Toolkit Items

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.

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.

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 atomic force sensing technique is an assay method for dynamically probing protein conformational changes with microsecond time resolution. In the cited 1997 study, it was applied to light-induced conformational changes in bacteriorhodopsin.

Automated 96-well microplate illumination and measurement is an assay method for high-throughput optogenetic characterization of cultures under controlled light input. In the cited Saccharomyces cerevisiae workflow, it supported construction and characterization of split transcription factors containing cryptochrome and Enhanced Magnet light-sensitive dimerizers.

The Bessel beam stimulation source integrated into lattice light-sheet microscopy (LLSM) is an optical assay configuration that adds Bessel-beam-based optogenetic stimulation to LLSM without changing the microscope optical configuration. It enables three-dimensional photoactivation with improved spatiotemporal control and has been used to manipulate subcellular membrane ruffling and guide cell migration.

This tool is a bioreactor-based assay platform coupled to automated cytometry measurements for monitoring intracellular protein levels and secretory stress during production of hard-to-secrete proteins. It was reported as a real-time measurement platform to identify an optimal secretory-stress regime during protein production.

Biosensing is mentioned only as an emerging assay-related strategy expected to shape future directions in the field. The supplied evidence does not define a specific biosensor modality, analyte, or experimental implementation.

Bisulfite pyrosequencing is an assay method used to quantify promoter CpG DNA methylation after bisulfite treatment. In the cited study, it was used to measure methylation in the CAMK1D, CRY2, and CALM2 promoter regions in peripheral blood from patients with type 2 diabetes and matched healthy controls.

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.

Cas12aVIP is a rapid visual nucleic acid detection assay that integrates recombinase polymerase amplification, a CRISPR/Cas12a detection system, and a PMNT plus single-stranded DNA color reporter. It was proposed for visual readout of target nucleic acids in a format intended to be rapid and directly observable.

A cDNA microarray is a gene-expression profiling assay used in Arabidopsis to examine how phyA pathway mutations affect far-red light control of genome-wide expression. In the cited study, it was applied to profile transcriptional responses associated with phytochrome A signaling and to compare mutant expression patterns.

Cell-free chromatin immunoprecipitation (cfChIP) is an assay method that immunoprecipitates histone mark-associated cell-free chromatin from blood plasma. In the cited study, cfChIP targeting H3K36me3-associated cfDNA was used with droplet digital PCR to infer transcriptional activity of specific genes, including EGFR, in the cells that released the cfDNA.

cfDNA fragmentomics evaluation is an assay method that analyzes plasma cell-free DNA fragment length distributions and fragment end motifs to identify signatures associated with active gene expression. In a 2024 study, integrating short-fragment frequency with end-motif information improved enrichment for highly expressed genes in plasma samples from lung cancer patients and healthy individuals.

Chlorophyll fluorescence lifetime measurements are an optical assay method used to detect free chlorophyll. In Arabidopsis chaos leaves, this method detected free chlorophyll before visible symptoms of oxidative stress appeared.

Chromatin immunoprecipitation sequencing (ChIP-seq) is an assay method that combines chromatin immunoprecipitation with sequencing-based genomic localization to map protein-associated genomic regions. In the cited study, it was used to identify genome-wide ZFHX3-binding sites in suprachiasmatic nucleus chromatin, revealing occupancy concentrated near transcription start sites and co-localization with known histone modifications.

Chromatin in vivo imaging is identified in a 2018 review as a CRISPR/Cas9-based epigenetic technique for imaging chromatin in living systems. The supplied evidence supports its existence as a method category within the CRISPR/Cas9 epigenetics toolkit, but does not describe a specific construct, protocol, or performance profile.

CIDNP (chemically induced dynamic nuclear polarization) is a phenomenon in which chemical reactions generate nuclear hyperpolarization. Photo-CIDNP is the light-driven form of this phenomenon and is discussed in electron-transfer systems that often use flavins as electron acceptors.

Confocal microscopy is an in vivo fluorescence imaging assay method described as part of microscopy platforms tailored to larval zebrafish research. In the cited review context, it is used with fluorescent probes for real-time monitoring of cell identity, fate, and physiology in living larvae, including pancreatic and islet studies.

