Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.
47 items matching 1 filter
Mechanism Branch
Layer 1
Mechanisms
Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.
Layer 2
Architectures
Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.
Layer 3
Components
Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.
Technique Branch
Layer 1
Approaches
High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.
Layer 2
Methods
Concrete methods used to design, build, verify, or characterize engineered systems.
Showing 1-47 of 47
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.
As a tool component, CIB1 is most directly supported as the cryptochrome-interacting bHLH partner used with CRY2 to create blue-light-controlled protein association systems. In these systems, CIB1 is typically fused to localization, transcriptional, or enzymatic modules so that blue light drives CRY2–CIB1 binding and light withdrawal reverses the interaction.
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.
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.
DNA nanostructures, such as DNA origami, provide nanoscale spatial precision for regulating receptor valency and oligomerization.
OptoSTIM1 is an optogenetic protein tool engineered by combining the STIM1 SOAR region with a plant photoreceptor LOV2 domain. It manipulates intracellular Ca2+ levels by light-dependent activation of endogenous Ca2+-selective CRAC channels.
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.
Intrinsically disordered regions (IDRs) are protein domains used in engineered synthetic condensates to drive constitutive oligomerization and cluster formation. In the cited modular membraneless organelle design, IDR-mediated assembly is separated from cargo recruitment by fused interaction domains, enabling tunable control of condensate composition and function.
We investigated the G-quadruplex (G4) binding selectivity of short aromatic oligoamide helical foldamers comprising quinoline (Q) and pyridine (P) units... Mixed quinoline-pyridine foldamers are thus a promising class of selective G4 ligands
Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings.
The oligomerizing CRY2 component is a modified CRY2-based optogenetic construct tested in Drosophila melanogaster as a tool for negative regulation of targeted proteins. The available evidence indicates that it was evaluated in the context of adapting CRY2/CIB optogenetic components to Drosophila-specific constructs.
Q-PAS1 is an engineered single-domain binding partner for the bacterial phytochrome BphP1 that enables near-infrared-light-inducible protein interactions. It was developed as a smaller, non-oligomerizing alternative to the natural BphP1 partner PpsR2 and has been applied to transcription regulation, chromatin state modification, and spectral multiplexing.
The theoretical probability of neighbor density (PND) is a computational method introduced to discern protein oligomeric states in cellular environments. It is described as robust, precise, and adaptable for analyzing oligomerization scenarios spanning monomers to hexamers.
Light-inducible oligomerization of Eps15 is an optogenetic engineering method used to tune Eps15 initiator-protein assembly strength in real time during endocytosis. In mammalian Eps15 knockout cells, low light produced liquid-like Eps15 assemblies that restored normal endocytic rates, whereas higher light produced solid-like assemblies that stalled vesicle budding.
The autodisplay system was developed on the basis of the natural Escherichia coli autotransporter protein AIDA-I (adhesin involved in diffuse adherence). Autodisplay has been used for the surface display of random peptide libraries to successfully screen for novel enzyme inhibitors. The autodisplay system was also used for the surface display of functional enzymes... Autodisplay of epitopes on the surface of attenuated Salmonella carriers has also provided a novel way to induce immune protection after oral vaccination.
The Arabidopsis CRY2 photosensory domain is a light-responsive protein domain from plant cryptochrome-2 whose active-state crystal structure was determined in a tetrameric form. Structural analysis indicates that this domain undergoes photo-induced oligomerization and contains specific structural elements and residues that participate in activation.
Caenorhabditis elegans light-induced coclustering (CeLINC) is a fluorescence-based optical binary protein-protein interaction assay for testing whether two proteins interact in vivo in C. elegans. It uses light-induced coclustering as the assay readout for protein association.
The optogenetic Amyloid-β2 peptide is a fluorescently tagged construct, also referred to as Aβ2-CRY2-mCherry, designed for blue-light-controlled oligomerization of an amyloid-β species in vivo. It enables inducible amyloid-β oligomerization for neurodegeneration-related studies.
Photoactivatable cyclic caged morpholino oligomers (ccMOs) are light-responsive antisense morpholino reagents engineered in a cyclic, caged format to suppress target binding until photoactivation. In the reported design, brief 405-nm illumination photocleaves the cage and restores antisense activity, enabling spatiotemporal regulation of gene expression.
Defined oligomers of CENP-T are genetically engineered multimeric assemblies of the inner kinetochore protein CENP-T produced using two distinct systems in human cells. These higher-order CENP-T assemblies increase recruitment of outer kinetochore components and, when configured to mimic centromeric density, can induce functional cytoplasmic kinetochore-like particles.
The PHR domain of Arabidopsis thaliana cryptochrome 2 is a blue-light-responsive protein domain that self-oligomerizes upon illumination. In the cited optogenetic application, it was fused into a construct that rapidly modulated caspase-8 activation, leading to caspase-3 accumulation and induction of apoptosis.
Oligomerization reactions are a fundamental engineering strategy for optogenetic control of bacterial gene expression. In this context, light regulates signaling through oligomerization-based processes to drive upregulation or downregulation of expression outputs.
