Toolkit Items

LiCre is a single-chain light-inducible Cre recombinase optogenetic switch. The supplied evidence supports that blue light can activate Cre-dependent recombination outputs, including induction of antibiotic resistance gene expression in Escherichia coli.

FUN-LOV is a fungal light-oxygen-voltage optogenetic switch for yeast built from Neurospora crassa photoreceptors WC-1 and VVD. It uses the photon-regulated interaction of these components to drive light-dependent target gene activation, including GPD1 and ADH1 expression in a wine yeast strain.

Cry2 is a blue-light photoreceptor cryptochrome from Arabidopsis used as a light-responsive multi-component optogenetic switch. The supplied evidence supports blue-light-dependent photoactivation linked to regulation of transcription factor control and to CRY2 degradation.

The CRISPR/Cas9 system is a multi-component genome engineering platform derived from a bacterial defense system that uses Cas9 and guide RNA to manipulate genomic loci in living cells. It has been widely adopted for mutagenesis and genome research, with reported applications spanning basic biology, biotechnology, agriculture, medicine, epigenetic perturbation, and disease models.

CRY2/CIB1 is a blue-light-inducible multi-component interaction switch composed of the photoreceptor CRY2 and its interacting partner CIB1. It is used for acute light-dependent protein recruitment, including plasma-membrane recruitment and clustering, to control protein localization and downstream signaling with high spatial and temporal resolution.

synaptoPAC is a presynaptically targeted version of the photoactivated adenylyl cyclase bPAC developed as a light-responsive optogenetic tool for induction of presynaptic plasticity. It is reported to increase action potential-evoked transmission in some neuronal contexts, but this potentiation was not observed in non-granule hippocampal cultures or at Schaffer collateral synapses in CA1 acute slices.

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.

EL222 is a blue light-activated LOV-HTH transcription factor from the marine bacterium Erythrobacter litoralis HTCC2594 that functions as a light-dependent DNA-binding protein for optical control of transcription. Its flavin mononucleotide chromophore photodynamics have been characterized in free solution and when embedded in EL222 variants.

iLID/SspB is a blue-light-inducible heterodimerization system built from an engineered iLID module and the SspB binding partner. It is used to reversibly recruit proteins in cells for control of localization and signaling, including membrane recruitment, neurotrophin receptor construction, microtubule plus-end targeting, and perturbation of small GTPase pathways.

Channelrhodopsin-2 (ChR2) is a light-activated ion channel used as an optogenetic switch to depolarize membranes and activate electrically excitable cells. The supplied evidence also indicates that light-activated ChR2 can modulate CaV1.3 calcium channel activity.

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.

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.

PhyB/PIF is a genetically encoded red/far-red light-inducible dimerization system built from phytochrome B and phytochrome-interacting factor. It enables reversible light-controlled protein association and dissociation on the second time scale and has been applied to gene regulation, protein transport, and subcellular recruitment.

BcLOV4 is a blue-light-responsive photoreceptor from Botrytis cinerea that functions as a single-component optogenetic module for rapid plasma membrane recruitment. Illumination drives cytosol-to-membrane translocation through direct protein-lipid electrostatic interaction, and fused cargo such as RhoA GTPase or RhoA-activating GEFs can be relocalized to the membrane with light.

The Cib1−/− mouse model is a genetic loss-of-function system in which calcium- and integrin-binding protein 1 (CIB1) is deleted to study its role in megakaryocyte and platelet biology. In the cited Blood 2011 study, Cib1 deficiency altered megakaryocyte adhesion, migration, and proplatelet formation and attenuated platelet recovery after depletion.

The CcaS/CcaR system is a green/red light-responsive two-component optogenetic switch used to control transcription in Synechococcus sp. PCC 7002. In the cited work, its output was tuned through genetic modification of the pCpcG2 promoter and its transcriptional response kinetics were quantified by qRT-PCR.

The yeast optogenetic toolkit (yOTK) is a modular construct system for light-controlled gene expression in Saccharomyces cerevisiae. It integrates optogenetic parts into an existing yeast toolkit and supports rapid assembly of light-controlled circuits, including split transcription factors built from cryptochrome and Enhanced Magnet dimerizers.

OptoRAF1 is a blue light-responsive optogenetic RAF1 system built on the CRY2/CIB1 dimerizer pair. It reversibly activates the RAF/MEK/ERK pathway by recruiting RAF1 to the plasma membrane.

