Toolkit Items

A NIMPLY B gates are compressed two-input mixed-phenotype transcriptional logic operations reported in a 2023 ACS Synthetic Biology study on performance prediction of fundamental transcriptional programs. The study indicates that their behavior can be modeled and predicted from experimentally characterized single-input logical operations and associated metrology.

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.

Allosteric Cre regulation with NS3 ligands is a chemical multi-component recombination switch in which an NS3-based ligand-responsive system is used to allosterically regulate Cre recombinase. It was reported as an orthogonal recombination control strategy in eukaryotic cells and as a way to control prokaryotic recombinase activity across divergent organisms.

The antagonistic genetic circuit is a light-responsive multi-component mammalian synthetic switch that enables stringent transcriptional regulation. In the cited study context, it was reported to provide high spatiotemporal resolution with extremely low leaky expression and was proposed for light-regulated control of Diphtheria toxin A expression.

AQTrip is an engineered EL222 variant carrying V41I, L52I, A79Q, and V121I substitutions in the blue-light-responsive LOV–HTH transcription factor. It stabilizes the photoactivated state and, in the reported study, oligomerizes without DNA and forms an EL222 dimer–DNA complex in the presence of DNA substrates.

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.

ArrayG is a fluorogenic nanobody array tag built from linear repeats of GFP nanobodies that recruit free monomeric wild-type GFP. GFP fluorescence increases by approximately 15-fold upon array binding, enabling prolonged live-cell single-molecule imaging.

AsLOV2 REST-inhibitory chimeras are optogenetic fusion proteins that couple REST-inhibitory domains to the Avena sativa LOV2 photosensory module. In Neuro2a cells they enabled light-dependent modulation of REST target genes, and in primary neurons light-mediated REST inhibition increased Na+ currents and neuronal firing.

AsLOV2-Jα-Rac1 is an artificial fusion protein that connects the Avena sativa AsLOV2-Jα photosensor to the Rac1 GTPase to create a light-responsive signaling switch. Light-triggered structural changes in the LOV2 module disrupt steric inhibition of Rac1 and permit binding of the effector protein PAK1.

Associating photoreceptors are light-responsive receptors defined by changes in oligomeric state as part of light-regulated allostery. In engineered systems, they provide a multi-component switch architecture based on light-controlled association behavior.

The AtCRY2-TopBP1 optogenetic DNA damage checkpoint switch is a fusion of Arabidopsis thaliana cryptochrome 2 (AtCRY2) to the DNA damage checkpoint protein TopBP1. In mammalian nuclei, light-induced AtCRY2 photobody formation is used to activate DNA damage signaling in the absence of DNA damage.

The AUREO1 bZIP-LOV truncated construct (ZL) is an N-terminally truncated aureochrome-1 derivative that retains the bZIP DNA-binding region and the LOV photosensory domain. It binds DNA in a sequence-specific manner and undergoes a blue-light-induced conformational response measurable as an approximately 5% increase in hydrodynamic radius without a detectable change in secondary structure.

B NIMPLY A gates are compressed mixed-phenotype two-input transcriptional logic operations reported in a 2023 ACS Synthetic Biology study on performance prediction of fundamental transcriptional programs. In that context, their behavior was modeled and predicted from single-input data and metrology rather than described as a separately detailed molecular construct.

BACCS is a genetically engineered blue light-activated Ca2+ channel switch developed as an optogenetic tool for generating intracellular Ca2+ signals. It acts by opening Ca2+-selective ORAI ion channels in response to blue light and has been used to drive downstream cellular and physiological responses.

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.

BcLOV4-ARHGEF11 is a single-transgene optogenetic fusion in which the upstream RhoA activator ARHGEF11 is fused to BcLOV4. It enables light-inducible, spatiotemporally precise control of RhoA signaling through dynamic membrane localization without requiring a separate protein binding partner.

