Designing biological circuits

2021 ◽  
pp. 275-292
Author(s):  
Karthik Raman
Keyword(s):  
Biological Circuits

Joint DAC/IWBDA special session design and synthesis of biological circuits

2011 ◽  
Author(s):  
Douglas Densmore ◽  
Mark Horowitz ◽  
Smita Krishnaswamy ◽  
Xiling Shen ◽  
Adam Arkin ◽  
...  
Keyword(s):  
Special Session ◽  
Design And Synthesis ◽  
Biological Circuits

scholarly journals Functional tunability of biological circuits from additional toggle switches

2013 ◽  
Vol 7 (5) ◽  
pp. 126-134 ◽  
Author(s):  
Changhong Shi ◽  
Tianshou Zhou ◽  
Zhanjiang Yuan
Keyword(s):  
Biological Circuits

scholarly journals Independent control of amplitude and period in a synthetic oscillator circuit with modified repressilator

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Fengyu Zhang ◽  
Yanhong Sun ◽  
Yihao Zhang ◽  
Wenting Shen ◽  
Shujing Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Synthetic Biology ◽  
Biological Systems ◽  
Reporter Genes ◽  
Quantitative Model ◽  
Theoretical Level ◽  
Independent Control ◽  
Oscillator Circuit ◽  
Biological Circuits

AbstractSynthetic Biology aims to create predictable biological circuits and fully operational biological systems. Although there are methods to create more stable oscillators, such as repressilators, independently controlling the oscillation of reporter genes in terms of their amplitude and period is only on theoretical level. Here, we introduce a new oscillator circuit that can be independently controlled by two inducers in Escherichia coli. Some control components, including σECF11 and NahR, were added to the circuit. By systematically tuning the concentration of the inducers, salicylate and IPTG, the amplitude and period can be modulated independently. Furthermore, we constructed a quantitative model to forecast the regulation results. Under the guidance of the model, the expected oscillation can be regulated by choosing the proper concentration combinations of inducers. In summary, our work achieved independent control of the oscillator circuit, which allows the oscillator to be modularized and used in more complex circuit designs.

scholarly journals Toeholder: a software for automated design and in silico validation of toehold riboswitches

2021 ◽  
Author(s):  
Angel Fernando Cisneros Caballero ◽  
Francois D. Rouleau ◽  
Carla Bautista ◽  
Pascale Lemieux ◽  
Nathan Dumont-Leblond
Keyword(s):  
In Silico ◽  
Dynamic Range ◽  
Regulatory Elements ◽  
Automated Design ◽  
Design And Optimization ◽  
Potential Applications ◽  
Dynamics Simulations ◽  
Effective Use ◽  
Biological Circuits ◽  
High Throughput Experiments

Synthetic biology aims to engineer biological circuits, which often involve gene expression. A particularly promising group of regulatory elements are riboswitches because of their versatility with respect to their targets, but early synthetic designs were not as attractive because of a reduced dynamic range with respect to protein regulators. Only recently, the creation of toehold switches helped overcome this obstacle by also providing an unprecedented degree of orthogonality. However, a lack of automated design and optimization tools prevents the widespread and effective use of toehold switches in high-throughput experiments. To address this, we developed Toeholder, a comprehensive open-source software for toehold design and in silico benchmarking. Toeholder takes into consideration sequence constraints as well as data derived from molecular dynamics simulations of a toehold switch. We describe the software and its in silico validation results, as well as its potential applications and impacts on the management and design of toehold switches.

Prototyping of microbial chassis for the biomanufacturing of high-value chemical targets

2021 ◽  
Author(s):  
Christopher J. Robinson ◽  
Jonathan Tellechea-Luzardo ◽  
Pablo Carbonell ◽  
Adrian J. Jervis ◽  
Cunyu Yan ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Potential Role ◽  
Design Space ◽  
Scale Up ◽  
Combinatorial Design ◽  
Design Build ◽  
Biological Circuits ◽  
Genetic Constructs ◽  
Host Strains

Metabolic engineering technologies have been employed with increasing success over the last three decades for the engineering and optimization of industrial host strains to competitively produce high-value chemical targets. To this end, continued reductions in the time taken from concept, to development, to scale-up are essential. Design–Build–Test–Learn pipelines that are able to rapidly deliver diverse chemical targets through iterative optimization of microbial production strains have been established. Biofoundries are employing in silico tools for the design of genetic parts, alongside combinatorial design of experiments approaches to optimize selection from within the potential design space of biological circuits based on multi-criteria objectives. These genetic constructs can then be built and tested through automated laboratory workflows, with performance data analysed in the learn phase to inform further design. Successful examples of rapid prototyping processes for microbially produced compounds reveal the potential role of biofoundries in leading the sustainable production of next-generation bio-based chemicals.

scholarly journals Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems

2019 ◽  
Vol 2 (2) ◽  
pp. 39 ◽  
Author(s):  
Dohyun Jeong ◽  
Melissa Klocke ◽  
Siddharth Agarwal ◽  
Jeongwon Kim ◽  
Seungdo Choi ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Free Expression ◽  
Dna Nanostructures ◽  
Expression Systems ◽  
Natural Systems ◽  
The Past ◽  
Current Cell ◽  
Recent Developments ◽  
Biological Circuits

Synthetic biology integrates diverse engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription–translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.

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