Toolkit Items

The (C120)5-CYC102 responsive promoter architecture is a blue-light-inducible transcriptional output module comprising five copies of the C120 upstream activation sequence fused to the minimal promoter CYC102. In an EL222-based single-component system in Yarrowia lipolytica, it mediated blue-light-dependent expression of the GFPMut3 reporter.

15N and 1H liquid-state high-resolution NMR is an assay method used to detect light-induced photo-CIDNP signals in engineered Mr4511 flavoproteins. In the cited study, it reported nuclear hyperpolarization arising from a light-driven transient paramagnetic state in variants containing tryptophan at canonical or newly introduced positions.

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 2D silicene-based nonviral vector, termed silicene-Cas9, is a NIR-II light-controlled CRISPR/Cas9 nanosystem built from 2D silicene nanosheets. It is designed to harness the photothermal-conversion capability of biosafe, biodegradable silicene for nonviral genome-editing delivery.

The 5-deazaFMN-based Avena sativa LOV2 photoswitch is an AsLOV2 protein domain in which the native FMN chromophore is replaced by the flavin analogue 5-deazaFMN. Upon illumination, this cofactor-exchanged construct forms a thermodynamically stable adduct, and recovery to the dark-adapted state can be induced by light, enabling a repeatable photoswitching cycle.

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.

The A. sativa LOV2 domain is a light-responsive protein domain used as a regulatory module in engineered optogenetic switches. In a DHFR/LOV2 fusion, photoactivation thermally destabilized the fusion and lowered the catalytic transition free energy of the lit state relative to the dark state.

The A'α-helix is an N-terminal upstream element of the Arabidopsis thaliana phototropin1 LOV2 photosensory module that interacts with the Jα-helix and contributes to blue-light signal transmission to the downstream serine/threonine kinase. Truncation of this region or Ala substitution of conserved A'α/Aβ-gap residues Glu474 and Lys475 impairs blue-light-induced kinase activation in phot1 LOV2-STK polypeptides.

The A'α-LOV2-Jα photosensory module is a light-responsive domain from Arabidopsis phototropin 1 that primarily controls light-induced activation of the C-terminal kinase domain and subsequent receptor autophosphorylation. Available evidence links LOV2-dependent photosensory input to regulation of phot1 kinase activity.

The A'α/Aβ gap is a structurally defined region N-terminal to the LOV2 core of Arabidopsis thaliana phototropin1. In LOV2-serine/threonine kinase polypeptides, this region contributes to blue-light signal transmission from LOV2 to kinase activation, and conserved residues Glu474 and Lys475 are required for efficient light-induced kinase activation.

AAV-based viral vectors are adeno-associated virus delivery systems used to introduce optogenetic transgenes for expression in target cell types. In the cited therapeutic optogenetics context, they are presented as promising for human trials but still limited by barriers to general use.

AAV-PA-Cre 3.0 is an adeno-associated viral delivery resource for the photoactivatable Cre recombinase 3.0 system, generated and validated for in vivo mouse applications. It delivers a blue-light-gated Cre/lox recombination system engineered for mammalian expression with reduced background recombination.

AAV9-mediated CIB1 transduction is an in vivo gene delivery approach that uses adeno-associated virus serotype 9 to drive CIB1 gain-of-function expression. In hepatocellular carcinoma patient-derived xenografts, this manipulation promoted lenvatinib resistance.

Accelerated MD simulation is an in silico computational method reported for elucidating the photoactivation mechanism of the AsLOV2 light-responsive domain. The available evidence supports its use as a mechanistic analysis approach for a protein photosensor rather than as a deployable biological reagent.

AcrIIA4 is an anti-CRISPR protein characterized in Nicotiana benthamiana as an inhibitor of CRISPR/Cas9 function. In plant assays, it blocks Cas9-mediated site-directed mutagenesis and represses CRISPR/dCas-based transcriptional activation, including when delivered by Tobacco etch virus.

AcrIIC3 is an anti-CRISPR protein that inhibits Neisseria meningitidis Cas9 (NmeCas9). Engineered AcrIIC3-Avena sativa LOV2 hybrids function as blue-light-switchable NmeCas9 inhibitors, blocking genome editing in the dark and permitting robust editing under blue light.

