Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch

Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes

Bacteriophage RNA polymerases, in particular T7 RNA polymerase (RNAP), are well-characterized and popular enzymes for many RNA applications in biotechnology both in vitro and in cellular settings. These monomeric polymerases are relatively inexpensive and have high transcription rates and processivity to quickly produce large quantities of RNA. T7 RNAP also has high promoter-specificity on double-stranded DNA (dsDNA) such that it only initiates transcription downstream of its 17-base promoter site on dsDNA templates. However, there are many promoter-independent T7 RNAP transcription reactions involving transcription initiation in regions of single-stranded DNA (ssDNA) that have been reported and characterized. These promoter-independent transcription reactions are important to consider when using T7 RNAP transcriptional systems for DNA nanotechnology and DNA computing applications, in which ssDNA domains often stabilize, organize, and functionalize DNA nanostructures and facilitate strand displacement reactions. Here we review the existing literature on promoter-independent transcription by bacteriophage RNA polymerases with a specific focus on T7 RNAP, and provide examples of how promoter-independent reactions can disrupt the functionality of DNA strand displacement circuit components and alter the stability and functionality of DNA-based materials. We then highlight design strategies for DNA nanotechnology applications that can mitigate the effects of promoter-independent T7 RNAP transcription. The design strategies we present should have an immediate impact by increasing the rate of success of using T7 RNAP for applications in DNA nanotechnology and DNA computing.

Phototriggered Equilibrated and Transient Orthogonally Operating Constitutional Dynamic Networks Guiding Biocatalytic Cascades

The photochemical deprotection of structurally engineered o-nitrobenzylphosphate-caged hairpin nucleic acids is introduced as a versatile method to evolve constitutional dynamic networks, CDNs. The photogenerated CDNs, in the presence of fuel strands, interact with auxiliary CDNs, resulting in their dynamically equilibrated reconfiguration. By modification of the constituents associated with the auxiliary CDNs with glucose oxidase (GOx)/horseradish peroxidase (HRP) or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) cofactor, the photogenerated CDN drives the orthogonal operation upregulated/downregulated operation of the GOx/HRP and LDH/NAD+ biocatalytic cascade in the conjugate mixture of auxiliary CDNs. Also, the photogenerated CDN was applied to control the reconfiguration of coupled CDNs, leading to upregulated/downregulated formation of the antithrombin aptamer units, resulting in the dictated inhibition of thrombin activity (fibrinogen coagulation). Moreover, a reaction module consisting of GOx/HRP-modified o-nitrobenzyl phosphate-caged DNA hairpins, photoresponsive caged auxiliary duplexes, and nickase leads upon irradiation to the emergence of a transient, dissipative CDN activating in the presence of two alternate auxiliary triggers, achieving transient operation of up- and downregulated GOx/HRP biocatalytic cascades.

Dynamic monitoring of an enzymatically driven dissipative toehold-mediated strand displacement reaction

A general strategy to program self-resettable and dissipative toehold-mediated strand displacement reactions was proposed, using DNA strands as the fuel and lambda exonuclease as the fuel-consuming unit. This non-equilibrium system is reversible and temporally controllable. Furthermore, it can be well integrated into a DNA network to temporally control its cascade reaction or dynamic behaviour.

Dynamic DNA Networks-Guided Directional and Orthogonal Transient Biocatalytic Cascades

