Toolkit Items

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.

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.

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.

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.

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.

The AS1411 aptamer-modified cell membrane biomimetic core-shell system is a light-augmented delivery harness for CRISPR-Cas9 plasmid cargo (pCas9). It consists of a cell membrane-camouflaged shell modified with AS1411 aptamers and photosensitizers to promote tumor targeting, reactive oxygen species-mediated lysosomal escape, and light-controllable pCas9 release for enhanced gene editing.

Bioelectronic implants are delivery-harness systems that combine light-interfaced electronic devices with optogenetic systems. The cited literature describes them as portable, personalized precision bioelectronic medical tools.

Biofunctional nanodot arrays (bNDAs) are nanoscale surface-patterned delivery harnesses designed to spatially control dimerization and clustering of cell-surface receptors. In live cells, they were used to capture extracellularly GFP-tagged Lrp6 and drive assembly of active Wnt signalosomes at the plasma membrane.

Bioreactor designs for optogenetic stimulation are light-delivery and culture-platform configurations used to stimulate optogenetic systems across experimental formats ranging from simple illumination set-ups to microscopy, microtiter plate, and bioreactor designs. These platforms support applications spanning single-cell stimulation to whole-culture illumination and can be integrated with automated measurement and stimulation for computer-controlled experiments.

Camouflage nanoparticle-based vectors are biomimetic delivery systems developed for in situ bioluminescence-driven optogenetic therapy of retinoblastoma. In the cited 2023 ACS Nano study, this system enabled optogenetic treatment and showed greater tumor inhibition than external blue light irradiation.

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.

Ce-doped Gd3(Al,Ga)5O12 (Ce:GAGG) microparticles are injectable yellow-emitting inorganic scintillators used to convert X-ray irradiation into local optical output in vivo. In the cited study, this scintillation activated the red-shifted opsins ChRmine and GtACR1, enabling remote bidirectional control of neural activity.

Ce-doped Gd3(Al,Ga)5O12 (Ce:GAGG) microparticles are injectable yellow-emitting inorganic scintillators used as implanted transducers for X-ray-driven optogenetic control. In the cited study, they converted X-ray irradiation into local light sufficient to activate ChRmine and inhibit via GtACR1, enabling bidirectional modulation of neural activity in mice.

The cell membrane biomimetic core-shell system is a membrane-camouflaged delivery harness developed for light-controllable, precise gene editing. In the cited study, it was used as a CRISPR-Cas9 delivery strategy for tumor cell reprogramming and cancer therapy.

Core-shell fluorescent upconversion nanoparticles are a near-infrared-responsive delivery harness that converts highly penetrating near-infrared excitation into simultaneous ultraviolet and visible emission. In the cited study, these nanoparticles functioned as remote nanotransducers to promote endosomal escape and enhance photomorpholino-mediated gene knockdown.

The CRISPR-Cas9 piggyBac system is a regulatable genome engineering delivery harness reported in human cells. It combines CRISPR-Cas9 with a piggyBac-based system to enable site-specific randomization of the endogenous genome.

NP2 denotes decitabine nanomicelles incorporated into a tumor-specific, light-controlled nanotheranostic platform. In the reported 2023 Advanced Materials study, NP2 is used together with oxidation-sensitive nanoparticles loaded with TBE to combine epigenetic therapy with photodynamic therapy for tumor photoimmunotherapy.

This entry describes delivery-system choice as a genome-editing optimization strategy rather than a single defined molecular reagent. In the cited 2022 review, delivery-system selection is presented as one approach for improving the efficiency of CRISPR/Cas-induced mutations.

Diya is a universal light illumination platform for multiwell plate cultures that is compatible with a wide range of cell culture plates and dishes. It provides programmable optical induction and has been used to drive light-controlled operation of an in vivo biomolecular feedback circuit.

Down-conversion phosphors are material-based light-delivery harnesses explored for remote optogenetic control of neuronal activity in living animals. They are used in wireless, less invasive optical stimulation strategies to control cellular functions in the brain and other tissues.

Drug-inducible lentiviral and transposon vectors were used to deliver the PhyB-PIF light-inducible dimerization system together with the synPCB phycocyanobilin synthesis module. In the cited study, doxycycline treatment induced PCB synthesis and enabled PhyB-PIF light-inducible dimerization function.

Engineered endosymbionts (EES) are engineered intracellular bacteria that escape endosomal destruction, reside in the mammalian cell cytoplasm, and secrete proteins that are transported to the nucleus. In the reported 2021 system, EES were engineered to express mammalian transcription factors and thereby direct host cell gene expression and modulate host cell fate.

Ex vivo stem cell modification and re-transplantation is a clinical delivery workflow in which a patient's own stem cells are isolated, genetically modified outside the body with CRISPR-based approaches, and returned to the same patient. The supplied evidence identifies this format as common among current clinical CRISPR trials.

EXPLORs is an exosome-based intracellular protein delivery platform that couples exosome biogenesis to a blue-light-controlled reversible protein–protein interaction module. It is designed to load soluble cargo proteins into newly generated exosomes and increase their intracellular delivery and functional activity in recipient cells in vitro and in vivo.

