Toolkit Items

Chimeric antigen receptor natural killer (CAR-NK) cells represent a promising "off-the-shelf" alternative to CAR-T cells.

This review examines recent advancements in nanoparticle( s) (NPs) delivery systems, with a focus on ... lipid nanoparticles (LNPs)... We discussed various NP platforms and their applications, such as ... dry powder formulations of mRNA-loaded LNPs for pulmonary delivery, and LNP-mediated siRNA delivery for respiratory infections.

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.

CRY1 is a blue-light-sensing cryptochrome protein from the Arabidopsis cryptochrome family, and the name cry1 is also used for a Drosophila-like insect cryptochrome gene family. The supplied evidence indicates that CRY1 mediates blue light responses, contributes to regulation of early blue light-induced genes, and has functional overlap with CRY2.

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.

Arabidopsis cryptochrome 2 (AtCRY2) is a blue-light-responsive plant photoreceptor domain that has been heterologously expressed in mammalian cells. In that context, blue light induces AtCRY2 photobody formation and also triggers AtCRY2 degradation, providing a light-controlled module linked to protein clustering and turnover.

MALAT1 is a long noncoding RNA reported in trophoblasts to promote cell migration and invasion by reducing CRY2 protein abundance. In the cited study, MALAT1 recruits the E3 ubiquitin ligase FBXW7, impairing CRY2 protein stability and inducing ubiquitin-mediated CRY2 degradation.

Halorhodopsin (NpHR) is a microbial rhodopsin optogenetic tool described as a hyperpolarizing light-driven chloride ion pump. It is used for optical silencing and artificial modulation of neuronal activity, and has been combined with channelrhodopsin-2 (ChR2) for multimodal remote control of neurons in culture, tissue, and living animals.

LOVdeg is an engineered protein tag that is appended to a protein of interest to enable blue-light-inducible degradation in Escherichia coli. It provides optically controlled post-translational regulation by coupling light exposure to loss of the tagged protein.

The photosensitive degron (psd) is a protein-domain tool that confers acute light-induced degradation on fused proteins. Available evidence indicates activity in the nervous system and a construct requirement that the psd be placed at the carboxy terminus of the target protein.

its cognate stem-loop RNA (Cas6 binding site, termed CBS)

Here, we developed a genetically encoded biosensor, cdiGEBS, based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH.

The CRY2-lacZ gene fusion is a Saccharomyces cerevisiae reporter construct used to measure how CRY2 sequence features regulate reporter expression. It was applied to identify cis-acting elements involved in repression of CRY2, linking CRY2-derived nucleotide information to lacZ output.

The development of KEAP1-recruiting PROTACs utilizing ligands derived from different classes of known KEAP1 inhibitors-including short peptides, covalent small molecules (e.g., CDDO derivatives), and non-covalent inhibitors (e.g., KI696)-is discussed.

A non-linear disturbance observer (NDO) is an engineering control method used within a feedback linearisation framework to estimate lumped uncertainty. In the cited in-wheel motor drive study, it was implemented as part of a DSP-based intelligent control system for a six-phase permanent magnet synchronous motor.

First, we developed a constitutive excitatory synapse ablator, PFE3, analogous to the inhibitory synapse ablator GFE3. PFE3 targets the RING domain of the E3 ligase Mdm2 and the proteasome-interacting region of Protocadherin 10 to the scaffolding protein PSD-95, leading to efficient ablation of excitatory synapses.

The TRIM21 RING domain is a catalytic protein domain whose ubiquitination activity is activated by substrate-induced clustering that promotes intermolecular RING dimerization. In the cited 2020 study, this activation mechanism underlies TRIM21-dependent antiviral responses and Trim-Away-mediated protein degradation.

We used DNA array technology to decipher the interplay between these responses in P. putida KT2440 subjected to a short challenge (15 min) with toluene.

Here, we consider the potential of macrocyclic peptides to overcome this limitation.

Synthetic, light-induced RNA condensation is an engineering method that uses light to induce RNA condensation in cells. In the cited study, this perturbation was sufficient to fluidize the cytoplasm, supporting a causal role for RNA condensation in increasing mesoscale particle diffusivity.

Between 2020 and 2025, major progress has been achieved across five modalities: ... autophagy-targeting chimeras (AUTACs) and related tethering strategies...

Bacterial degraders are a proposed construct pattern for targeted protein degradation in bacteria. They are discussed as tools to interrogate protein function and as potential antimicrobial modalities.

Bacterial degrons are proteolysis-targeting signals that are appended to proteins to direct their degradation in bacterial cells. They are described as tools to interrogate and control protein function through targeted protein depletion.

Base editors are identified in the supplied evidence as a bacterial genome-editing tool category discussed alongside CRISPR nickases and Cas12a. The evidence establishes their inclusion within genome-editing approaches in bacteria but does not describe their molecular composition or specific editing outcomes.

CRISPR-associated transposases are identified in the cited review as a bacterial genome-editing method category within the broader landscape of CRISPR-Cas and related approaches. The supplied evidence establishes only their inclusion as an editing approach and does not provide mechanistic or performance detail.

MCs are embedded in the final product and therefore need to be edible... the third scenario appears to be the most promising one for a production process. Indeed, using an edible material can limit or completely eliminate dissociation/degradation/separation steps and even promote organoleptic qualities when embedded in the final product.

Between 2020 and 2025, major progress has been achieved across five modalities: ... lysosome-targeting chimeras (LYTACs)... Each exploits endogenous degradation or regulatory pathways using chemically engineered bifunctional or monofunctional small molecules.

