by chemical caging of carbohydrate-related inducers and characterized photochemically. In the cited ChemBioChem study, six photocaged carbohydrates were synthesized, and related photocaged compounds were used to place bacterial gene expression under optical control as light-activated inducers.

we previously developed a Francisella novicida Cas12a variant (FnoCas12a) by introducing double proline substitutions (K969P/D970P) in a conserved arginine-rich helix called the bridge helix (BH)

2A is a short viral oligopeptide sequence that mediates a ribosome skipping effect during translation, causing co-translational cleavage of polyproteins. It is used in heterologous co-expression systems to separate proteins of biotechnological interest from a single coding sequence.

CRISPR-Cas technology comprises CRISPR-associated effector proteins that recognize specific DNA or RNA sequences and cleave them. In the cited review, it is presented primarily as a platform for rapid pathogen nucleic acid detection that leverages Cas trans-cleavage activity together with signal amplification and signal transformation strategies.

GFP-PHR-caspase8/Flag-CIB1N-caspase8 is a blue light-responsive two-component optogenetic caspase-8 system composed of GFP-PHR-caspase8 and Flag-CIB1N-caspase8 fusion proteins. Under blue light, the two components interact more strongly and undergo light-dependent cleavage, consistent with inducible caspase-8 activation.

PS Intein is a photoswitchable intein engineered by allosterically modulating the small autocatalytic gp41-1 intein with a tandem Vivid photoreceptor. It enables light control of covalent protein binding and cleavage in cells.

The alkynyl-functionalized photocleavable linker is a construct pattern used in caged antisense morpholino reagents, in which an ethynyl-bearing photocleavable linker is coupled to an oligonucleotide. In the caged state it inhibits DNA binding, and brief 405-nm illumination restores antisense activity through linker photocleavage.

Auxiliary photocleavable oligodeoxyribonucleotides complementary to crRNA (PC-DNAs) are inhibitory oligonucleotide components of a photoactivatable nanoCRISPR/Cas9 system. They hybridize to crRNA to suppress Cas9 function before illumination and are photocleaved by 365 nm UV light to release crRNA and restore gene-editing activity.

Caged guide RNAs are synthetic CRISPR guide RNAs containing photolabile nucleobase substitutions in the 5′ protospacer that enable light-activated control of Cas9 function. They were developed to conditionally regulate genome editing in mammalian cells and zebrafish embryos by suppressing guide RNA binding to target DNA until optical activation.

The caged NF-κB DNA decoy is a photoregulated oligonucleotide decoy in which photoremovable protecting groups are installed on nucleobases within an NF-κB decoy sequence. UV irradiation removes the caging groups, restores decoy hybridization and NF-κB binding activity, and enables light-controlled regulation of NF-κB-driven transcription in mammalian cells.

Carbon nanoparticles, particularly carbon-encapsulated iron nanoparticles, were developed as a photoactivatable nanoCRISPR/Cas9 delivery harness in which photocleavable oligodeoxyribonucleotides are immobilized on the nanoparticle surface to reversibly block crRNA. UV irradiation at 365 nm cleaves the blocking oligonucleotides, releases crRNA, and restores Cas9 editing activity.

CRISPR-plus is a light-activated CRISPR/Cas9 strategy in which guide RNA activity is suppressed by photocleavable protectors and restored by illumination. It enables optical control of genome editing and was reported to be compatible with simultaneous targeting of multiple DNA sequences.

Engineered MT-cleaving enzymes are recruitment-based perturbation tools that acutely disassemble selected microtubule subtypes in living cells. Reported implementations use chemogenetic or optogenetic recruitment to localize microtubule-cleaving activity and thereby control microtubule disassembly.

The enzymatically crosslinked marine collagen-alginate hydrogel blend is an orthogonally crosslinked composite for visible-light-triggered, on-demand BMP-2 release. It combines microbial transglutaminase-crosslinked marine collagen with leachable alginate to generate microporosity, increase oxygen diffusion, and enhance osteogenic responses in dental pulp stem cells.

This tool is a light-mediated implementation of lac promoter-based gene expression that uses photocaged isopropyl β-D-thiogalactopyranoside (IPTG) as a synthetic inducer. In Corynebacterium glutamicum, it was applied for light-mediated optimization of lac promoter-driven expression and (+)-valencene biosynthesis.

This assay method combines a lateral flow assay strip test with a CRISPR/Cas12a sensing system to visualize nucleic acid cleavage signals. In the cited 2024 Analytical Chemistry study, it was presented within a photoactivatable CRISPR/Cas12a platform for DNA and RNA detection with point-of-care diagnostic potential.

The LHCII N-terminal domain is the region of the light-harvesting complex II chlorophyll-protein substrate that contains the phosphothreonine site. In thylakoid studies, illumination induces a reversible conformational change that increases exposure of this N-terminal region, enabling access by endogenous thylakoid protein kinase(s) and increasing susceptibility to tryptic cleavage.

Light-activated plasmids are engineered DNA constructs in which photocleavable biotinylated nucleobases are installed at defined positions in T7 or CMV promoters and occupied by streptavidin to suppress transcription until light exposure. They were reported to control gene expression in both cell-free systems and mammalian cells.

Here, we report the development of a photocaged derivative of L-lactate, 4-methoxy-7-nitroindolinyl-L-lactate (MNI-L-lac), that releases L-lactate upon illumination.

In addition, we developed a light-inducible version of GFE3, paGFE3, using a novel photoactivatable complex based on the photocleavable protein PhoCl2c. paGFE3 degrades Gephyrin and ablates inhibitory synapses in response to 400 nm light.

pc-PROTAC3 is a photocaged PROTAC constructed against Bruton's tyrosine kinase (BTK) within a light-inducible protein degradation strategy. The available evidence states that this approach was successfully applied to generate pc-PROTAC3 and that photocaged PROTACs can activate degradation activity upon light exposure.

PhoCl is a light-responsive protein domain that cleaves upon 405 nm illumination. In the SPLIT system, it was fused between maltose-binding protein and a tandem RGG coacervation module to trigger light-induced assembly of synthetic membraneless organelles in Saccharomyces cerevisiae after a single light pulse.

Phosphorothioate-caged antisense oligonucleotides are mixed-backbone antisense oligonucleotides in which phosphorothioate linkages are modified with 2-nitroveratryl photocages. In the caged state, these modifications suppress target RNA duplex formation and RNase H activity, and UV uncaging restores antisense function to enable light-controlled knockdown of cell-free protein synthesis.

Photoactivatable cyclic caged morpholino oligomers (ccMOs) are light-responsive antisense morpholino reagents engineered in a cyclic, caged format to suppress target binding until photoactivation. In the reported design, brief 405-nm illumination photocleaves the cage and restores antisense activity, enabling spatiotemporal regulation of gene expression.

Photo-caged mRNA is an mRNA engineering strategy in which small-molecule caging groups are tethered to the 5′ untranslated region to suppress translation until illumination. Photocleavage of the cages activates translation and enables single-cell spatiotemporal control in mammalian cells.

The photocaged salicylic acid derivative is an optochemical inducer developed to place benzoate-based bacterial expression systems under light control. It is a caged small-molecule regulator that enables light-triggered bacterial gene expression.