Magnets are engineered pairs of distinct light-responsive protein modules derived from the Neurospora crassa photoreceptor Vivid. They act as a multi-component optogenetic switch by converting a native Vivid homodimerization interface into complementary light-dependent heterodimers for protein interaction and recruitment in subcellular volumes.

Opto-Rho1DN is a multi-component optogenetic switch that inhibits Rho1 by light-dependent recruitment of a dominant-negative Rho1 construct to the plasma membrane. The listed components are CIBN-pmGFP and CRY2-Rho1DN.

dCas9*_PhlF is a bacterial CRISPR-based transcriptional switch comprising a non-toxic dCas9* variant with the R1335K PAM-binding mutation fused to the PhlF repressor. The fusion recovered DNA-binding-dependent repression and enabled sgRNA-programmed NOT gate behavior that depends on both an sgRNA target site and a PhlF operator.

Set2-LANS is an optogenetic fusion of the yeast H3K36 methyltransferase Set2 with the light-activated nuclear shuttle (LANS) domain. It provides rapid and reversible light control of Set2, enabling inducible nuclear localization and control of H3K36 methylation in vivo.

The human CIB1-EVER1-EVER2 complex is a multicomponent protein complex in keratinocytes composed of CIB1, EVER1, and EVER2. It is reported to govern keratinocyte-intrinsic immunity to β-papillomaviruses, and disruption of this complex-dependent pathway is linked to selective susceptibility to β-HPVs in epidermodysplasia verruciformis.

Vivid-fused light-inducible recombinases are engineered Cre, Dre, and Flp variants generated by combining each site-specific recombinase with the fungal light-inducible protein Vivid. These constructs confer blue-light-driven recombinase activity and were used for light-induced genomic modification in live mouse brain, including under one-photon or two-photon illumination according to the provided summary.

The YF1/FixJ system is a blue light-repressible multi-component optogenetic switch evaluated for transcriptional control in the cyanobacterium Synechococcus sp. PCC 7002. In the cited PCC 7002 study, it was tested as a heterologously expressed light-input gene regulation system and showed limited performance, with a reported maximum dynamic range of 1.5-fold.

The split Cas9 logic gate is a synthetic multi-component circuit that uses split Cas9 halves to sense biological events through conditional reconstitution of Cas9 activity. In the reported 2023 implementation, self-assembling inteins reconstituted split Cas9 and enabled reporter activation only when specified transcriptional or cell-state inputs were present.

ArchT is an archaerhodopsin-based optogenetic actuator used for light-driven intracellular alkalinization in single cells. In the cited 2021 study, ArchT activation raised intracellular pH and was sufficient to trigger localized membrane ruffling and increased protrusion-retraction dynamics within seconds.

CRY2-BIC1 is a multi-component blue-light-dependent interacting protein pair derived from Arabidopsis thaliana cryptochrome 2 (CRY2) and Blue-light Inhibitor of Cryptochromes 1 (BIC1). It functions as a light-input protein interaction switch, and phage-assisted continuous evolution was applied to increase the dynamic range of the blue-light-dependent CRY2-BIC1 interaction.

This tool is a tunable optogenetic, light-inducible gene expression system used to control morphogen production in vitro. It was reported to generate long-range Sonic hedgehog (Shh) gradients that pattern neural progenitors into spatially distinct progenitor domains resembling vertebrate neural tube organization in vivo.

AcrIIC3-LOV2 is an engineered light-switchable anti-CRISPR protein formed by fusing the Neisseria meningitidis Cas9 inhibitor AcrIIC3 to the Avena sativa LOV2 blue-light sensory domain. In mammalian cells, two reported hybrids strongly inhibit NmeCas9 in the dark and allow robust genome editing under blue-light irradiation.

Light Activated BioID (LAB) is an optically controlled proximity-labeling system in which the two halves of split-TurboID are fused to the photodimerizing proteins CRY2 and CIB1. Blue light induces CRY2–CIB1 association, reconstituting split-TurboID and enabling proximity-dependent biotinylation of nearby proteins.

This tool is a genetically encoded optogenetic switch that uses light to regulate biological function. The supplied evidence supports its use to control central metabolic flux in Escherichia coli and to drive spatiotemporally controlled shape change in yeast with pulses of dim blue light.

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.

The optimized CRISPR-Cas9-based light-inducible gene expression device is a multi-component light-on transcription system built on CRISPR-Cas9-based engineering. It was reported to control gene transcription in a dose-dependent manner and was applied to induce P53 expression in bladder cancer cells.