Fiber optic technologies are described as a delivery harness used to develop implantable devices for generating and recording signals in excitable tissues. In the cited optogenetics context, they support light-based monitoring of biochemical processes and control of cellular activity.

The flexible implantable piezoelectric nanogenerator (i-PENG) is an implantable energy-harvesting component of a self-powered optogenetic system for blood glucose control. It converts biomechanical energy into electricity to provide long-term power for a biocompatible far-red light source that interfaces with FRL-triggered transgene-expressing cells.

Focused ultrasound (FUS) is a noninvasive physical delivery and control modality that penetrates deep biological tissues and induces confined mild hyperthermia to activate heat-sensitive genetic modules. In the cited 2023 study, FUS was coupled to heat-sensitive CRISPR, CRISPRa, and CRISPRi systems to enable remote spatiotemporal regulation of genome and epigenome function in live cells and animals.

The GelMA-Macrophages-LED system is a composite delivery harness composed of a light-crosslinked GelMA hydrogel, gene-modulated macrophages, and a wireless LED device. In the cited study, it was used for in situ light regulation of cardiac inflammation in murine lipopolysaccharide-induced sepsis models, with macrophage photoactivation linked to suppression of inflammatory cytokine production.

High-velocity microprojectile-mediated gene transfer, or particle bombardment, is a physical DNA delivery harness used to establish a rapid transient expression assay. In the cited 1989 study, it introduced an oat phy-CAT reporter construct into rice, enabling analysis of phytochrome-regulated phy gene expression within less than 24 hours after bombardment.

HiRet is a lentiviral system for highly efficient retrograde gene transfer that targets specific neural circuits. It supports neural circuit-selective, stable transgene expression and has been used with optogenetic tools to manipulate neuronal activity and behavior.

Hydrogen-rich water (HRW) is a dissolved-gas treatment reported to enhance anthocyanin accumulation in immature radish microgreens when combined with short-wavelength light, including blue light and UV-A. In the cited study, this response was associated with altered anthocyanin-biosynthetic enzyme activity and transcript abundance.

Lanthanide-doped upconversion nanoparticles are a near-infrared-responsive delivery harness that converts NIR light into visible light to modulate neurons expressing classical opsins. They act as a wireless optical transducer that couples deeper-penetrating NIR illumination to conventional optogenetic actuators.

The LED illumination system is a low-cost, versatile, and customizable light-delivery harness for optogenetic experiments. It provides programmable illumination with automated precise timing and pulsing through an open-source user interface running on a personal computer or inexpensive tablet.

lentiSLiCES is a lentiviral implementation of the self-limiting Cas9 editing system SLiCES. It delivers genome-editing activity to target cells and then promotes self-neutralization by inactivating SpCas9 after editing.

The lentiviral platform is a delivery harness used to implement an optimized Light-On system for light-controlled gene expression in neurons. The available evidence supports its use for optically regulated transgene expression in neuronal contexts, but does not provide further construct-level or performance details.

LAVA is a set of engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes. It delivers user-defined light intensity, temporal sequences, and spatial patterns to control signaling responses, including optogenetic Wnt/beta-catenin pathway activation.

Light emitting diodes (LEDs) are a light-delivery harness discussed in a 2022 review as part of light-engineering technology for modulating plant biology. In that context, LEDs are presented as a potential approach for fine-tuning crop defense and yield.

The Light Plate Apparatus (LPA) is an open-source light delivery device engineered for 24-well plates that provides two independent optical inputs to each well. It delivers wavelengths spanning 310 to 1550 nm with intensity control over three orders of magnitude and millisecond temporal resolution, and it has been used for spectral and dynamical calibration experiments in optogenetics and photobiology.

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.

The light-controlled bioreactor is a light-input production platform reported for optogenetic control of gene expression in Corynebacterium glutamicum. In that context, it was used to drive chito-oligosaccharide (CHOS) biosynthesis to 6.2 g/L, which the source describes as the highest recorded CHOS titer to date.

Light-emitting diode illumination is a light-delivery harness used with a photoactivatable CRISPR-Cas9 system to provide optical input for temporally and spatially controlled genome editing in mice. In the cited in vivo study, it was applied in the context of embryo implantation and reproductive function.

Light-induction hardware-software platforms are optogenetic delivery systems that provide controlled illumination using formats ranging from simple illumination set-ups to microscopy, microtiter plate, and bioreactor designs. They are used to stimulate biological systems with light, and automated implementations can support computer-controlled experiments with in silico feedback control.

Light-responsive nano-regulators are light-activatable nanoplatforms used to manipulate cellular functions with high spatiotemporal precision. The cited 2019 review describes their application to neuromodulation, stem cell monitoring, immunomanipulation, cancer therapy, and other biological target interventions.

LITOS is a LED Illumination Tool for Optogenetic Stimulation built from an assembled printed circuit board that controls a commercially available 32×64 LED matrix. It serves as a programmable light-delivery harness for optogenetic stimulation and is reported to support flexible temporal illumination schemes across multiple culture vessel formats.