Source 1primary paper2024Angewandte Chemie
Toolkit/three-stranded DNAzyme probe
three-stranded DNAzyme probe
Also known as: TSDP
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The three-stranded DNAzyme probe (TSDP) is a CRISPR/Cas9-inducible DNA construct engineered with a 20-bp Cas9 recognition site that suppresses DNAzyme activity until cleavage. It was developed for in situ imaging of nuclear Zn2+ in living cells and was further combined with photoactivation and Boolean logic control for spatiotemporal imaging.
Usefulness & Problems
Why this is useful
TSDP is useful for conditional activation of a DNAzyme signal in the nucleus, enabling in situ imaging of nuclear Zn2+ in living cells. Integration with photoactivation and Boolean logic gating was reported to provide superior spatiotemporal control for dynamic monitoring in HeLa cells and mice.
Source:
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
Problem solved
TSDP addresses the problem of keeping a DNAzyme probe inactive until a defined trigger is present, using a CRISPR/Cas9 recognition sequence to block catalytic function before cleavage. This design supports controlled nuclear Zn2+ imaging with added spatial and temporal regulation when coupled to photoactivation and logic gating.
Source:
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
Problem links
Need controllable genome or transcript editing
DerivedThe three-stranded DNAzyme probe (TSDP) is a CRISPR/Cas9-inducible DNA construct engineered with a 20-bp Cas9 recognition site that suppresses DNAzyme activity until cleavage. It was developed for in situ imaging of nuclear Zn2+ in living cells and was further combined with photoactivation and Boolean logic control for spatiotemporal imaging.
Need inducible protein relocalization or recruitment
DerivedThe three-stranded DNAzyme probe (TSDP) is a CRISPR/Cas9-inducible DNA construct engineered with a 20-bp Cas9 recognition site that suppresses DNAzyme activity until cleavage. It was developed for in situ imaging of nuclear Zn2+ in living cells and was further combined with photoactivation and Boolean logic control for spatiotemporal imaging.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A reusable architecture pattern for arranging parts into an engineered system.
Mechanisms
boolean logic gatingcrispr/cas9-mediated cleavagednazyme catalytic activationPhotocleavageTechniques
Computational DesignTarget processes
editinglocalizationImplementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: regulatorswitch architecture: cleavage
The construct is described as a three-stranded DNAzyme probe containing a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus. Reported use includes living cells, specifically HeLa cells, and mice, but the supplied evidence does not detail delivery methods, expression systems, or the specific photoactivation chemistry.
The supplied evidence is limited to a single 2024 study and does not provide detailed quantitative performance metrics, such as sensitivity, kinetics, background suppression, or off-target effects. The available text also does not specify sequence architecture beyond the 20-bp recognition site or define how broadly the construct has been validated across cell types or targets other than nuclear Zn2+.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The CRISPR/Cas9-inducible DNAzyme design enables in situ imaging of nuclear Zn2+ in living cells.
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
The CRISPR/Cas9-inducible DNAzyme design enables in situ imaging of nuclear Zn2+ in living cells.
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
The CRISPR/Cas9-inducible DNAzyme design enables in situ imaging of nuclear Zn2+ in living cells.
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
The CRISPR/Cas9-inducible DNAzyme design enables in situ imaging of nuclear Zn2+ in living cells.
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
The CRISPR/Cas9-inducible DNAzyme design enables in situ imaging of nuclear Zn2+ in living cells.
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
The CRISPR/Cas9-inducible DNAzyme design enables in situ imaging of nuclear Zn2+ in living cells.
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
The CRISPR/Cas9-inducible DNAzyme design enables in situ imaging of nuclear Zn2+ in living cells.
With this design, the CRISPR/Cas9‐inducible imaging of nuclear Zn 2+ is demonstrated in living cells.
Integrating the CRISPR-DNAzyme system with photoactivation strategy and Boolean logic gate provided superior spatiotemporal control imaging for dynamic monitoring of nuclear Zn2+ in HeLa cells and mice.
Moreover, the superiority of CRISPR‐DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn 2+ in both HeLa cells and mice.
Integrating the CRISPR-DNAzyme system with photoactivation strategy and Boolean logic gate provided superior spatiotemporal control imaging for dynamic monitoring of nuclear Zn2+ in HeLa cells and mice.
Moreover, the superiority of CRISPR‐DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn 2+ in both HeLa cells and mice.
Integrating the CRISPR-DNAzyme system with photoactivation strategy and Boolean logic gate provided superior spatiotemporal control imaging for dynamic monitoring of nuclear Zn2+ in HeLa cells and mice.