Cryogenic-temperature ENDOR spectroscopy is a spectroscopic assay method applied to LOV domains to interrogate the local environment of the flavin mononucleotide (FMN) cofactor. It does so by measuring temperature-dependent hyperfine couplings associated with hindered rotation of the methyl group attached at C(8) of the FMN isoalloxazine ring.

dcFCCS is a dual-color fluorescence cross-correlation spectroscopy assay method used to quantify interactions relevant to cGAS phase separation. In the cited study, it was applied to systematically examine binding among cGAS, double-stranded DNA, and accessory proteins in relation to condensate formation and enzymatic activity.

The directional reaching for water behavioral framework is a head-fixed mouse assay in which animals make center-out-like reaches toward water droplets presented at multiple spatial locations. It enables structured study of cortex-dependent reaching, sensorimotor processing, and decision making, and has been used with optogenetic motor cortex inactivation.

The droplet microfluidic platform is an assay method for screening and separating cell populations based on the in vivo fluorescence response of expressed biosensors after addition of an exogenous analyte. It was applied to HeLa-cell genetic linker libraries for genetically encoded Zn2+ sensors to assess library diversity and detect response heterogeneity.

The dual transient visible absorption (visTA)/FSRS set-up is a broadband time-resolved spectroscopic assay that combines transient visible absorption with femtosecond stimulated Raman spectroscopy. It covers approximately 200–2200 cm^-1 and supports pump–probe delays from a few femtoseconds to several hundreds of microseconds after actinic light excitation, enabling monitoring of photoinduced dynamics.

Electron paramagnetic resonance (EPR) is an assay method used to monitor light-induced paramagnetic signals. In the cited study, it measures the kinetics of appearance and disappearance of signals assigned to P700+ and iron-sulfur protein(s) at low temperature.

Electron-electron double resonance (ELDOR) spectroscopy is a structural assay method that, when combined with site-directed spin labelling, was used to chart light-induced structural transitions in the engineered LOV histidine kinase YF1. In the cited study, it provided pairwise distance information used to model blue-light-driven quaternary rearrangements in a signaling photoreceptor.

Electron-transfer/higher-energy collision dissociation (EThcD) is a top-down mass spectrometry fragmentation method used in a combined workflow with 213 nm ultraviolet photodissociation (UVPD) to characterize covalent insulin dimers. In the cited study, this workflow identified cross-link chemical composition and, with MS3 analysis of informative MS2 fragments, enabled residue-level localization of interchain cross-link sites.

Electrophysiology is used as a functional assay in a multimodal study of gasdermin D pore behavior, alongside optogenetic tools and live-cell fluorescence biosensing. In the cited work, it supports measurement of pore conductance dynamics and the conclusion that gasdermin pores show phosphoinositide-dependent, repeated fast opening-closing behavior.

The endometrial receptivity assay (ERA) is a clinical assay intended to assess endometrial receptivity during the window of implantation. The supplied evidence indicates that, as a current test of the window of implantation, it does not consistently improve clinical outcomes measured by live birth rates.

Endometrial thickness measurement is a current clinical assay method used as a marker of the window of implantation and endometrial receptivity. The cited evidence indicates that, as a current test of the window of implantation, it does not consistently improve clinical outcomes measured by live birth rates.

EndoV-seq is an assay method reported for genome-wide profiling of adenine base editor specificity. The available evidence supports its use as a functional assay to identify where adenine base editing occurs across the genome.

Epigenetic element screening is described in a 2018 review as a CRISPR/Cas9-based epigenetic technique. The supplied evidence establishes only that it belongs to the set of CRISPR/Cas9-enabled approaches used in epigenetics, without further methodological detail.

This assay-method profile describes genomic analysis used to study light-regulated gene expression in plants. The cited review states that such studies revealed epigenetic regulation, massive transcriptome reprogramming in response to light, and genome-wide binding sites for pivotal light-signaling transcription factors.

An expressed sequence tag-based microarray is a microarray expression-profiling assay used to measure genome-scale transcript patterns in Arabidopsis. In the cited study, it was applied to profile gene expression underlying light-controlled development across different light conditions.

