Source 1primary paper2019
Toolkit/caged guide RNA
caged guide RNA
Also known as: caged gRNAs, light-activated guide RNA, photochemically activated, caged guide RNAs
Taxonomy: Mechanism Branch / Component. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
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.
Usefulness & Problems
Why this is useful
This tool is useful for conditional, spatiotemporal control of CRISPR/Cas9-mediated gene editing. The source literature presents it as a way to investigate physiologically complex events and dynamic gene regulation in systems where precise timing and localization of editing are important.
Source:
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Problem solved
Caged guide RNAs address the problem of controlling when and where CRISPR/Cas9 editing occurs. Specifically, they provide a light-responsive guide RNA format that keeps Cas9 inactive at a target site until illumination restores guide RNA-target DNA hybridization.
Source:
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Problem links
Need controllable genome or transcript editing
DerivedCaged 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.
Need precise spatiotemporal control with light input
DerivedCaged 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.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Component: A low-level RNA part used inside a larger architecture that realizes a mechanism.
Mechanisms
light-gated suppression and restoration of grna-target dna hybridizationlight-gated suppression of grna-target dna hybridizationlight-triggered restoration of grna-target dna hybridizationPhotocleavageTechniques
Computational DesignTarget processes
editingInput: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: regulatorswitch architecture: cleavage
Caged guide RNAs are generated during chemical synthesis by substituting four nucleobases evenly distributed throughout the 5′ protospacer region with caged nucleobases. Practical use requires optical activation and pairing with CRISPR/Cas9 in mammalian cells or zebrafish embryos, but the supplied evidence does not specify the photolabile chemistry, activation wavelength, or delivery format.
The supplied evidence is limited to a single 2019 source and does not provide quantitative performance metrics, illumination parameters, editing efficiencies, or off-target analyses. Evidence also does not describe performance with Cas variants beyond Cas9 or validation across a broad range of targets and organisms.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Caged guide RNAs are presented as tools for conditional control of gene editing to investigate spatiotemporally complex physiological events and dynamic gene regulation.
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Caged guide RNAs are presented as tools for conditional control of gene editing to investigate spatiotemporally complex physiological events and dynamic gene regulation.
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Caged guide RNAs are presented as tools for conditional control of gene editing to investigate spatiotemporally complex physiological events and dynamic gene regulation.
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Caged guide RNAs are presented as tools for conditional control of gene editing to investigate spatiotemporally complex physiological events and dynamic gene regulation.
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Caged guide RNAs are presented as tools for conditional control of gene editing to investigate spatiotemporally complex physiological events and dynamic gene regulation.
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Caged guide RNAs are presented as tools for conditional control of gene editing to investigate spatiotemporally complex physiological events and dynamic gene regulation.
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Caged guide RNAs are presented as tools for conditional control of gene editing to investigate spatiotemporally complex physiological events and dynamic gene regulation.
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Caged guide RNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged guide RNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged guide RNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged guide RNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged guide RNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged guide RNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged guide RNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caging completely suppresses gRNA-target double-stranded DNA hybridization and optical activation rapidly restores CRISPR/Cas9 function.
Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation.
Caging completely suppresses gRNA-target double-stranded DNA hybridization and optical activation rapidly restores CRISPR/Cas9 function.
Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation.
Caging completely suppresses gRNA-target double-stranded DNA hybridization and optical activation rapidly restores CRISPR/Cas9 function.
Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation.
Caging completely suppresses gRNA-target double-stranded DNA hybridization and optical activation rapidly restores CRISPR/Cas9 function.
Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation.
Caging completely suppresses gRNA-target double-stranded DNA hybridization and optical activation rapidly restores CRISPR/Cas9 function.
Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation.
Caging completely suppresses gRNA-target double-stranded DNA hybridization and optical activation rapidly restores CRISPR/Cas9 function.
Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation.
Caging completely suppresses gRNA-target double-stranded DNA hybridization and optical activation rapidly restores CRISPR/Cas9 function.
Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation.
Photochemically activated caged guide RNAs were developed as a method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos.
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Photochemically activated caged guide RNAs were developed as a method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos.
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Photochemically activated caged guide RNAs were developed as a method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos.
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Photochemically activated caged guide RNAs were developed as a method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos.
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Photochemically activated caged guide RNAs were developed as a method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos.
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Photochemically activated caged guide RNAs were developed as a method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos.
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Photochemically activated caged guide RNAs were developed as a method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos.
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Caged guide RNAs provide high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving Cas9:gRNA ribonucleoprotein complex formation.
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
Caged guide RNAs provide high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving Cas9:gRNA ribonucleoprotein complex formation.
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
Caged guide RNAs provide high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving Cas9:gRNA ribonucleoprotein complex formation.
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
Caged guide RNAs provide high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving Cas9:gRNA ribonucleoprotein complex formation.
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
Caged guide RNAs provide high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving Cas9:gRNA ribonucleoprotein complex formation.
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
Caged guide RNAs provide high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving Cas9:gRNA ribonucleoprotein complex formation.
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
Caged guide RNAs provide high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving Cas9:gRNA ribonucleoprotein complex formation.
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
Approval Evidence
1 source5 linked approval claimsfirst-pass slug caged-guide-rna
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Source:
application scopesupports
Caged guide RNAs are presented as tools for conditional control of gene editing to investigate spatiotemporally complex physiological events and dynamic gene regulation.
caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.
Source:
design descriptionsupports
Caged guide RNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5’-protospacer region with caged nucleobases during synthesis.
Source:
mechanismsupports
Caging completely suppresses gRNA-target double-stranded DNA hybridization and optical activation rapidly restores CRISPR/Cas9 function.
Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation.
Source:
method developmentsupports
Photochemically activated caged guide RNAs were developed as a method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos.
We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs.
Source:
performance statementsupports
Caged guide RNAs provide high spatiotemporal specificity in cells and zebrafish embryos, excellent off-to-on switching, and stability by preserving Cas9:gRNA ribonucleoprotein complex formation.
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
Source:
Comparisons
Source-backed strengths
The reported design completely suppresses guide RNA-target double-stranded DNA hybridization in the caged state and rapidly restores CRISPR/Cas9 function after optical activation. The method was demonstrated for conditional regulation in both mammalian cells and zebrafish embryos, supporting use across cultured cells and an embryonic vertebrate model.
Source:
This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes.
caged guide RNA and auxiliary photocleavable oligodeoxyribonucleotides complementary to crRNA address a similar problem space because they share editing.
Shared frame: same top-level item type; shared target processes: editing; shared mechanisms: photocleavage; same primary input modality: light
Compared with light-controlled crRNA
caged guide RNA and light-controlled crRNA address a similar problem space because they share editing.
Shared frame: same top-level item type; shared target processes: editing; shared mechanisms: photocleavage; same primary input modality: light
Compared with photo-sensitive circular gRNAs
caged guide RNA and photo-sensitive circular gRNAs address a similar problem space because they share editing.
Shared frame: same top-level item type; shared target processes: editing; shared mechanisms: photocleavage; same primary input modality: light
Ranked Citations
- 1.