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.

3 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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polymerase chain reaction amplification

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qRT-PCR

Assay Method

Since 2024fluorescence-based nucleic acid quantification polymerase chain reaction amplification reverse 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

real-time reverse transcription polymerase chain reaction

Assay Method

Since 2000fluorescence-based real-time kinetic detection polymerase chain reaction amplification reverse transcriptionComputational DesignFunctional Assay

The recent introduction of fluorescence-based kinetic RT-PCR procedures significantly simplifies the process of producing reproducible quantification of mRNAs and promises to overcome these limitations.

CFBacMamMusHumTxRep

Ev 20Rep 9Pr 71

reverse transcription polymerase chain reaction

Assay Method

Since 2000polymerase chain reaction amplification reverse 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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