Toolkit Items

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.

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.

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.

Auxiliary photocleavable oligodeoxyribonucleotides complementary to crRNA (PC-DNAs) are inhibitory oligonucleotide components of a photoactivatable nanoCRISPR/Cas9 system. They hybridize to crRNA to suppress Cas9 function before illumination and are photocleaved by 365 nm UV light to release crRNA and restore gene-editing activity.

Biliverdin is described in the supplied evidence as a chromophore used by biliverdin-binding phytochromes, where it is covalently attached to the protein. The attachment site is located in the N-terminal region and differs from that of plant phytochromes.

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%.

The bow-knot-type gRNA is a light-responsive guide RNA format for CRISPR-Cas editing developed within a cyclically caged gRNA strategy. It is reported to enable optical control of gene editing, including light-mediated MSTN editing in embryos, while showing no background editing without light irradiation.

Caged guide RNAs are synthetic CRISPR guide RNAs containing photolabile nucleobase substitutions in the 5′ protospacer that enable light-activated control of Cas9 function. They were developed to conditionally regulate genome editing in mammalian cells and zebrafish embryos by suppressing guide RNA binding to target DNA until optical activation.

The caged NF-κB DNA decoy is a photoregulated oligonucleotide decoy in which photoremovable protecting groups are installed on nucleobases within an NF-κB decoy sequence. UV irradiation removes the caging groups, restores decoy hybridization and NF-κB binding activity, and enables light-controlled regulation of NF-κB-driven transcription in mammalian cells.

The chalcone synthase promoter is a plant light-responsive promoter used to control expression of a foreign gene in tobacco BY-2 cells. The available evidence supports its function as a promoter-based light-regulated gene expression tool in this heterologous plant cell context.

The CIb1 promoter is a Bombyx mori gene promoter characterized by firefly luciferase reporter assays in the ovary-derived BmN cell line. Deletion analysis identified promoter fragments with transcriptional activity, including an 82 bp region from -72 to +10 nt that retains basic promoter function, and an upstream segment with strong negative regulatory effects.

CircZNF367 is a circular RNA reported to promote osteoclast differentiation and osteoporosis. The available evidence indicates that it acts through interaction with the RNA-binding protein FUS to maintain CRY2 mRNA stability.

Cis-acting sequences are endogenous regulatory DNA elements implicated in controlling downstream light-regulated gene expression during seedling development. The cited literature places them within red- and blue-light signal transduction pathways that influence leaf and chloroplast development and expression of nuclear genes encoding chloroplast-destined proteins in dicots.

CRY2 mRNA is described in the cited study as a post-transcriptionally regulated RNA whose stability is maintained through a CircZNF367–FUS interaction. In that reported context, this regulatory relationship is linked to osteoclast differentiation and osteoporosis.

The enzyme-activatable antisense oligonucleotide is an engineered antisense component used within a nanosystem for gene regulation. Available evidence indicates that it is combined with an upconversion nanoparticle-based photodynamic system and a mitochondria localization signal in a remotely controlled therapeutic platform.

Fluorescently labeled synthetic guide RNAs are engineered CRISPR guide RNAs bearing covalently attached fluorophores. They are described as enabling highly specific nuclear staining and imaging, including mechanistic studies of chromosomal dynamics and genomic mapping.

Functional nucleic acid (FNA) probes are nucleic-acid-based biosensing probes used in environmental monitoring, food analysis, clinical diagnosis, and biological imaging. The cited evidence specifically emphasizes two-photon-based FNA probes as fluorescence biosensing formats with improved optical performance over one-photon-based FNA probes in biomedical sensing.

Fusion guide RNAs are engineered RNA elements reported for orthogonal gene manipulation with the CRISPR effectors Cas9 and Cpf1. The available evidence indicates that they are designed to interface with both systems within a single guide-RNA framework for gene control.

A nested group II intron has been described as an RNA regulatory element for controlling homing endonuclease expression. In Escherichia coli, altering the splicing efficiency of a homing endonuclease ORF-embedded group II intron was reported to modulate homing endonuclease expression in vivo.