Moreover, the superiority of CRISPR‐DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn 2+ in both HeLa cells and mice.
Integrating the CRISPR-DNAzyme system with photoactivation strategy and Boolean logic gate provided superior spatiotemporal control imaging for dynamic monitoring of nuclear Zn2+ in HeLa cells and mice.
Moreover, the superiority of CRISPR‐DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn 2+ in both HeLa cells and mice.
Integrating the CRISPR-DNAzyme system with photoactivation strategy and Boolean logic gate provided superior spatiotemporal control imaging for dynamic monitoring of nuclear Zn2+ in HeLa cells and mice.
Moreover, the superiority of CRISPR‐DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn 2+ in both HeLa cells and mice.
Integrating the CRISPR-DNAzyme system with photoactivation strategy and Boolean logic gate provided superior spatiotemporal control imaging for dynamic monitoring of nuclear Zn2+ in HeLa cells and mice.
Moreover, the superiority of CRISPR‐DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn 2+ in both HeLa cells and mice.
Integrating the CRISPR-DNAzyme system with photoactivation strategy and Boolean logic gate provided superior spatiotemporal control imaging for dynamic monitoring of nuclear Zn2+ in HeLa cells and mice.
Moreover, the superiority of CRISPR‐DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn 2+ in both HeLa cells and mice.
The three-stranded DNAzyme probe contains a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus.
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure.
recognition site length 20 bp
The three-stranded DNAzyme probe contains a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus.
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure.
recognition site length 20 bp
The three-stranded DNAzyme probe contains a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus.
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure.
recognition site length 20 bp
The three-stranded DNAzyme probe contains a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus.
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure.
recognition site length 20 bp
The three-stranded DNAzyme probe contains a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus.
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure.
recognition site length 20 bp
The three-stranded DNAzyme probe contains a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus.
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure.
recognition site length 20 bp
The three-stranded DNAzyme probe contains a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus.
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure.
recognition site length 20 bp
This conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and provides new analytical methods for nuclear metal-associated biology.
Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal‐associated biology.
This conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and provides new analytical methods for nuclear metal-associated biology.
Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal‐associated biology.
This conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and provides new analytical methods for nuclear metal-associated biology.
Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal‐associated biology.
This conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and provides new analytical methods for nuclear metal-associated biology.
Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal‐associated biology.
This conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and provides new analytical methods for nuclear metal-associated biology.
Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal‐associated biology.
This conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and provides new analytical methods for nuclear metal-associated biology.
Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal‐associated biology.
This conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and provides new analytical methods for nuclear metal-associated biology.
Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal‐associated biology.
Approval Evidence
1 source2 linked approval claimsfirst-pass slug three-stranded-dnazyme-probe
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity.
Source:
design mechanismsupports
The three-stranded DNAzyme probe contains a 20-bp CRISPR/Cas9 recognition site that blocks DNAzyme activity until Cas9/sgRNA cleavage forms the catalytic DNAzyme structure in the nucleus.
We developed a three‐stranded DNAzyme probe (TSDP) that contained a 20‐base‐pair (20‐bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure.
Source:
toolbox expansionsupports
This conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and provides new analytical methods for nuclear metal-associated biology.
Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal‐associated biology.
Source:
Comparisons
Source-backed strengths
The reported design uses a 20-bp CRISPR/Cas9 recognition site to prevent premature DNAzyme activity and to enable catalytic activation after Cas9/sgRNA cleavage in the nucleus. The source literature states that the photoactivatable, Boolean-gated CRISPR-DNAzyme system achieved superior spatiotemporal control for dynamic nuclear Zn2+ imaging in HeLa cells and mice.
Source:
Moreover, the superiority of CRISPR‐DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn 2+ in both HeLa cells and mice.
Compared with nCas9ERT2
three-stranded DNAzyme probe and nCas9ERT2 address a similar problem space because they share editing, localization.
Shared frame: same top-level item type; shared target processes: editing, localization
Compared with synthetic promoters
three-stranded DNAzyme probe and synthetic promoters address a similar problem space because they share editing, localization.
Shared frame: same top-level item type; shared target processes: editing, localization
Relative tradeoffs: appears more independently replicated; looks easier to implement in practice.
Compared with transcription activator-like effector nucleases
three-stranded DNAzyme probe and transcription activator-like effector nucleases address a similar problem space because they share editing.
Shared frame: same top-level item type; shared target processes: editing; shared mechanisms: photocleavage
Relative tradeoffs: appears more independently replicated; looks easier to implement in practice.
Ranked Citations
- 1.