The BcLOV4-RhoA optogenetic fusion is a single-transgene light-responsive construct in which RhoA GTPase, or its upstream activator ARHGEF11, is fused to BcLOV4. It enables spatiotemporally precise optical control of RhoA signaling and associated cytoskeletal and mechanotransductive responses without requiring a separate protein binding partner for dynamic membrane localization.

BcWCL1 PASΔ is a PAS-domain-deleted variant of the Botrytis cinerea blue-light photoreceptor BcWCL1 that functions in yeast as a blue-light-activated transcription switch. The reported activity depends on the BcWCL1 N-terminal region, which supports light-stimulated self-dimerization and contains a functional 9aaTAD-family transcriptional activation domain.

The benzoate-/vanillate-responsive mammalian gene switch is a dual-input transgene control system engineered for mammalian cells that is induced and repressed by the food additives benzoate and vanillate. It was also reported to function as a modular component in higher-order gene control networks and to regulate a SEAP reporter in implanted designer cells in mice.

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.

Bioluminescence resonant energy transfer (BRET) is a multi-component light-activation strategy that uses bioluminescence to induce photochemical activation for photodynamic therapy. In the cited 2015 cancer study, BRET-driven therapy produced cytotoxicity comparable to external red laser irradiation and was applied against deep-tissue tumors, metastases, and tumor-bearing lymph nodes.

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.

BLISS is a blue-light-inducible SpyTag system generated by inserting SpyTag into different positions of the AsLOV2 Jα-helix. In this design, blue light exposure enables conditional SpyTag reactivity with SpyCatcher, allowing light-gated coupling.

The blue light-activated PKC isozyme recruitment system is a multi-component optogenetic switch that uses the plant-derived CRY2-CIB1 interaction to recruit PKC isozyme catalytic domains to the cell surface under blue light. In the reported format, CRY2-tagged PKC catalytic domains undergo light-triggered membrane translocation, and a PKCε implementation robustly activates GIRK1/4 potassium channels.

The blue light-dependent switch is a multi-component optogenetic control element used in the Lockdown system to induce expression of CRISPR/Cas13b in response to blue light. In this context, it enables light-triggered control of RNA levels through Cas13b-mediated mRNA knockdown.

The blue light-inducible cryptochrome-based dimerization system is a light-responsive multi-component switch that uses blue light to induce protein dimerization. The cited evidence supports its use for spatiotemporally precise control of signaling or cytoskeletal events.

The blue light-inducible LOV domain-based dimerization system is a light-responsive multi-component switch in which blue light induces dimerization to control intracellular signaling or cytoskeletal events. The cited literature describes this class of systems as providing spatiotemporally precise perturbation of cell behavior.

The blue light-responsive and rapidly reversible expression system is an optogenetic multi-component gene switch for mammalian cells that enables blue light-controlled transgene expression. It was developed as a rapidly reversible blue-light module and used within an orthogonal UV-B/blue/red-far-red triple-gene control framework.

BLINK1 is a blue-light-induced potassium channel engineered by fusing the plant LOV2-Jα photosensory module to the small viral K+ channel Kcv. It is reversibly photoactivated by blue light and channel opening drives membrane hyperpolarization toward the potassium equilibrium potential.

Boolean logic gates are synthetic genetic circuits that integrate multiple biological inputs into a defined output state. The supplied evidence indicates that such circuits have been developed with up to six inputs and are discussed as components within synthetic circuits of varying complexity.

BphP1-Q-PAS1 is a near-infrared-light-inducible optogenetic interaction pair composed of BphP1 and Q-PAS1. It enables light-controlled protein regulation, including transcription-related applications and modification of chromatin epigenetic state, and it can be combined with blue-light LOV-domain systems with negligible spectral crosstalk.

BphP1-QPAS1 is a near-infrared light-inducible protein interaction system in which the bacterial phytochrome BphP1 binds an engineered partner, QPAS1, for optical protein regulation in mammalian cells. It has been incorporated into multi-component optogenetic tools for transcriptional control and protein targeting, including use in neurons and non-neuronal cells.