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.

AcrVA1 is an anti-CRISPR protein functionally characterized in Nicotiana benthamiana as an inhibitor of Cas12a-dependent activities. In the cited plant study, transient co-expression of AcrVA1 suppressed both CRISPR/Cas12a-mediated genome editing and CRISPR/dCas-based transcriptional activation reporter output.

The active phytochrome binding (APB) domain is a protein interaction module present in most phytochrome-interacting factors (PIFs) that mediates binding to light-activated phytochrome B (phyB). In Arabidopsis PIF4 and PIF5, this domain is required for phyB-associated, phosphorylation-preceded, proteasome-sensitive degradation in a light-regulated shade-avoidance pathway.

Adeno-associated virus (AAV) is a viral delivery harness used to package and express CRISPR genome-editing components in vivo. In the cited literature, AAV supports single-vector delivery when smaller Cas9 orthologues and their chimeric guide RNAs fit within AAV packaging constraints, enabling robust in vivo genome editing.

Adeno-associated virus (AAV) particles were used as a delivery harness for the BphP1-QPAS1-based TA optogenetic system in neurons. In the cited ChemBioChem study, this application was enabled by the small size of the QPAS1 component.

Adeno-associated virus delivery is a viral gene delivery harness used to deploy the far-red light-induced split-Cre recombinase (FISC) system in vivo. In the cited study, AAV delivery enabled implementation of optogenetically controlled genome engineering in living systems.

Adenoviral infection is a viral delivery harness used in vitro to introduce the optogenetic actuators ChR2(H134R) and ArchT into primary cardiac fibroblasts. In the cited Methods in Molecular Biology protocol, it enables quick, robust, and consistent opsin expression and supports generation of light-responsive cardiac fibroblast preparations.

Adenovirus is described here as a viral delivery harness used in optogenetic experiments to introduce genes encoding photosensitive proteins into specific neural regions. This delivery enables subsequent light-gated control of ion passage for neuronal activation or inhibition.

The Aer PAS domain is the FAD-binding sensory domain from the dimeric Escherichia coli aerotaxis receptor Aer. It monitors cellular respiration through a redox-sensitive flavin cofactor and is structurally characterized in the Aer-PAS-GVV variant at 2.4 Å resolution.

Affinity-based purification of caged DNA is a preparation method for caged linear double-stranded DNA in which a minimal protein-expression cassette is reacted with Bio-Bhc-diazo and the caged DNA is isolated by affinity separation. The reported application context is light-controlled gene expression in mammalian cells.

The Affymetrix ATH1 microarray is a transcript expression assay for genome-scale expression profiling in Arabidopsis thaliana. In the cited AtGenExpress study, it was used to generate a comprehensive transcript dataset across abiotic stress conditions including UV-B light, drought, and cold.

AKAR3EV is a previously developed genetically encoded Förster resonance energy transfer (FRET) biosensor for protein kinase A activity that comprises a CFP/YFP fluorescent protein pair. In the cited 2020 ACS Sensors study, it served as the benchmark comparator for the red-shifted Booster-PKA biosensor.

Algal-mediated nanoparticles are presented in a 2023 review as a delivery-related concept at the intersection of microalgal gene editing and CRISPR/Cas system delivery. The available evidence identifies a proposed tool class relevant to editing, but does not define a specific nanoparticle formulation, cargo architecture, or experimentally demonstrated delivery workflow.

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.

All-atom replica exchange discrete molecular dynamics is a computational docking method used to generate structural models of calcium and integrin binding protein 1 (CIB1) bound to α-integrin cytoplasmic tails. In the cited CIB1 study, it predicted that multiple α-integrin tails engage the same hydrophobic binding pocket on CIB1.

The all-optical framework for functional testing of opsin responsiveness in cardiac fibroblasts is an assay method described to evaluate whether virally introduced optogenetic actuators are functionally responsive in primary cFB. In the cited study, it provides an optical functional readout for opsin-expressing cardiac fibroblasts and is associated with co-culture conditions that can yield a light-sensitive excitable cardiac syncytium.

