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.

4 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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reverse transcription

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qRT-PCR

Assay Method
Since 2024fluorescence-based nucleic acid quantificationpolymerase chain reaction amplificationreverse transcriptionFunctional Assay

qRT-PCR is a quantitative reverse-transcription PCR assay used to measure transcript abundance, here applied to GFP mRNA during light-controlled gene expression in Synechococcus sp. PCC 7002. In the cited study, it quantified transcriptional activation and deactivation kinetics of optogenetic systems under green/red and light/dark illumination cycles.

CFBacMamMusHumTxRep
Ev 83Rep 43Pr 71

prime-editing

Multi-Component Switch
Since 2021Degradationdouble-strand-break-free editingPhotocleavagereverse transcriptiontemplate-programmed genome editingTranslation ControlDirected EvolutionStructural Characterization

Prime editing is mentioned in the cited review as part of the broader set of genome-editing approaches considered in bacterial genome engineering. The supplied evidence does not describe its molecular architecture, target scope, or editing outcomes.

CFBacMamMusHumTxRep
Ev 70Rep 54Pr 37

reverse transcription polymerase chain reaction

Assay Method
Since 2000polymerase chain reaction amplificationreverse transcriptionFunctional Assay

The reverse transcription polymerase chain reaction (RT-PCR) is the most sensitive method for the detection of low-abundance mRNA, often obtained from limited tissue samples. However, it is a complex technique, there are substantial problems associated with its true sensitivity, reproducibility and specificity and, as a quantitative method, it suffers from the problems inherent in PCR.

CFBacMamMusHumTxRep
Ev 20Rep 9Pr 71
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