Toolkit Items

Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.

5 items matching 1 filter

Mechanism Branch

Layer 1

Mechanisms

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Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.

Layer 2

Architectures

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Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.

Layer 3

Components

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Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.

Technique Branch

Layer 1

Approaches

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High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.

Layer 2

Methods

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Concrete methods used to design, build, verify, or characterize engineered systems.

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boolean logic gating

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three-stranded DNAzyme probe

Construct Pattern

Since 2024boolean logic gating crispr/cas9-mediated cleavage dnazyme catalytic activationPhotocleavageComputational Design

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.

CFBacMamMusHumTxRep

Ev 28Rep 9Pr 71

Boolean logic gate

Construct Pattern

Since 2024boolean logic gating conditional dnazyme activation crispr/cas9-mediated cleavage photoactivation

The Boolean logic gate is a construct pattern incorporated into a photoactivatable CRISPR/Cas9-inducible DNAzyme probe. In the reported system, it contributed to superior spatiotemporal control for dynamic imaging of nuclear Zn2+ in HeLa cells and mice.

CFBacMamMusHumTxRep

Ev 28Rep 9Pr 59

photoactivation strategy

Engineering Method

Since 2024boolean logic gating conditional activation of dnazyme catalysis crispr/cas9-mediated cleavage photoactivation

The photoactivation strategy is a light-input engineering method integrated with a CRISPR/Cas9-inducible DNAzyme probe to improve spatiotemporal control of imaging. In the cited 2024 study, this integrated system enabled dynamic monitoring of nuclear Zn2+ in HeLa cells and mice.

CFBacMamMusHumTxRep

Ev 28Rep 9Pr 59

CRISPR/Cas9-inducible DNAzyme probe

Engineering Method

Since 2024boolean logic gating conditional dnazyme activation crispr/cas9-mediated cleavage photoactivationPhotocleavageComputational Design

CRISPR-DNAzyme is a three-stranded DNAzyme probe engineered for in situ imaging of nuclear Zn2+ in living cells. Its catalytic activity is initially blocked by a 20-bp CRISPR/Cas9 recognition site and is activated in the nucleus after Cas9/sgRNA cleavage forms the active DNAzyme structure.

CFBacMamMusHumTxRep

Ev 36Rep 9Pr 47

Synthetic Notch receptor

Multi-Component Switch

Since 2023boolean logic gating conditional activation contact-dependent signaling ligand-dependent receptor activation transcriptional activationComputational Design

Synthetic Notch (synNotch) receptors are modular engineered receptors expressed in mammalian cells that detect signals presented by neighboring cells or ligand-bearing materials and activate prescribed transcriptional programs. In the cited work, synNotch was used as a programmable material-to-cell signaling interface for spatial control of cell phenotypes in multicellular constructs.

CFBacMamMusHumTxRep

Ev 22Rep 9Pr 49

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