DNA frameworks, consisting of constitutional dynamic networks (CDNs) undergoing fuel-driven reconfiguration, are coupled to a dissipative reaction module that triggers the reconfigured CDNs into a transient intermediate CDNs recovering the parent CDN state. Biocatalytic cascades consisting of the glucose oxidase (GOx)/horseradish peroxidase (HRP) couple or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) couple are tethered to the constituents of two different CDNs, allowing the CDNs-guided operation of the spatially confined GOx/HRP or LDH/NAD+ biocatalytic cascades. By applying two different fuel triggers, the directional transient CDN-guided upregulation/downregulation of the two biocatalytic cascades are demonstrated. By mixing the GOx/HRP-biocatalyst-modified CDN with the LDH/NAD+-biocatalyst-functionalized CDN, a composite CDN is assembled. Triggering the composite CDN with two different fuel strands results in orthogonal transient upregulation of the GOx/HRP cascade and transient downregulation of the LDH/NAD+ cascade or vice versa. The transient CDNs-guided biocatalytic cascades are computationally simulated by kinetic models, and the computational analyses allow the prediction of the performance of transient biocatalytic cascades under different auxiliary conditions. The concept of orthogonally triggered temporal, transient, biocatalytic cascades by means of CDN frameworks is applied to design an orthogonally operating CDN for the temporal upregulated or downregulated transient thrombin-induced coagulation of fibrinogen to fibrin.

Alternate Strategies to Induce Dynamically Modulated Transient Transcription Machineries

Emulating native transient transcription machineries modulating temporal gene expression by synthetic circuits is a major challenge in the area of systems chemistry. Three different methods to operate transient transcription machineries and to modulate the gated transcription processes of target RNAs are introduced. One method involves the design of a reaction module consisting of transcription templates being triggered by promoter fuel strands transcribing target RNAs and in parallel generating functional DNAzymes in the transcription templates, modulating the dissipative depletion of the active templates and the transient operation of transcription circuits. The second approach involves the application of a reaction module consisting of two transcription templates being activated by a common fuel promoter strand. While one transcription template triggers the transcription of the target RNA, the second transcription template transcribes the anti-fuel strand, displacing the promoter strand associated with the transcription templates, leading to the depletion of the transcription templates and to the dynamic transient modulation of the transcription process. The third strategy involves the assembly of a reaction module consisting of a reaction template triggered by a fuel promoter strand transcribing the target RNA. The concomitant nickase-stimulated depletion of the promoter strand guides the transient modulation of the transcription process. Via integration of two parallel fuel-triggered transcription templates in the three transcription reaction modules and application of template-specific blocker units, the parallel and gated transiently modulated transcription of two different RNA aptamers is demonstrated. The nickase-stimulated transiently modulated transcription reaction module is applied as a functional circuit guiding the dynamic expression of gated, transiently operating, catalytic DNAzymes.

Transient Transcription Machineries Modulate Dynamic Functions of G-Quadruplexes: Temporal Regulation of Biocatalytic Circuits, Gene Replication and Transcription

Native G-quadruplex-regulated temporal biocatalytic circuits, gene polymerization, and transcription processes are emulated by biomimetic, synthetically engineered transcription machineries coupled to reconfigurable G-quadruplex nanostructures. These are addressed by the following example: (i) A reaction module demonstrates the fuel-triggered transcription machinery-guided transient synthesis of G-quadruplex nanostructures. (ii) A dynamically triggered and modulated transcription machinery that guides the temporal separation and reassembly of the anti-thrombin G-quadruplex aptamer/thrombin complex is introduced, and the transient thrombin-catalyzed coagulation of fibrinogen is demonstrated. (iii) A dynamically fueled transient transcription machinery for the temporal activation of G-quadruplex-topologically blocked gene polymerization circuits is introduced. (iv) Transcription circuits revealing G-quadruplex-promoted or G-quadruplex-inhibited cascaded transcription machineries are presented. Beyond advancing the rapidly developing field of dynamically modulated G-quadruplex DNA nanostructures, the systems introduce potential therapeutic applications.