Between 2020 and 2025, major progress has been achieved across five modalities: proteolysis-targeting chimeras (PROTACs), molecular glues... Each exploits endogenous degradation or regulatory pathways using chemically engineered bifunctional or monofunctional small molecules.

Orthogonal degrons are bacterial construct patterns used in tunable degradation systems to direct targeted proteolysis of proteins of interest. The cited literature places them among recent advances that enable large screens and functional interrogation through regulated protein degradation.

PROteolysis TArgeting Chimeras (PROTACs) are heterobifunctional molecules consisting of two ligands; an "anchor" to bind to an E3 ubiquitin ligase and a "warhead" to bind to a protein of interest, connected by a chemical linker.

The development of proteolysis targeting chimeras (PROTACs) that trigger degradation of the target proteins provides a conceptually novel approach to address drug targets that remained previously elusive.

Between 2020 and 2025, major progress has been achieved across five modalities: ... and ribonuclease-targeting chimeras (RIBOTACs). Each exploits endogenous degradation or regulatory pathways using chemically engineered bifunctional or monofunctional small molecules, thereby expanding the druggable proteome and transcriptome.

Synthetically engineered guide RNAs are chemically modified or conjugated CRISPR guide RNAs used in mammalian cells to improve the performance and functional scope of CRISPR-Cas9 systems. Reported implementations increase guide stability and specificity, support donor DNA tethering to enhance homology-directed repair, and enable fluorescent genomic imaging.

This entry refers broadly to imaging-oriented tools and sensors associated with bacterial degron and degrader concepts. The supplied evidence only states that bacterial degrons can be used to interrogate and control protein function and mentions “tools and sensors for imaging,” without defining a specific construct, sensor architecture, or imaging readout.

These heterobifunctional molecules are comprised of three units: a ligand for the protein of interest (POI), a ligand for an E3 ubiquitin ligase, and a linker that tethers the two motifs together. Von Hippel-Lindau (VHL) is one of the most widely employed E3 ligases in PROTACs development.

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.

The blue light-inducible degradation (B-LID) domain is a light-activated degron used to trigger loss of a fused protein in vivo. Available evidence indicates that it must be fused to the carboxy terminus of the target protein and can elicit light-dependent loss of Cactus function in developing Drosophila embryos.

The blue light-responsive Cas13b mRNA knockdown system is an optogenetic RNA-control platform in which blue light induces expression of an engineered Cas13b that specifically degrades target mRNAs. In the reported application, combining three blue light-inducible switches reduced protein levels by more than 99%.

In the present study, transgenic tobacco lines with constitutive SsDHN expression (SsDHN-OE) were employed to examine its influence on seedling development under water-limited conditions.

CRISPRoff is an engineering method for light-induced degradation of single-guide RNA (sgRNA) that inactivates the CRISPR ribonucleoprotein. It enables spatiotemporal attenuation of CRISPR-Cas9 genome editing in cells through selective illumination.

CRY2-GFP is a C-terminal green fluorescent protein fusion of Arabidopsis cryptochrome 2 used to probe CRY2 blue-light responses. In the cited Plant Cell study, this fusion displayed constitutive biochemical and physiological activity and underwent blue-light-induced degradation more slowly than GFP-CRY2 or endogenous CRY2.

GFP-CRY2 is an N-terminal green fluorescent protein fusion to Arabidopsis CRY2. In the cited Plant Cell study, this fusion retained blue light-dependent biochemical and physiological activities similar to endogenous CRY2 and showed blue light-responsive degradation behavior more similar to native CRY2 than the reciprocal CRY2-GFP construct.

Jalpha helix point mutations disrupting LOV-domain interaction are a phototropin construct pattern in which residues along the Jα helix are mutated to weaken LOV–Jα intramolecular association. In full-length phototropin, these mutations displace or unfold the Jα helix and produce constitutive kinase activation in the absence of illumination.

The LOV2 domain-based optogenetic tool is a light-responsive protein-domain system reported to control protein degradation and cellular function. The supplied evidence identifies a LOV2-based optogenetic platform but does not specify the exact construct architecture or experimental context.

Here, we constructed lysosome-localized optogenetic actuators, named lyso-NpHR3.0, lyso-ArchT, and lyso-ChR2, to achieve optogenetic manipulation of lysosomes.

Here, we constructed lysosome-localized optogenetic actuators, named lyso-NpHR3.0, lyso-ArchT, and lyso-ChR2, to achieve optogenetic manipulation of lysosomes. Notably, lyso-ChR2 activation induces autophagy through the mTOR pathway, promotes Aβ clearance in an autophagy-dependent manner in cellular models, and alleviates Aβ-induced paralysis in the Caenorhabditis elegans model of Alzheimer's disease.

Here, we constructed lysosome-localized optogenetic actuators, named lyso-NpHR3.0, lyso-ArchT, and lyso-ChR2, to achieve optogenetic manipulation of lysosomes.

Nanobody-mediated proteolysis-targeting chimeras are a degradation-based engineering method used in an optogenetically coordinated platform to regulate the intracellular factor Survivin in cancer cells. In the cited study context, they are combined with split-Cas9-based targeted gene editing for multi-level control of cancer cell fate.

opto-PROTAC is a light-inducible PROTAC design in which a photolabile caging group is installed on pomalidomide-based degraders to block activity in the dark and permit target protein degradation after ultraviolet A irradiation. It was demonstrated using caged pomalidomide and the PROTACs dBET1 and dALK to achieve spatiotemporal control of protein destruction.

In addition, we developed a light-inducible version of GFE3, paGFE3, using a novel photoactivatable complex based on the photocleavable protein PhoCl2c. paGFE3 degrades Gephyrin and ablates inhibitory synapses in response to 400 nm light.