Guide RNA is the programmable RNA component of the CRISPR/Cas9 system that directs Cas9 to sequence-defined genomic sites. Altering the guide RNA sequence retargets Cas9 to new DNA loci for sequence-specific genome editing.

The hypoxanthine switch is a small molecule-responsive RNA element described as a hypoxanthine-sensitive switch. Available evidence indicates that its intracellular switch activity correlates with aptamer binding properties measured biochemically.

Ligand-activated and ligand-deactivated sgRNAs are engineered single-guide RNAs that place CRISPR-Cas9-based gene repression under small-molecule control. In the reported 2019 Nature Communications study, sgRNA function was activated or deactivated in a dose-dependent manner by two different ligands, with regulation acting directly at the level of each target-specific sgRNA.

Light-controlled crRNA is a chemically modified CRISPR guide RNA in which vitamin E is attached to the 5' terminus through a photolabile linker, creating a caged crRNA that inactivates CRISPR/Cas9 until light exposure. Upon irradiation, this design restores CRISPR/Cas9 activity and supports genome editing of VEGFA and knockdown of EGFP expression in human cells.

Long non-coding RNAs (lncRNAs) are non-protein-coding RNA elements within the broader non-coding RNA landscape. In plants, available reports indicate that lncRNAs participate in light-dependent processes including photomorphogenesis, cotyledon greening, and photoperiod-regulated flowering.

Long noncoding RNAs are RNA elements with broad regulatory functions in gene expression and cellular activity. The cited review describes lncRNAs as biomolecule-interacting regulators that affect mRNA stability, translational control, splicing, DNA triplex formation, and chromatin organization.

The main ORF (mORF) is the protein-coding open reading frame in a transcript whose translation can be repressed by upstream ORFs (uORFs). In Arabidopsis, transcripts initiated from downstream alternative transcription start sites can bypass uORFs and thereby support expression of the mORF, including in blue-light-responsive genes.

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.

Methylated guide RNA for CRISPR-Cas12a is a chemically modified crRNA bearing m6A or m1A marks that suppresses Cas12a activity. The methylated guide inhibits both cis- and trans-DNA cleavage, and activity can be reactivated through guide RNA demethylation.

The methylation-deactivated and demethylase-activated CRISPR-Cas12a guide RNA strategy is an RNA-level control system in which m6A or m1A modification of the Cas12a guide RNA suppresses CRISPR-Cas12a activity, while demethylation restores function. It was reported as a way to regulate Cas12a for controllable gene editing, gene expression regulation, and demethylase imaging in living cells.

MicroRNAs are small non-coding RNAs that participate in light-regulated biological processes. The supplied evidence supports a role for miRNAs in mediating light-dependent pathways, but does not define a specific engineered construct or application format.

miR-181d is a microRNA reported in colorectal cancer that is induced by c-Myc signaling and promotes glycolytic metabolism. The available evidence describes it as a post-transcriptional regulator involved in metabolic reprogramming in CRC cells.

miR-27a-3p is a microRNA reported to promote osteogenic differentiation through activation of the CRY2/ERK1/2 signaling axis. The available evidence supports a functional role in regulating an osteogenesis-associated pathway.

miR-7-5p is a microRNA reported to directly target CRY2 and thereby modulate osteoblast differentiation. In the cited 2019 study, miR-7-5p overexpression promoted osteogenic marker expression and osteoblast differentiation, consistent with repression of CRY2 and activation of CLOCK/BMAL1/P300 signaling.

Phosphorothioate-caged antisense oligonucleotides are mixed-backbone antisense oligonucleotides in which phosphorothioate linkages are modified with 2-nitroveratryl photocages. In the caged state, these modifications suppress target RNA duplex formation and RNase H activity, and UV uncaging restores antisense function to enable light-controlled knockdown of cell-free protein synthesis.

