Source 1primary paper2011Journal of the American Chemical Society
Toolkit/caged NF-κB DNA decoy
caged NF-κB DNA decoy
Also known as: caged DNA decoy, NF-κB DNA decoy
Taxonomy: Mechanism Branch / Component. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
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.
Usefulness & Problems
Why this is useful
This tool enables temporal optical control over NF-κB decoy function rather than constitutive transcription factor sequestration. It is useful for probing NF-κB-dependent transcriptional programs in mammalian cells with externally applied light as the activating input.
Source:
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Problem solved
Conventional NF-κB DNA decoys lack precise on-demand activation once delivered to cells. This tool addresses that limitation by keeping the decoy inactive until UV exposure restores transcription factor binding and decoy-mediated inhibition of NF-κB-driven transcription.
Problem links
Need conditional recombination or state switching
DerivedThe 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.
Need precise spatiotemporal control with light input
DerivedThe 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.
Need tighter control over gene expression timing or amplitude
DerivedThe 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.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Component: A low-level RNA part used inside a larger architecture that realizes a mechanism.
Mechanisms
light-gated restoration of dna:dna hybridizationlight-gated restoration of transcription factor bindingPhotocleavagetranscriptional decoy sequestration of nf-κbTechniques
No technique tags yet.
Target processes
recombinationtranscriptionInput: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: regulatorswitch architecture: cleavage
The construct is an NF-κB DNA decoy oligonucleotide bearing photoremovable protecting groups on nucleobases. Functional activation depends on UV irradiation to remove the caging groups, and the reported cellular validation was performed in mammalian cells using an NF-κB-driven secreted alkaline phosphatase reporter assay.
The available evidence is limited to a single cited study and a mammalian-cell reporter context. Activation requires UV irradiation, and the supplied evidence does not describe broader target validation, in vivo use, quantitative performance, or applications beyond NF-κB-driven transcription.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Photoremovable protecting groups on nucleobases of NF-κB DNA decoys enable light-controlled regulation of NF-κB-driven transcription of secreted alkaline phosphatase.
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Photoremovable protecting groups on nucleobases of NF-κB DNA decoys enable light-controlled regulation of NF-κB-driven transcription of secreted alkaline phosphatase.
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Photoremovable protecting groups on nucleobases of NF-κB DNA decoys enable light-controlled regulation of NF-κB-driven transcription of secreted alkaline phosphatase.
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Photoremovable protecting groups on nucleobases of NF-κB DNA decoys enable light-controlled regulation of NF-κB-driven transcription of secreted alkaline phosphatase.
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Photoremovable protecting groups on nucleobases of NF-κB DNA decoys enable light-controlled regulation of NF-κB-driven transcription of secreted alkaline phosphatase.
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Photoremovable protecting groups on nucleobases of NF-κB DNA decoys enable light-controlled regulation of NF-κB-driven transcription of secreted alkaline phosphatase.
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Photoremovable protecting groups on nucleobases of NF-κB DNA decoys enable light-controlled regulation of NF-κB-driven transcription of secreted alkaline phosphatase.
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Incorporation of caging groups into an NF-κB decoy disrupts DNA:DNA hybridization and inhibits transcription factor binding until UV irradiation removes the caging groups and restores oligonucleotide activity.
Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide.
Incorporation of caging groups into an NF-κB decoy disrupts DNA:DNA hybridization and inhibits transcription factor binding until UV irradiation removes the caging groups and restores oligonucleotide activity.
Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide.
Incorporation of caging groups into an NF-κB decoy disrupts DNA:DNA hybridization and inhibits transcription factor binding until UV irradiation removes the caging groups and restores oligonucleotide activity.
Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide.
Incorporation of caging groups into an NF-κB decoy disrupts DNA:DNA hybridization and inhibits transcription factor binding until UV irradiation removes the caging groups and restores oligonucleotide activity.
Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide.
Incorporation of caging groups into an NF-κB decoy disrupts DNA:DNA hybridization and inhibits transcription factor binding until UV irradiation removes the caging groups and restores oligonucleotide activity.
Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide.