Field-domain rapid-scan EPR at 240 GHz is a high-frequency electron paramagnetic resonance assay method reported for studying protein functional dynamics at room temperature. The available evidence identifies it specifically as a field-domain rapid-scan EPR approach operating at 240 GHz.

The five-primary photostimulator is a light-delivery assay method that generates stimuli to selectively modulate melanopsin, rod, and S-, M-, and L-cone excitations in isolation or combination. It was used to measure human flicker pupillary responses and to examine how luminance and chromatic signals interact with melanopsin in control of the pupil light response.

Flash-and-freeze is an assay method that induces neuronal activity with a flash of light and captures membrane dynamics by rapid freezing. It was developed to visualize activity-evoked synaptic membrane trafficking with millisecond temporal resolution and was used to identify ultrafast endocytosis during neurotransmission.

FLIPR (Fluorometric Imaging Plate Reader) is a fluorescence-analysis instrument used as a miniaturized optogenetic assay platform in 384-well plates. In the cited study, FLIPR LEDs provided optical modulation to support recombinant cellular assays, including Channelrhodopsin-2 control of CaV1.3.

Fluorescence line narrowing (FLN) is a spectroscopic assay method used in the cited study to interrogate the electronic structure of flavin mononucleotide (FMN) within phototropin LOV2 domains. In this context, FLN was applied to support mechanistic analysis of how the conserved cysteine near FMN perturbs the chromophore ground state and promotes photochemistry.

The fluorescence method is a signal transformation modality used in CRISPR-Cas pathogen nucleic acid diagnostic platforms. In the cited context, Cas effector proteins recognize and cleave specific DNA or RNA targets, and fluorescence is combined with signal amplification and transformation technologies to report detection.

Fluorescence microscopy is an imaging assay method used to detect and localize fluorescent signals in living biological specimens. In the supplied evidence, it is described for larval zebrafish as a means to achieve subcellular fluorescence localization and real-time monitoring of cell identity, fate, physiology, and organ pathophysiology.

Fluorescence recovery after photobleaching (FRAP) is proposed as a functional assay readout for liquid-like molecular mobility within the pathological condensate termed the addivosome. In this context, FRAP is intended to detect restoration of mobility, or reliquefaction, during compound screening.

Fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM) is an assay method that combines fluorescence resonance energy transfer with fluorescence lifetime imaging to detect molecular proximity in living cells. In the cited Arabidopsis study, it was used to support a physical interaction between CRY2 and SPA1 in nuclei.

Fluorescent polarization is an assay method provided as a protocol for validating, improving, and using newly designed photoswitches in the context of LOV2-based optogenetic engineering. In the cited source, it is presented alongside phage display and microscopy as part of the experimental toolkit for photoswitch development.

Fluorescent probes are described as an expanding assay toolbox that can be combined with larval zebrafish for real-time in vivo monitoring of cell identity, cell fate, and physiology. In the cited review, this use context is framed for organ pathophysiology studies, including the pancreas and islets of Langerhans.

Fluorescent-protein-based methods are assay approaches discussed for evaluating the efficacy of CRISPR-based genome-editing systems in bacteria. The available evidence supports their use as fluorescence-based functional readouts of bacterial editing performance, but does not specify particular reporter proteins, construct architectures, or assay workflows.

FMN fluorescence is an optical metabolic imaging assay based on flavin mononucleotide autofluorescence. The supplied evidence indicates potential use for visualization and classification of brain tumor tissue during surgery.

The FRET-based RhoA biosensor is an assay method developed to visualize RhoA activity during optical control experiments using photoswitchable RhoGEF (psRhoGEF). The available evidence supports its use for monitoring RhoA signaling in the context of endogenous RhoA manipulation.

Full-length transcriptome analysis is an assay method used to examine transcriptomic features associated with shade-induced promotion of tuber production in Pinellia ternata. The available evidence supports its application in this specific plant developmental context, but does not provide methodological detail beyond the study focus.

Genetically encoded red fluorescence intensity-based small GTPase biosensors are assay reagents used to characterize optogenetic regulators of small GTPase activity. In the cited 2021 Journal of Biological Chemistry study, they were used to assess and confirm the specificities of iLID-based optogenetic small GTPase control tools.