Photo-caged mRNA is an mRNA engineering strategy in which small-molecule caging groups are tethered to the 5′ untranslated region to suppress translation until illumination. Photocleavage of the cages activates translation and enables single-cell spatiotemporal control in mammalian cells.

Photo-sensitive circular gRNAs are cyclically caged guide RNAs that enable light-activated CRISPR/Cas9- and Cpf1-mediated genome editing. They are designed for spatiotemporal control of editing and are activated by photocleavage of the circularized guide.

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.

Photolabile-modified small interfering RNA is a chemically caged siRNA reagent whose RNA interference activity is suppressed before illumination and restored by light exposure. Upon irradiation, the modified siRNA is released into an active state that suppresses target gene expression.

Phytochrome mRNA is a native light-responsive RNA output measured in etiolated Avena seedlings. Its translatable abundance decreases after red-light exposure and this effect is reversed by an immediately subsequent far-red pulse, indicating phytochrome-mediated autoregulation of translatable phytochrome mRNA levels.

The PORC promoter is an Arabidopsis promoter element that functions as an in vivo binding target of the scarecrow-like transcription factor SCL27. Available evidence indicates that SCL27 binds GT cis-elements within this promoter and regulates PORC promoter activity, with DELLA proteins reducing SCL27 promoter binding.

The RhVI1 promoter is an 895 bp promoter fragment from Rosa hybrida Vacuolar Invertase 1 that mediates transcriptional responses to light, sugars, and gibberellins. A 468 bp subfragment is sufficient for reporter activation by these inputs, and a 127 bp region from -595 to -468 bp is critical for combinatorial regulation by light with sugar or gibberellin signals.

This tool is an RNA aptamer-based component for light-controlled, reversible gene transactivation in a CRISPR/dCas9-based system. It is built on the interaction between the photoreceptor PAL and an RNA aptamer to regulate gene expression with light.

This RNA platform is described as a general class of synthetic biology tools for modular, dynamic, and multi-output control over mammalian cells. The cited 2015 study also states that synthetic RNA devices were used to control the mammalian cell cycle.

sgRNA (single-guide RNA) is the RNA guide element in CRISPR systems that directs sequence-specific targeting for RNA or DNA manipulation. In the cited review, sgRNA design and modification are highlighted as central determinants of effective virus-targeted gene knock-in, gene knock-out, and CRISPR/Cas mutation efficiency.

SIBR is an inducible RNA-based regulatory element proposed to provide universal control of gene expression and gene regulation in bacteria. In the reported SIBR-Cas configuration, it regulates CRISPR-Cas counterselection with a temporal delay that improves genome editing in non-model bacterial hosts.

Small interfering RNA (siRNA) is a short RNA modality used to transiently downregulate expression of a target gene by exploiting the RNA interference pathway. In the supplied evidence, siRNA is described as a gene-therapy approach for altering gene expression rather than a genome-editing reagent.

Small interfering RNA modified at the 5' antisense phosphate is an siRNA variant evaluated as a potential light-responsive RNAi switch. Evidence from a 2007 Oligonucleotides study indicates that this modification is tolerated by the RNA interference machinery and still supports RNAi, although at lower activity than fully native siRNA.

Small interfering RNA with randomly incorporated photolabile groups is a chemically modified RNAi reagent whose gene-silencing activity can be modulated by light. Available evidence indicates that siRNA can retain RNA interference activity despite certain chemical modifications, including modification at the 5′ antisense phosphate, although activity is reduced relative to native siRNA.

Small molecule regulated sgRNAs are engineered single-guide RNAs that confer small-molecule control over Cas9-mediated genome editing in Escherichia coli. The available evidence supports their function as RNA-level regulators of CRISPR-Cas9 editing activity in a bacterial system.

Smart RNA guides (SmartGuides) are engineered CRISPR-Cas9 guide RNAs that become active only in the presence of a specific RNA opener. They provide conditional RNA-responsive control of guide function and were reported in miRNA-responsive formats and Boolean logic circuit compositions.