OptoINVRT7 is a rapid optogenetic inverter circuit for controlling gene expression in Saccharomyces cerevisiae. In combination with the engineered promoter P_GAL1-S, it enables light-tunable expression that is induced in darkness and has been applied to regulate metabolic pathway enzymes.

mOptoT7 is a mammalian optogenetic transcription system composed of a split T7 RNA polymerase fused to the blue-light-inducible nMag/pMag Magnets photodimerization system. Blue light drives reconstitution of the split polymerase to activate transcription from orthogonal T7 promoters in mammalian cells, and the system has been used to produce protein-coding mRNA, shRNA, and the Pepper RNA aptamer.

Cytoplasmically diffuse CRY2 with membrane-anchored CIBN is a proof-of-concept CRY2/CIB optogenetic configuration adapted into Drosophila-oriented vector systems. It was proposed to use blue light to recruit CRY2 fusion proteins, including a possible CRY2-Rho1 fusion, to the plasma membrane.

pCpcG2 is a modified output promoter used in the green/red light-responsive CcaS/CcaR optogenetic system in Synechococcus sp. PCC 7002. Targeted changes to this promoter were reported to increase system activity under green light, improving light-controlled transcriptional output.

BOS is a bifunctional optogenetic transcriptional control system developed in Escherichia coli by combining the light-inducible transcriptional regulator LEVI mutant with the chemical-inducible repressor LacI. It enables blue-light-responsive regulation of target genes and has been applied to metabolic engineering for shikimic acid and l-valine production.

BLADE, or Boolean Logic and Arithmetic through DNA Excision, is a platform that multiplexes light-inducible recombinases in mammalian cells. In the cited study, it was used as a DNA-excision-based control framework for Boolean logic and arithmetic operations and in a light-responsive recombinase context for cell patterning applications.

Channelrhodopsins are light-activated ion channels from algae used as optogenetic tools to control membrane potential. Reported channelrhodopsin variants conduct either cations or anions, enabling light-driven depolarization or hyperpolarization.

Cry2/CIB is a genetically encoded blue-light-activated protein dimerization module derived from Arabidopsis thaliana. It is used to optically induce protein-protein interactions and has been applied to control transcription, protein localization, protein secretion, and, when coupled to BAX, light-triggered apoptosis.

The CRY2-CIB1 optogenetic PIP3 production system is a blue-light-responsive multi-component switch built from Arabidopsis CRY2 and CIB1. It recruits a CRY2-fused constitutively active PI3-kinase from the cytosol to the plasma membrane through light-induced CRY2-CIB1 interaction, enabling sub-second spatiotemporal control of PIP3 production.

CRY2/CIB1 is a light-responsive multi-component switch derived from Arabidopsis thaliana that uses CRY2-CIB1 association to control protein localization and kinase regulation. It has been reported to rapidly redirect proteins within living E. coli cells and to serve as the basis for light-regulated protein kinase designs.

The combined EL222 and LOVdeg system is a light-responsive multi-component optogenetic system developed in Escherichia coli by pairing the existing EL222 module with the LOVdeg blue-light-inducible degradation tag. It is intended to enhance optogenetic performance by combining EL222-based control with post-translational light-inducible protein degradation.

The iLID N414L variant is a modified iLID light-inducible dimerization system in which an N414L point mutation in the LOV domain lengthens the reversion half-life. In combination with SspB binding partners, it supports blue-light-dependent control of protein colocalization and has been used in reengineered iLID-SspB systems for processes including transmembrane protein localization.

Lockdown is a blue light-operated, multi-component CRISPR/Cas13b system for optical control of RNA abundance in mammalian cells. It uses a blue light-dependent switch to induce CRISPR/Cas13b expression, enabling sequence-specific knockdown of exogenous and endogenous mRNA.

LOOMINA is a light off-operated modular inducer of transcriptional activation engineered for mammalian cells. It is an optogenetic transcriptional control platform that efficiently terminates transcriptional activation in response to blue light and can be coupled to dCas9 for regulation from endogenous promoters.

LOV2-based photoswitches are optogenetic switches engineered from the LOV2 photoreceptor domain to control biological activities with light. They repurpose endogenous light-induced conformational changes in LOV2 to generate new cellular outputs and have been developed on the basis of detailed biophysical characterization of the isolated domain.

LOVpep/ePDZb is a blue-light-inducible heterodimerization system examined as one of three optogenetic dimer variants in a comparative cellular optogenetics study. It mediates light-dependent protein association that was used to control cellular localization and activity in assays including transcription, intracellular localization, and GTPase signaling.