Dynamic Transcription Machineries Guide the Synthesis of Temporally Operating DNAzymes, Gated and Cascaded DNAzyme Catalysis

Transient transcription machineries play important roles in the dynamic modulation of gene expression and the sequestered regulation of cellular networks. The present study emulates such processes by designing artificial reaction modules consisting of transcription machineries that guide the transient synthesis of catalytic DNAzymes, the transient operation of gated DNAzymes, and the temporal activation of an intercommunicated DNAzyme cascade. The reaction modules rely on functional constituents that lead to the triggered activation of transcription machineries in the presence of the nucleoside triphosphates oligonucleotide fuel, yielding the transient formation and dissipative depletion of the intermediate DNAzyme(s) products. The kinetics of the transient DNAzyme networks are computationally simulated, allowing to predict and experimentally validate the performance of the systems under different auxiliary conditions. The study advances the field of systems chemistry by introducing transcription machinery-based networks for the dynamic control over transient catalysis─a primary step toward life-like cellular assemblies.

Autoinhibited transient, gated, and cascaded dynamic transcription of RNAs

Following transient spatiotemporal misregulation of gene expression programs by native transcription machineries, we introduce a versatile biomimetic concept to design transient dynamic transcription machineries, revealing gated and cascaded temporal transcription of RNAs. The concept is based on the engineering of the reaction module consisting of malachite green (MG) and/or DFHBI {(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylene]-3,5-dihydro-2,3-dimethyl-4H-imidazol-4-one} DNA scaffolds, T7 RNA polymerase (RNAP) aptamer transcription scaffold, and the inhibited T7 RNAP-aptamer complex. In the presence of the counter RNAP aptamer strand and ribonucleoside triphosphates, the triggered activation of the three transcription scaffolds are activated, leading to the transcription of the MG and/or DFHBI RNA aptamer and to the transcription of the RNAP aptamer acting as an autoinhibitor that leads to the transient temporal, dissipative, and blockage of all transcription. By appropriate design of the transcription scaffolds and the inhibitors/coupler, transient gated and cascaded transcription processes are demonstrated, and a bimodal transcription module synthesizing a transient operating ribozyme is introduced.

Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks

Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network's various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.

Dissipative DNA nanotechnology

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature.

Dynamic self-assembly of compartmentalized DNA nanotubes

Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets. We develop methods to encapsulate and assemble different types of DNA nanotubes from programmable DNA monomers, and demonstrate temporal control of assembly via designed pathways of RNA production and degradation. We examine the dynamic response of encapsulated nanotube assembly and disassembly with the support of statistical analysis of droplet images. Our study provides a toolkit of methods and components to build increasingly complex and functional NA materials to mimic life-like functions in synthetic cells.

A strategy for programming the regulation of in vitro transcription with application in molecular circuits

In vitro transcription is a convenient platform for fabricating nanodevices and has been used for assembling synthetic networks. However, it remains challenging to regulate synthetic cell-free in vitro transcription by multiple stimuli in a simple and programmable way. We proposed a strategy to regulate in vitro transcription by controlling the transcription templates' promoter domain via variable DNA inputs. To demonstrate the utility of this strategy, various logic circuits and cascading circuits were implemented. With the advantage of simplicity, modularity, programmability, and extensibility, the proposed strategy has potential in biocomputing, bioanalytical, and therapeutic applications.

Constitutional Dynamic Networks-Guided Synthesis of Programmed "Genes", Transcription of mRNAs, and Translation of Proteins

