Biomolecular Computing Devices in Synthetic Biology

2010 ◽  
Vol 2 (2) ◽  
pp. 47-64
Author(s):  
Jesús M. Miró ◽  
Alfonso Rodríguez-Patón
Keyword(s):  
Synthetic Biology ◽  
Gene Expression Regulation ◽  
Logic Gates ◽  
Restriction Enzymes ◽  
Regulatory Proteins ◽  
Biomolecular Computing ◽  
Gene Circuits ◽  
Building Information ◽  
Competitive Hybridization ◽  
Standard Molecular Biology

Synthetic biology and biomolecular computation are disciplines that fuse when it comes to designing and building information processing devices. In this chapter, we study several devices that are representative of this fusion. These are three gene circuits implementing logic gates, a DNA nanodevice and a biomolecular automaton. The operation of these devices is based on gene expression regulation, the so-called competitive hybridization and the workings of certain biomolecules like restriction enzymes or regulatory proteins. Synthetic biology, biomolecular computation, systems biology and standard molecular biology concepts are also defined to give a better understanding of the chapter. The aim is to acquaint readers with these biomolecular devices born of the marriage between synthetic biology and biomolecular computation.

scholarly journals Contextual dependencies expand the re-usability of genetic inverters

2020 ◽  
Author(s):  
Huseyin Tas ◽  
Lewis Grozinger ◽  
Ruud Stoof ◽  
Victor de Lorenzo ◽  
Angel Goñi-Moreno
Keyword(s):  
Synthetic Biology ◽  
Computational Analysis ◽  
Logic Gate ◽  
Logic Gates ◽  
Boolean Logic ◽  
Regulatory Proteins ◽  
Genetic Circuits ◽  
Genetic Construct ◽  
Genetic Components ◽  
Logic Functions

The design and implementation of Boolean logic functions in living cells has become a very active field within synthetic biology. By controlling networks of regulatory proteins, novel genetic circuits are engineered to generate predefined output responses. Although many current implementations focus solely on the genetic components of the circuit, the host context in which the circuit performs is crucial for its outcome. Here, we characterise 20 genetic NOT logic gates (inverters) in up to 7 bacterial-based contexts each, to finally generate 135 different functions. The contexts we focus on are particular combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each NOT logic gate shows seven different logic behaviours, depending on the context. That is, gates can be reconfigured to fit response requirements by changing only contextual parameters. Computational analysis shows that this range of behaviours improves the compatibility between gates, because there are considerably more possibilities for combination than when considering a unique function per genetic construct. Finally, we address the issue of interoperability and portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expand the scope of the functions that can be engineered in complex cellular environments, and advocate for considering context as a fundamental design parameter for synthetic biology.

scholarly journals Engineering orthogonal dual transcription factors for multi-input synthetic promoters

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Andreas K. Brödel ◽  
Alfonso Jaramillo ◽  
Mark Isalan
Keyword(s):  
Transcription Factors ◽  
Synthetic Biology ◽  
Directed Evolution ◽  
Logic Gates ◽  
Bacteriophage Λ ◽  
Gene Circuits ◽  
Synthetic Promoters ◽  
Core Set ◽  
Artificial Gene ◽  
Current Engineering

Abstract Synthetic biology has seen an explosive growth in the capability of engineering artificial gene circuits from transcription factors (TFs), particularly in bacteria. However, most artificial networks still employ the same core set of TFs (for example LacI, TetR and cI). The TFs mostly function via repression and it is difficult to integrate multiple inputs in promoter logic. Here we present to our knowledge the first set of dual activator-repressor switches for orthogonal logic gates, based on bacteriophage λ cI variants and multi-input promoter architectures. Our toolkit contains 12 TFs, flexibly operating as activators, repressors, dual activator–repressors or dual repressor–repressors, on up to 270 synthetic promoters. To engineer non cross-reacting cI variants, we design a new M13 phagemid-based system for the directed evolution of biomolecules. Because cI is used in so many synthetic biology projects, the new set of variants will easily slot into the existing projects of other groups, greatly expanding current engineering capacities.

scholarly journals Mammalian synthetic biology: emerging medical applications

2015 ◽  
Vol 12 (106) ◽  
pp. 20141000 ◽  
Author(s):  
Zoltán Kis ◽  
Hugo Sant'Ana Pereira ◽  
Takayuki Homma ◽  
Ryan M. Pedrigi ◽  
Rob Krams
Keyword(s):  
Drug Delivery ◽  
Synthetic Biology ◽  
Gene Networks ◽  
Regulatory Networks ◽  
Logic Gates ◽  
Boolean Logic ◽  
Synthetic Gene ◽  
Medical Applications ◽  
Synthetic Gene Networks ◽  
Gene Circuits

In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON–OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes.

Synthetic Biology: From Gene Circuits to Novel Biological Tools

2017 ◽  
pp. 371-388
Author(s):  
Nina G. Argibay ◽  
Eric M. Vazquez ◽  
Cortney E. Wilson ◽  
Travis J.A. Craddock ◽  
Robert P. Smith
Keyword(s):  
Synthetic Biology ◽  
Gene Circuits

scholarly journals Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinyi Wan ◽  
Filipe Pinto ◽  
Luyang Yu ◽  
Baojun Wang
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Protein Binding ◽  
Gene Networks ◽  
Dynamic Range ◽  
Gene Expression Regulation ◽  
Single Layer ◽  
Regulation Mechanism ◽  
Gene Circuits ◽  
Synthetic Dna

AbstractVersatile tools for gene expression regulation are vital for engineering gene networks of increasing scales and complexity with bespoke responses. Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in Escherichia coli. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by >20-fold, increasing system output amplitude by >130-fold and dynamic range by >70-fold, and mitigating host growth inhibition by >20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications.