The allelic series of Cry mutants is a panel of 22 cryptochrome variants, each carrying a single amino acid substitution identified by random mutagenesis and a cell-based screen. The series was used to generate diverse deficiencies across CRY functions and to identify residues involved in protein-protein interaction and CRY2-specific repression.

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.

ALovD-1 is an archaeal LOV protein domain functionally characterized as a blue-light-responsive photoreceptor. In heterologous expression, it retained conserved dark- and light-adapted state photophysics, exhibited slow photocycle recovery, and remained active at 0.5 M monovalent salt.

The alpha-helical domain linker is a construct pattern in which a rigid alpha-helical segment is placed between fused protein domains to couple their functions. In the cited design context, it is proposed to act as a helical allosteric lever arm that transmits conformational information between domains.

AlphaFold3 is a computational structure-prediction method used in the cited study to model the MagMboI–DNA complex. In that work, it was applied to infer interactions with the 5'-GATC-3' recognition sequence and to guide optimization of the photoactivatable endonuclease variant MagMboI-plus for top-down genome engineering.

AM1_1557 is a typical red/green cyanobacteriochrome domain from Acaryochloris marina that can bind biliverdin at a level almost comparable to phycocyanobilin. In its biliverdin-bound form, the Pfr state is reported to fluoresce at room temperature with an emission maximum at 730 nm.

Am1_c0023g2 is a cyanobacteriochrome photosensory domain from Acaryochloris marina that covalently binds either phycocyanobilin or biliverdin with high binding efficiency. It has been used as the light-responsive target for engineered, state-selective binders that enable green-, orange-, red-, and far-red-controlled protein-protein interactions and transcriptional regulation in yeast.

AM1_C0023g2 Ser334Gly mutant is a cyanobacteriochrome-derived protein domain variant in which Ser334 is replaced by Gly. It retains the AM1_C0023g2 scaffold’s covalent bilin-binding and light-dependent photoconversion properties, and the mutation was reported to significantly improve the yield of the biliverdin-binding holoprotein, supporting its use as a platform for future optogenetic switch development.

The Anderson-Darling test is a nonparametric computational method applied in genome-wide association studies of complex quantitative traits. In an enlarged maize association panel, it identified loci across 17 agronomic traits, including both previously known loci and additional candidate loci detected only by this test.

Animal opsin-based pigments are light-responsive receptor systems composed of an opsin protein bound to the chromophore 11-cis retinal. Most are typical G protein-coupled receptors, and their diversity, particularly among nonconventional visual pigments, has been proposed as a basis for optogenetic modulation of GPCR signaling.

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.

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.

The antiGFP nanobody is used as a targeting domain in an iLID fusion to localize the light-inducible iLID module to GFP-tagged proteins. In this configuration, blue-light illumination induces iLID-SspB heterodimerization while recruitment remains efficient at the GFP-labeled target.

Antisense morpholino oligonucleotides are synthetic antisense reagents used for gene knockdown in sea urchin embryos. In the cited literature, microinjection into the egg is described as the most widely used delivery approach, and membrane-permeable vivo-MOs extend knockdown to later developmental stages.

The antisense oligodeoxynucleotide against Per1 is a nucleic acid perturbation reagent used in the rat suprachiasmatic nucleus to suppress Per1 function during circadian signaling experiments. In the cited study, this antisense ODN blocked glutamate-induced phase advances, implicating Per1 in light-responsive clock resetting.

Antisense RNA is an RNA-based regulatory tool reported in tobacco to restore fertility in genetically engineered male sterile plants. The available evidence indicates a functional phenotype in this plant system, but does not specify the target gene, antisense construct design, or molecular implementation.

APC is a cationic polymer-coated gold nanorod used in the nanoCRISPR platform as the delivery harness for a Cas9 plasmid driven by a heat-inducible promoter. Within this system, it supports near-infrared-programmable genome editing by coupling plasmid delivery to photothermal control of Cas9 expression.

Aptazyme-embedded guide RNAs are engineered CRISPR guide RNA constructs that confer ligand-responsive control over CRISPR outputs. Reported functions include ligand-responsive genome editing and ligand-responsive transcriptional activation.