C-terminal iLID fusion is a commonly used anchor configuration within the iLID optogenetic recruitment system. In the cited study, it functions as a baseline membrane-anchor design for light-controlled recruitment of components to subcellular locations, including micron-scale regions of the plasma membrane.

The C120 promoter is a TAEL-responsive regulatory element used in the zebrafish TAEL optogenetic transcription system. Blue light induces TAEL transcription factor dimerization, which activates transcription from the C120 promoter.

The Ca2+/cAMP response element decoy oligodeoxynucleotide (CRE-decoy ODN) is an oligodeoxynucleotide perturbation reagent used in the rat suprachiasmatic nucleus to interfere with CREB-dependent transcription. In the cited study, it blocked glutamate-induced Per1 mRNA accumulation and prevented glutamate-induced phase advances of the circadian clock, implicating CREB-dependent Per1 activation in light-responsive circadian signaling.

Caging/uncaging events are optogenetic control strategies in which light is used to regulate the functional state of signaling proteins. In the cited review, they are presented as one of two broad routes, alongside light-regulated protein-protein interactions, for steering signal transduction.

Caspase-LOV is an engineered light-activated human caspase-3 created by rational insertion of a light-sensitive LOV2 domain into caspase-3. Illumination triggers LOV2 expansion and enables optical activation of caspase-3, leading to apoptotic cell death and neuron ablation in vivo.

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.

CcaS/R is an optimized chromatic acclimation sensor/regulator module used as a light-input induction system in a dual light-controlled co-culture platform. In the cited implementation, it operates alongside the blue light-activated YF1-FixJ-PhlF module to regulate population composition.

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.

ChR2/C128X/D156A denotes engineered channelrhodopsin-2 variants carrying mutations at residue C128 or the D156A substitution. The supplied evidence identifies this class as part of the channelrhodopsin variant toolkit but does not provide direct functional characterization for these specific variants.

Channelrhodopsin-2 E123T, also called ChETA, is an engineered variant of the algal light-activated channel Channelrhodopsin-2 generated by point mutagenesis at residue E123. It is described in a comparative review as one of several channelrhodopsin optogenetic variants.

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.

ChemHEAL is a small-molecule-inducible variant of the HEAL dCas12f-based CRISPR activation platform for programmable transcriptional control. It uses a multi-component architecture in which transcriptional activators are recruited through MS2 coat protein binding to MS2 aptamers embedded in the sgRNA scaffold.

Chemical-controlled molecular switches are multi-component research tools in mammalian cell biology whose activity is regulated by chemical inducers. The supplied evidence establishes their general role as central instruments and identifies chemical input as the control modality, but does not specify particular switch architectures or target processes.

The chemically inducible RTK platform is a multi-component chemical switch that enables tunable, background-minimized activation of receptor tyrosine kinases. Upon chemical induction, it drives RTK clustering at the plasma membrane and elicits ERK-dependent cellular responses while allowing activation to be intentionally triggered.

ChETA-SFO co-expression strategy is a multi-component optogenetic design that co-expresses a fast channelrhodopsin with a step-function opsin to improve neuronal optical switching. In a 2022 theoretical study, this approach was proposed to support sustained low-power, high-frequency, high-fidelity spiking by combining fast channelrhodopsin-driven excitation with sustained step-function opsin photocurrent.

chimera D (ChD) is an engineered channelrhodopsin variant identified in a comparative review of channelrhodopsin tools. The supplied evidence indicates that it emerged from chimeragenesis, mutagenesis, and bioinformatic engineering efforts, but does not describe its specific functional properties or application behavior.

chimera EF (ChEF) is an engineered channelrhodopsin variant identified in a 2010 review as part of the broader set of modified channelrhodopsins. The supplied evidence indicates that it was introduced through chimeragenesis, mutagenesis, and bioinformatic approaches, but does not provide its specific design or functional characterization.

chimera EF I170V is an engineered channelrhodopsin variant described as a ChEF chimera carrying the I170V mutation. The supplied evidence identifies it as an optogenetic light-gated ion channel variant but does not provide direct functional characterization for this specific construct.