The optogenetic zebrafish ALS model is an in vivo construct pattern in zebrafish in which light illumination is used to control oligomerization, phase transition, and aggregation of the ALS-associated DNA/RNA-binding protein TDP-43. It is presented as an optogenetic disease model for studying ALS-related TDP-43 protein state changes.
Second-messenger signaling is a fundamental engineering strategy used for optogenetic control of bacterial gene expression. In this context, light input is coupled to intracellular second-messenger pathways to regulate bacterial expression programs.
Synthetic condensates are an engineered modular system for building synthetic membraneless organelles that separates condensate assembly from client recruitment. The framework uses constitutive oligomerization of intrinsically disordered regions to form clusters and fused interaction domains to define condensate composition.
Light-activated MLKL is an engineered optogenetic MLKL system that undergoes rapid light-triggered oligomerization and plasma membrane recruitment, causing rapid cell death. A re-engineered variant blocks the cell-killing activity while retaining light-mediated membrane recruitment, enabling single-component control of protein function at the plasma membrane.
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.
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.
CluMPS (Clusters Magnified by Phase Separation) is a fluorescent reporter strategy for high-sensitivity detection of protein clusters in cells. It is reported to visualize submicroscopic clusters, including small aggregates, and to track clusters of unmodified, tagged, and endogenous proteins.
The CRY2-CIB1 interaction system is a blue-light-responsive optogenetic multi-component switch built from the light-inducible CRY2-CIB1 interaction system in mammalian cells. Photoexcited CRY2 supports inducible CRY2-CIB1 heterodimerization and can also undergo concomitant CRY2-CRY2 homo-oligomerization, enabling light-controlled manipulation of signaling pathways and cellular processes with high spatiotemporal precision.
CRY2clust is an engineered CRY2-based optogenetic module that drives blue light-dependent homo-oligomerization and clustering of fused target proteins. It was reported as a new CRY2 variant that enables rapid and efficient protein clustering with spatiotemporal optical control.
The CRY2-CRY2 interaction system is a blue-light-responsive optogenetic switch in which photoexcited cryptochrome 2 undergoes homo-oligomerization. In mammalian cells, this light-inducible interaction has been used to manipulate signaling pathways and cellular processes with high spatiotemporal precision.
The CRY2-mCherry-Drosophila β-catenin optogenetic switch is a fusion protein comprising Arabidopsis thaliana CRY2, mCherry, and Drosophila β-catenin. Blue light induces oligomerization of the fusion protein, which inhibits downstream Wnt signaling in vitro and in vivo and enables temporal inactivation of β-catenin.
opto-Dab1 is a single-component, photoactivatable version of Disabled-1 (Dab1) created by exploiting the blue light-sensitive dimerization/oligomerization properties of Arabidopsis thaliana Cryptochrome 2 (Cry2). Upon blue light illumination, it enables rapid, local, and reversible activation of Dab1 downstream signaling.
OptoREACT is a light-dependent extracellular receptor activation system for nonengineered cells. It combines phytochrome B with a PIF6-coupled antibody fragment to bind cell-surface receptors and, upon illumination, drive receptor oligomerization and activation, including the T cell receptor on Jurkat and primary human T cells.
optoRET is an optogenetic RET signaling switch created by fusing the cytosolic region of human RET to a blue-light-inducible homo-oligomerizing protein. Blue-light stimulation modulates RET pathway output, including Grb2 recruitment and activation of AKT and ERK, and can also induce local filopodia-like F-actin structures through Cdc42 activation.
optoSynC is a non-ionic optogenetic silencer that uses light-evoked homo-oligomerization of cryptochrome CRY2 to cluster synaptic vesicles and silence synaptic transmission. It was benchmarked in Caenorhabditis elegans, zebrafish, and murine hippocampal neurons.
The re-engineered MLKL membrane recruitment tool is a single-component optogenetic system derived from MLKL that preserves light-mediated plasma membrane recruitment while blocking MLKL-associated cell-killing activity. It is intended to modulate protein function through light-controlled localization at the plasma membrane.
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.
OptoDroplet is an optogenetic multi-component switch that controls biomolecular phase separation by fusing disease-associated proteins to light-sensitive oligomerization domains. Light input enables induction or reversal of condensate formation with spatial and temporal control.
OptoLoop is an optogenetic multi-component switch for light-controlled manipulation of chromatin contacts. It is built from nuclease-dead Streptococcus pyogenes Cas9 fused to the light-inducible oligomerizing protein CRY2 and is reported to induce contacts between genomically distant repetitive DNA loci.
The paper explicitly names AlphaFold2 multimer modeling as part of the study workflow for AtaApore trimer prediction.
AlphaFold-Multimer improves multi-chain complex assembly prediction.
The prototype of these B12-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5'-deoxyadenosylcobalamin and light.
The supplied web research summary states that the anchor review explicitly lists LOVS1K as a named LOV2-based calcium actuator.
The supplied web research summary states that the anchor review explicitly lists Opto-CRAC1 as a LOV2-based STIM1/SOAR tool and describes it as a light-induced unfolding design for CRAC activation.
The supplied web research summary states that the anchor review explicitly lists Opto-CRAC2 designs using CRY2/CIBN and iLID/SspB and ties them to a mechanistic STIM1 engineering paper.