scholarly journals A Synthetic Microbial Operational Amplifier

2017 ◽  
Author(s):  
Ji Zeng ◽  
Jaewook Kim ◽  
Areen Banerjee ◽  
Rahul Sarpeshkar
Keyword(s):  
Transcription Factor ◽  
Synthetic Biology ◽  
Operational Amplifier ◽  
Biological Systems ◽  
Logic Gates ◽  
Living Cells ◽  
Output Stage ◽  
Cellular Circuits ◽  
Differential Transcription ◽  
Insight Into

AbstractSynthetic biology has created oscillators, latches, logic gates, logarithmically linear circuits, and load drivers that have electronic analogs in living cells. The ubiquitous operational amplifier, which allows circuits to operate robustly and precisely has not been built with bio-molecular parts. As in electronics, a biological operational-amplifier could greatly improve the predictability of circuits despite noise and variability, a problem that all cellular circuits face. Here, we show how to create a synthetic 3-stage inducer-input operational amplifier with a differential transcription-factor stage, a CRISPR-based push-pull stage, and an enzymatic output stage with just 5 proteins including dCas9. Our ‘Bio-OpAmp’ expands the toolkit of fundamental circuits available to bioengineers or biologists, and may shed insight into biological systems that require robust and precise molecular homeostasis and regulation.One Sentence SummaryA synthetic bio-molecular operational amplifier that can enable robust, precise, and programmable homeostasis and regulation in living cells with just 5 protein parts is described.

scholarly journals A framework for the modular and combinatorial assembly of synthetic gene circuits

2019 ◽  
Author(s):  
Javier Santos-Moreno ◽  
Yolanda Schaerli
Keyword(s):  
Restriction Enzymes ◽  
Synthetic Gene ◽  
Gibson Assembly ◽  
Gene Circuits ◽  
Synthetic Gene Circuits ◽  
Assembly Method ◽  
Design Build ◽  
Transcriptional Units ◽  
Combinatorial Assembly ◽  
Flanking Regions

ABSTRACTSynthetic gene circuits emerge from iterative design-build-test cycles. Most commonly, the time-limiting step is the circuit construction process. Here, we present a hierarchical cloning scheme based on the widespread Gibson assembly method and make the set of constructed plasmids freely available. Our two-step modular cloning scheme allows for simple, fast, efficient and accurate assembly of gene circuits and combinatorial circuit libraries inEscherichia coli. The first step involves Gibson assembly of transcriptional units from constituent parts into individual intermediate plasmids. In the second step, these plasmids are digested with specific sets of restriction enzymes. The resulting flanking regions have overlaps that drive a second Gibson assembly into a single plasmid to yield the final circuit. This approach substantially reduces time and sequencing costs associated with gene circuit construction and allows for modular and combinatorial assembly of circuits. We demonstrate the usefulness of our framework by assembling a double-inverter circuit and a combinatorial library of 3-node networks.

scholarly journals Contextual dependencies expand the re-usability of genetic inverters

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Huseyin Tas ◽  
Lewis Grozinger ◽  
Ruud Stoof ◽  
Victor de Lorenzo ◽  
Ángel Goñi-Moreno
Keyword(s):  
Escherichia Coli ◽  
Synthetic Biology ◽  
Pseudomonas Putida ◽  
Genetic Background ◽  
Design Parameter ◽  
Logic Gates ◽  
Logic Circuits ◽  
Boolean Logic ◽  
Genetic Components ◽  
Fundamental Design

AbstractThe implementation of Boolean logic circuits in cells have become a very active field within synthetic biology. Although these are mostly focussed on the genetic components alone, the context in which the circuit performs is crucial for its outcome. We characterise 20 genetic NOT logic gates in up to 7 bacterial-based contexts each, to generate 135 different functions. The contexts we focus on are combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each gate shows seven different dynamic behaviours, depending on the context. That is, gates can be fine-tuned by changing only contextual parameters, thus improving the compatibility between gates. Finally, we analyse portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expands functionality, and advocate for considering context as a fundamental design parameter.

G-protein-coupled receptors function as logic gates for nanoparticle binding using systems and synthetic biology approach

2019 ◽  
Vol 34 (11) ◽  
pp. 1854-1867 ◽  
Author(s):  
Aman Chandra Kaushik ◽  
Xueying Mao ◽  
Cheng-Dong Li ◽  
Yan Li ◽  
Dong-Qing Wei ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
G Protein ◽  
Logic Gates ◽  
G Protein Coupled Receptors ◽  
Image Position ◽  
G Protein Coupled ◽  
Synthetic Biology Approach

Abstract

scholarly journals Synthetic biology: paving the way with novel drug delivery

2019 ◽  
Vol 41 (3) ◽  
pp. 24-27 ◽  
Author(s):  
Lucas M. Bush ◽  
Chelsea Gibbs ◽  
Tara L. Deans
Keyword(s):  
Gene Expression ◽  
Drug Delivery ◽  
Synthetic Biology ◽  
Rational Design ◽  
Control Cell ◽  
Regulation Of Gene Expression ◽  
Modern Technology ◽  
Gene Circuits ◽  
Basic Concepts ◽  
Novel Drug

Synthetic biology is a multidisciplinary field that focuses on the rational design and construction of novel genetic tools for the purpose of engineering cells to behave in controllable and predictable ways. The promise of this modern technology relies on our understanding of basic genetics and gene expression to engineer cells with unique functions. This is accomplished by designing biological parts and assembling them into higher-order gene circuits that control cell operations through tight regulation of gene expression, effectively reprogramming and rewiring the cells. In this article, we review the basic concepts of gene expression, discuss the framework of how synthetic biologists reprogram cells and outline how cells can be engineered to function as new vehicles for delivering therapeutic proteins.

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