Dynamic Characterization of Synthetic Genetic Circuits
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Solution Overview
Problem
Current methods for characterizing synthetic genetic circuits in living cells are hindered by the complexity of biological systems, making it difficult to predict the behavior of genetic components and optimize new systems, as they do not account for metabolic state variations and dynamic behaviors.
Innovation Solution
A method that estimates intrinsic properties of DNA components by using mathematical models to analyze measurements of cell culture density and target signal production over time, allowing for dynamic characterization and optimization of genetic circuits before in vitro preparation.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional characterization methods are used to study genetic circuits in living cells, then experimental data can be obtained, but the metabolic state of the cell cannot be accounted for leading to inaccurate parameter estimation
Solution Approach 1:
The patent segments the characterization process into two distinct phases: a calibration phase where extrinsic parameters related to metabolic state are determined, and a measurement phase where intrinsic genetic circuit parameters are estimated. This separation allows accurate parameter estimation by accounting for metabolic variations without overwhelming complexity in a single step.
Solution Approach 2:
The patent performs preliminary calibration of the system by measuring cell metabolic state and determining extrinsic parameters before conducting the actual genetic circuit characterization. This preliminary action establishes the baseline conditions needed for accurate subsequent measurements.
2Reliability
If static ratiometric methods are used to normalize genetic circuit activity, then variations from metabolic differences can be mitigated, but dynamic behaviors cannot be captured
Solution Approach 1:
The patent transitions from static ratiometric methods to a dynamic approach by continuously monitoring both cell metabolic state and genetic circuit activity over time. The system captures temporal variations and uses time-resolved data to characterize both normalization factors and circuit dynamics simultaneously.
Solution Approach 2:
The patent implements feedback by using measured metabolic state information to continuously adjust and normalize genetic circuit activity measurements. The system feeds back the relationship between metabolic state and circuit performance to accurately separate intrinsic from extrinsic effects.
3Reliability
If extensive in vitro testing and modification are performed to optimize genetic circuits, then predictable behavior can be achieved, but time and resources are consumed
Solution Approach 1:
The patent enables self-service by allowing genetic circuits to characterize their own performance in living cells under physiologically relevant conditions. The system automatically measures and distinguishes between intrinsic circuit properties and extrinsic metabolic effects, providing reliable predictive data without extensive iterative in vitro optimization.
Solution Approach 2:
The patent changes the approach from fixing parameters through iterative in vitro modification to measuring parameters in situ under varying physiological conditions. By characterizing circuits across different metabolic states and growth phases, the system obtains comprehensive parameter data that predicts behavior without extensive optimization cycles.
4Ease of operation
If intrinsic properties of DNA components are determined without accounting for extrinsic factors, then measurement is simplified, but accurate characterization cannot be achieved
Solution Approach 1:
The patent introduces an intermediary measurement of cell metabolic state that mediates between the simple genetic circuit measurements and the complex biological environment. This intermediary data allows the system to account for extrinsic factors while maintaining operational simplicity through automated calibration and normalization.
Data Source
AI summary
The present invention relates to a method for determining one or more intrinsic properties of a DNA component from a plurality of measurements obtained over a time period from a cell culture, with each cell comprising the DNA component, wherein the DNA component is involved in transcription of one or more target signals, wherein the plurality of measurements comprises measurements relating to the density of the cell culture over the time period and measurements relating to the amount of the one or more target signals in the cell culture over the time period.