Inspired by nature, where dynamic networks control the levels of gene expression and the activities of transcribed/translated proteins, we introduce nucleic acid-based constitutional dynamic networks (CDNs) as functional modules mimicking native circuits by demonstrating CDNs-guided programmed synthesis of genes, controlled transcription of RNAs, and dictated transcription/translation synthesis of proteins. An auxiliary CDN consisting of four dynamically equilibrated constituents AA', AB', BA', and BB' is orthogonally triggered by two different inputs yielding two different compositionally reconfigured CDNs. Subjecting the parent auxiliary CDN to two hairpins, H_A and H_B, and two templates T_A and T_B and a nicking/replication machinery leads to the cleavage of the hairpins and to the activation of the nicking/replication machineries that synthesize two "genes", e.g., the histidine-dependent DNAzyme g1 and the Zn²⁺-ion-dependent DNAzyme g2. The triggered orthogonal reconfiguration of the parent CDN to the respective CDNs leads to the programmed preferred CDN-guided synthesis of g1 or g2. Similarly, the triggered reconfigured CDNs are subjected to two hairpins H_C and H_D, the templates I'/I and J'/J, and the RNA polymerase (RNAp)/NTPs machinery. While the cleavage of the hairpins by the constituents associated with the parent CDN leads to the transcription of the broccoli aptamer recognizing the DFHBI ligand and of the aptamer recognizing the malachite green (MG) ligand, the orthogonally triggered CDNs lead to the CDNs-guided enhanced transcription of either the DFHBI aptamer or the MG aptamer. In addition, subjecting the triggered reconfigured CDNs to predesigned hairpins H_E and H_F, the templates M'/M and N'/N, the RNAp/NTPs machinery, and the cell-free ribosome t-RNA machinery leads to the CDNs-guided transcription/translation of the green fluorescence protein (GFP) or red fluorescence protein (RFP).

Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules

The regulation of cellular dynamics and responses to stimuli by genetic regulatory networks suggests how in vitro chemical reaction networks might analogously direct the dynamics of synthetic materials or chemistries. A key step in developing genetic regulatory network analogues capable of this type of sophisticated regulation is the integration of multiple coordinated functions within a single network. Here, we demonstrate how such functional integration can be achieved using in vitro transcriptional genelet circuits that emulate essential features of cellular genetic regulatory networks. By successively incorporating functional genelet modules into a bistable circuit, we construct an integrated regulatory network that dynamically changes its state in response to upstream stimuli and coordinates the timing of downstream signal expression. We use quantitative models to guide module integration and develop strategies to mitigate undesired interactions between network components that arise as the size of the network increases. This approach could enable the construction of in vitro networks capable of multifaceted chemical and material regulation.

Aptamer-based regulation of transcription circuits

We propose synthetic DNA/RNA transcription circuits based on specific aptamer recognition. By mimicking transcription factor regulation, combined with specific enzyme/DNA aptamer binding, multiple biomolecules including DNA, RNA, polymerase, restriction enzymes and methylase were used as regulators. In addition, multi-level cascading networks and methylation-switch circuits were also established. This regulation strategy has the potential to expand the toolkit of in vitro synthetic biology.

Dichotomous Nature of Bistability Generated by Negative Cooperativity in Receptor-Ligand Binding

Positive cooperativity in receptor-ligand binding plays an important role in cell signaling as it generates an ultrasensitive response, a requirement for nonlinear phenomena such as bistability and oscillations in feedback regulated reaction networks. On the other hand, negative cooperativity typically produces a hyperbolic response and is thus less explored. However, recently negative cooperativity was shown to generate an ultrasensitive response under the condition of strong ligand affinity. In this work, we have used mathematical modeling to investigate the effect of negative cooperativity in receptor-ligand interaction on the bistability in a positive feedback regulatory motif. We systematically investigated the effect of negative cooperativity, modifying the two equilibrium constants of the receptor-ligand binding, on the robustness and tunability of bistability. We show that in the regime where negative cooperativity exhibits robust bistability, positive cooperativity results in poor bistability and vice versa. Further we find that the robustness and tunability of bistability depend crucially on the stability of singly and doubly engaged receptors. Our modeling highlights the ability of negative cooperativity to produce complex phenomena with potential applications in designing synthetic devices or in explaining experimental observations in cell biology.

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

Synthetic biology brings 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.

Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology

Work on synthetic biology has largely used a component-based metaphor for system construction. While this paradigm has been successful for the construction of numerous systems, the incorporation of contextual design issues-either compositional, host or environmental-will be key to realising more complex applications. Here, we present a design framework that radically steps away from a purely parts-based paradigm by using aspect-oriented software engineering concepts. We believe that the notion of concerns is a powerful and biologically credible way of thinking about system synthesis. By adopting this approach, we can separate core concerns, which represent modular aims of the design, from cross-cutting concerns, which represent system-wide attributes. The explicit handling of cross-cutting concerns allows for contextual information to enter the design process in a modular way. As a proof-of-principle, we implemented the aspect-oriented approach in the Python tool, SynBioWeaver, which enables the combination, or weaving, of core and cross-cutting concerns. The power and flexibility of this framework is demonstrated through a number of examples covering the inclusion of part context, combining circuit designs in a context dependent manner, and the generation of rule, logic and reaction models from synthetic circuit designs.

