Toolkit Items

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.

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.

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.

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-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.

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.

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.

CRISPR-DNAzyme is a three-stranded DNAzyme probe engineered for in situ imaging of nuclear Zn2+ in living cells. Its catalytic activity is initially blocked by a 20-bp CRISPR/Cas9 recognition site and is activated in the nucleus after Cas9/sgRNA cleavage forms the active DNAzyme structure.

Cu-catalyzed azide-alkyne cycloaddition (CuAAC) is a click-chemistry method used to cyclize RNA through covalent intramolecular ligation. In a 2024 study on cyclic photocleavable RNA for a photoactivatable CRISPR/Cas9 system, CuAAC was tested alongside thiol-maleimide Michael reaction and was reported to have advantages for cyclic RNA preparation.

Duplex CRISPR/Cas9 technology is a genome-editing method that uses two guide RNAs to target intronic sequences flanking an exon, enabling excision of the intervening exon by Cas9-mediated cleavage. In human U-2 OS osteosarcoma cells, it was applied to generate CRY1 knockout, CRY2 knockout, and CRY1/CRY2 double knockout cell models.

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.

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.

The fluorescence method is a signal transformation modality used in CRISPR-Cas pathogen nucleic acid diagnostic platforms. In the cited context, Cas effector proteins recognize and cleave specific DNA or RNA targets, and fluorescence is combined with signal amplification and transformation technologies to report detection.

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.

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.

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.

Lateral flow technology is a signal transformation format used within CRISPR-Cas pathogen nucleic acid diagnostic platforms. In the supplied evidence, it functions alongside Cas protein-based sequence recognition and cleavage and with signal amplification approaches for rapid molecular diagnosis.

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-activatable nanoplatforms are light-responsive nano-regulators designed to modulate cellular events. The reviewed systems use light input, including UV-Vis-triggered photocleavage and photoisomerization, to control biological interventions across multiple application areas.

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.

The LOV-PvuII fusion enzyme is a genetically encoded light-controllable endonuclease created by fusing the Avena sativa phototropin1 LOV2 photosensory domain to the restriction enzyme PvuII. In analyzed variants, blue light modulated DNA cleavage activity relative to dark conditions, with the direction of regulation determined by the fusion interface.

The LOV2 domain from Avena sativa phototropin1 is a blue-light-responsive sensory domain that was fused to the restriction endonuclease PvuII to create a genetically encoded light-controllable chimeric nuclease. In this context, LOV2 modulates DNA cleavage activity in response to blue light, with the direction of regulation determined by the fusion interface.

MagMboI-plus is a redesigned photoactivatable endonuclease variant used as a light-controlled multi-component switch in Saccharomyces cerevisiae. In vivo, blue-light activation yields slightly increased DNA-cleavage activity relative to the original MagMboI construct, but also more pronounced genomic rearrangements.

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.

The near-infrared light activatable chemically induced split-Cas9/dCas9 system is a multi-component CRISPR switch in which split Cas9 or dCas9 is activated through a near-infrared photocleavable dimerization complex. It is intended to provide near-infrared light-gated control of CRISPR genome editing-related activity.

The NIR light-activated CRISPR-dCas9/Cas9 system is a multi-component optogenetic platform that controls CRISPR-dCas9/Cas9 gene regulation and editing with near-infrared light. It uses a chemically cleavable rapamycin dimer to confer precise and rapid light-dependent activity in living organisms.

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.

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.

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.

Photo-sensitive circular gRNAs are cyclically caged guide RNAs that enable light-activated CRISPR/Cas9- and Cpf1-mediated genome editing. They are designed for spatiotemporal control of editing and are activated by photocleavage of the circularized guide.

The photoactivatable CRISPR/Cas9 system is a light-gated genome-editing configuration comprising Cas9, either a synthetic 102-nt sgRNA or a crRNA/tracrRNA pair, and blocking photocleavable oligodeoxyribonucleotides. UV irradiation in the presence of the photomodified blocking oligodeoxyribonucleotides enables photoactivatable gene editing in vitro.

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.

The photoactivatable nanoCRISPR/Cas9 system is a light-gated CRISPR/Cas9 gene-editing platform built from crRNA, auxiliary photocleavable oligodeoxyribonucleotides complementary to the crRNA, and carbon nanoparticles. In this design, crRNA is immobilized in a blocked state before irradiation, and 365 nm UV exposure photocleaves the auxiliary oligonucleotides to release crRNA and restore Cas9 activity.

The photoactivated CRISPR/Cas12a strategy is a light-gated one-pot DETECTR nucleic acid detection system. It uses a photocleavable complementary ssDNA to transiently block crRNA activity during early recombinase polymerase amplification (RPA) and activates Cas12a after brief 365 nm ultraviolet exposure for sensitive detection.

Photocaged arabinose comprises two one-step cleavable arabinose derivatives used as light-sensitive inducers of transcription in bacteria. Upon UV-A illumination, these compounds undergo photocleavage to release active inducer and trigger arabinose-regulated gene expression with rapid and gradual control.

Photocleavable complementary ssDNA-blocked crRNA is a light-gated CRISPR/Cas12a construct design in which a photocleavable complementary single-stranded DNA transiently blocks crRNA function. In a one-pot DETECTR workflow, brief 365 nm ultraviolet exposure removes this block after recombinase polymerase amplification has progressed, thereby activating Cas12a at a controlled time.

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.

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.

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.

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.

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.

UV-Vis light-triggered photocleavage is a light-responsive engineering method used within nano-regulators to control biological activity. Upon UV-Vis illumination, responsive components undergo bond cleavage, enabling modulation of cellular events.

This tool is a pair of wavelength-selective photo-cages conjugated to the 5′-UTR of mRNA to suppress translation until illumination. Selective photocleavage with different wavelengths enables sequential optical activation of two distinct mRNAs in the same mammalian cell with single-cell spatiotemporal resolution.