Incorporation of caging groups into an NF-κB decoy disrupts DNA:DNA hybridization and inhibits transcription factor binding until UV irradiation removes the caging groups and restores oligonucleotide activity.
Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide.
Incorporation of caging groups into an NF-κB decoy disrupts DNA:DNA hybridization and inhibits transcription factor binding until UV irradiation removes the caging groups and restores oligonucleotide activity.
Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide.
This work reports the first example of a caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
This work reports the first example of a caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
This work reports the first example of a caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
This work reports the first example of a caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
This work reports the first example of a caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
This work reports the first example of a caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
This work reports the first example of a caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
The caged NF-κB DNA decoy showed excellent light-switching behavior of transcriptional regulation.
Excellent light-switching behavior of transcriptional regulation was observed.
light-switching behavior excellent
The caged NF-κB DNA decoy showed excellent light-switching behavior of transcriptional regulation.
Excellent light-switching behavior of transcriptional regulation was observed.
light-switching behavior excellent
The caged NF-κB DNA decoy showed excellent light-switching behavior of transcriptional regulation.
Excellent light-switching behavior of transcriptional regulation was observed.
light-switching behavior excellent
The caged NF-κB DNA decoy showed excellent light-switching behavior of transcriptional regulation.
Excellent light-switching behavior of transcriptional regulation was observed.
light-switching behavior excellent
The caged NF-κB DNA decoy showed excellent light-switching behavior of transcriptional regulation.
Excellent light-switching behavior of transcriptional regulation was observed.
light-switching behavior excellent
The caged NF-κB DNA decoy showed excellent light-switching behavior of transcriptional regulation.
Excellent light-switching behavior of transcriptional regulation was observed.
light-switching behavior excellent
The caged NF-κB DNA decoy showed excellent light-switching behavior of transcriptional regulation.
Excellent light-switching behavior of transcriptional regulation was observed.
light-switching behavior excellent
Approval Evidence
1 source4 linked approval claimsfirst-pass slug caged-nf-b-dna-decoy
application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys
Source:
functional modulationsupports
Photoremovable protecting groups on nucleobases of NF-κB DNA decoys enable light-controlled regulation of NF-κB-driven transcription of secreted alkaline phosphatase.
we report the application of photoremovable protecting groups on nucleobases of nuclear factor κB (NF-κB) DNA decoys to regulate NF-κB-driven transcription of secreted alkaline phosphatase using light as an external control element
Source:
mechanismsupports
Incorporation of caging groups into an NF-κB decoy disrupts DNA:DNA hybridization and inhibits transcription factor binding until UV irradiation removes the caging groups and restores oligonucleotide activity.
Through the direct incorporation of caging groups into an NF-κB decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide.
Source:
noveltysupports
This work reports the first example of a caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
Source:
performance statementsupports
The caged NF-κB DNA decoy showed excellent light-switching behavior of transcriptional regulation.
Excellent light-switching behavior of transcriptional regulation was observed.
Source:
Comparisons
Source-backed strengths
The reported design directly links photochemistry to restoration of both DNA:DNA hybridization and transcription factor binding. It was validated in mammalian cells by light-controlled regulation of an NF-κB-driven secreted alkaline phosphatase reporter, and the source describes it as the first caged DNA decoy for photochemical regulation of gene expression in mammalian cells.
Source:
This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells
Source:
Excellent light-switching behavior of transcriptional regulation was observed.
Compared with microRNA
caged NF-κB DNA decoy and microRNA address a similar problem space because they share transcription.
Shared frame: same top-level item type; shared target processes: transcription; same primary input modality: light
Compared with open-source microplate reader
caged NF-κB DNA decoy and open-source microplate reader address a similar problem space because they share recombination, transcription.
Shared frame: shared target processes: recombination, transcription; same primary input modality: light
Compared with Opto-Casp8-V2
caged NF-κB DNA decoy and Opto-Casp8-V2 address a similar problem space because they share recombination.
Shared frame: shared target processes: recombination; shared mechanisms: photocleavage; same primary input modality: light
Ranked Citations
- 1.