In Vitro Transcription Networks Based on Hairpin Promoter Switches

In vitro transcription networks are analogs of naturally occurring gene regulatory networks that consist of synthetic DNA templates that are cross-regulated by their own transcripts. This ability to design and execute in vitro transcription networks has allowed bottom-up construction of complex network topologies with predictable dynamic behavior. Here we describe the simplified design of an in vitro transcription network based on single-stranded synthetic DNA hairpin switches that function similar to molecular beacons, via toehold mediated strand displacement. Systematic construction of increasingly larger circuits was achieved by programming interactions between multiple switches through rational sequence design, and the dynamic behavior of networks was accurately predicted using a simple mathematical model. Ultimately, we engineered a cascade of switches that acted as a Boolean complete NAND gate capable of sensing both DNA and RNA inputs. The tools and framework that have been developed makes the execution of in vitro transcription circuits much simpler, which will enable them to more readily serve as testbeds for nucleic acid computations both in vitro and in vivo.

T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures

The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases.

A Robust Molecular Network Motif for Period-Doubling Devices

Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune. Circuits that can multiply the period of a clock signal (frequency dividers), such as binary counters and flip-flops, are commonly encountered in electronic systems, but design principles to obtain similar devices in biological systems are still unclear. We take inspiration from the architecture of electronic flip-flops, and we propose to build biomolecular period-doubling networks by combining a bistable switch with negative feedback modules that preprocess the circuit inputs. We identify a network motif and we show it can be "realized" using different biomolecular components; two of the realizations we propose rely on transcriptional gene networks and one on nucleic acid strand displacement systems. We examine the capacity of each realization to perform period-doubling by studying how bistability of the motif is affected by the presence of the input; for this purpose, we employ mathematical tools from algebraic geometry that provide us with valuable insights on the input/output behavior as a function of the realization parameters. We show that transcriptional network realizations operate correctly also in a stochastic regime when processing oscillations from the repressilator, a canonical synthetic in vivo oscillator. Finally, we compare the performance of different realizations in a range of realistic parameters via numerical sensitivity analysis of the period-doubling region, computed with respect to the input period and amplitude. Our mathematical and computational analysis suggests that the motif we propose is generally robust with respect to specific implementation details: functionally equivalent circuits can be built as long as the species-interaction topology is respected. This indicates that experimental construction of the circuit is possible with a variety of components within the rapidly expanding libraries available in synthetic biology.

Boosting functionality of synthetic DNA circuits with tailored deactivation

Molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. The function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. Here we introduce a mechanism to tune the nonlinearities associated with individual nodes of a synthetic network. This mechanism is based on programming deactivation laws using dedicated saturable pathways. We demonstrate this approach through the conversion of a single-node homoeostatic network into a bistable and reversible switch. Furthermore, we prove its generality by adding new functions to the library of reported man-made molecular devices: a system with three addressable bits of memory, and the first DNA-encoded excitable circuit. Specific saturable deactivation pathways thus greatly enrich the functional capability of a given circuit topology.

Nonlinearity in synthetic molecular circuits is usually achieved by manipulation of network topology or of production kinetics. Here, the authors achieve bistability and other nonlinear behaviours by manipulating the individual degradation rate laws of circuit components using saturable pathways.

Computational Design of a Circular RNA with Prionlike Behavior

RNA molecules engineered to fold into predefined conformations have enabled the design of a multitude of functional RNA devices in the field of synthetic biology and nanotechnology. More complex designs require efficient computational methods, which need to consider not only equilibrium thermodynamics but also the kinetics of structure formation. Here we present a novel type of RNA design that mimics the behavior of prions, that is, sequences capable of interaction-triggered autocatalytic replication of conformations. Our design was computed with the ViennaRNA package and is based on circular RNA that embeds domains amenable to intermolecular kissing interactions.

Automated design of programmable enzyme-driven DNA circuits

Molecular programming allows for the bottom-up engineering of biochemical reaction networks in a controlled in vitro setting. These engineered biochemical reaction networks yield important insight in the design principles of biological systems and can potentially enrich molecular diagnostic systems. The DNA polymerase-nickase-exonuclease (PEN) toolbox has recently been used to program oscillatory and bistable biochemical networks using a minimal number of components. Previous work has reported the automatic construction of in silico descriptions of biochemical networks derived from the PEN toolbox, paving the way for generating networks of arbitrary size and complexity in vitro. Here, we report an automated approach that further bridges the gap between an in silico description and in vitro realization. A biochemical network of arbitrary complexity can be globally screened for parameter values that display the desired function and combining this approach with robustness analysis further increases the chance of successful in vitro implementation. Moreover, we present an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis. Our in silico method has been tested on a previously reported network, the Oligator, and has also been applied to the design of a reaction network capable of displaying adaptation in one of its components. Finally, we experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. The strong nonlinearities in the degradation of active components caused by this unintended cross-coupling are shown computationally to have a positive effect on adaptation quality.

Computational design of nucleic acid feedback control circuits

The design of synthetic circuits for controlling molecular-scale processes is an important goal of synthetic biology, with potential applications in future in vitro and in vivo biotechnology. In this paper, we present a computational approach for designing feedback control circuits constructed from nucleic acids. Our approach relies on an existing methodology for expressing signal processing and control circuits as biomolecular reactions. We first extend the methodology so that circuits can be expressed using just two classes of reactions: catalysis and annihilation. We then propose implementations of these reactions in three distinct classes of nucleic acid circuits, which rely on DNA strand displacement, DNA enzyme and RNA enzyme mechanisms, respectively. We use these implementations to design a Proportional Integral controller, capable of regulating the output of a system according to a given reference signal, and discuss the trade-offs between the different approaches. As a proof of principle, we implement our methodology as an extension to a DNA strand displacement software tool, thus allowing a broad range of nucleic acid circuits to be designed and analyzed within a common modeling framework.

Negative autoregulation matches production and demand in synthetic transcriptional networks

We propose a negative feedback architecture that regulates activity of artificial genes, or "genelets", to meet their output downstream demand, achieving robustness with respect to uncertain open-loop output production rates. In particular, we consider the case where the outputs of two genelets interact to form a single assembled product. We show with analysis and experiments that negative autoregulation matches the production and demand of the outputs: the magnitude of the regulatory signal is proportional to the "error" between the circuit output concentration and its actual demand. This two-device system is experimentally implemented using in vitro transcriptional networks, where reactions are systematically designed by optimizing nucleic acid sequences with publicly available software packages. We build a predictive ordinary differential equation (ODE) model that captures the dynamics of the system and can be used to numerically assess the scalability of this architecture to larger sets of interconnected genes. Finally, with numerical simulations we contrast our negative autoregulation scheme with a cross-activation architecture, which is less scalable and results in slower response times.

Load capacity improvements in nucleic acid based systems using partially open feedback control

Synthetic biology is facilitating novel methods and components to build in vivo and in vitro circuits to better understand and re-engineer biological networks. Recently, Kim and Winfree have synthesized a remarkably elegant network of transcriptional oscillators in vitro using a modular architecture of synthetic gene analogues and a few enzymes that, in turn, could be used to drive a variety of downstream circuits and nanodevices. However, these oscillators are sensitive to initial conditions and downstream load processes. Furthermore, the oscillations are not sustained since the inherently closed design suffers from enzyme deactivation, NTP fuel exhaustion, and waste product build up. In this paper, we show that a partially open architecture in which an [Symbol: see text]1 adaptive controller, implemented inside an in silico computer that resides outside the wet-lab apparatus, can ensure sustained tunable oscillations in two specific designs of the Kim-Winfree oscillator networks. We consider two broad cases of operation: (1) the oscillator network operating in isolation and (2) the oscillator network driving a DNA tweezer subject to a variable load. In both scenarios, our simulation results show a significant improvement in the tunability and robustness of these oscillator networks. Our approach can be easily adopted to improve the loading capacity of a wide range of synthetic biological devices.

The emerging age of cell-free synthetic biology

The engineering of and mastery over biological parts has catalyzed the emergence of synthetic biology. This field has grown exponentially in the past decade. As increasingly more applications of synthetic biology are pursued, more challenges are encountered, such as delivering genetic material into cells and optimizing genetic circuits in vivo. An in vitro or cell-free approach to synthetic biology simplifies and avoids many of the pitfalls of in vivo synthetic biology. In this review, we describe some of the innate features that make cell-free systems compelling platforms for synthetic biology and discuss emerging improvements of cell-free technologies. We also select and highlight recent and emerging applications of cell-free synthetic biology.

Synthetic circuit for exact adaptation and fold-change detection

Biological organisms use their sensory systems to detect changes in their environment. The ability of sensory systems to adapt to static inputs allows wide dynamic range as well as sensitivity to input changes including fold-change detection, a response that depends only on fold changes in input, and not on absolute changes. This input scale invariance underlies an important strategy for search that depends solely on the spatial profile of the input. Synthetic efforts to reproduce the architecture and response of cellular circuits provide an important step to foster understanding at the molecular level. We report the bottom-up assembly of biochemical systems that show exact adaptation and fold-change detection. Using a malachite green aptamer as the output, a synthetic transcriptional circuit with the connectivity of an incoherent feed-forward loop motif exhibits pulse generation and exact adaptation. A simple mathematical model was used to assess the amplitude and duration of pulse response as well as the parameter regimes required for fold-change detection. Upon parameter tuning, this synthetic circuit exhibits fold-change detection for four successive rounds of two-fold input changes. The experimental realization of fold-change detection circuit highlights the programmability of transcriptional switches and the ability to obtain predictive dynamical systems in a cell-free environment for technological applications.

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator

In vitro compartmentalization of biochemical reaction networks is a crucial step towards engineering artificial cell-scale devices and systems. At this scale the dynamics of molecular systems becomes stochastic, which introduces several engineering challenges and opportunities. Here we study a programmable transcriptional oscillator system that is compartmentalized into microemulsion droplets with volumes between 33 fl and 16 pl. Simultaneous measurement of large populations of droplets reveals major variations in the amplitude, frequency and damping of the oscillations. Variability increases for smaller droplets and depends on the operating point of the oscillator. Rather than reflecting the stochastic kinetics of the chemical reaction network itself, the variability can be attributed to the statistical variation of reactant concentrations created during their partitioning into droplets. We anticipate that robustness to partitioning variability will be a critical challenge for engineering cell-scale systems, and that highly parallel time-series acquisition from microemulsion droplets will become a key tool for characterization of stochastic circuit function.

In vitro regulatory models for systems biology

The reductionist approach has revolutionized biology in the past 50 years. Yet its limits are being felt as the complexity of cellular interactions is gradually revealed by high-throughput technology. In order to make sense of the deluge of "omic data", a hypothesis-driven view is needed to understand how biomolecular interactions shape cellular networks. We review recent efforts aimed at building in vitro biochemical networks that reproduce the flow of genetic regulation. We highlight how those efforts have culminated in the rational construction of biochemical oscillators and bistable memories in test tubes. We also recapitulate the lessons learned about in vivo biochemical circuits such as the importance of delays and competition, the links between topology and kinetics, as well as the intriguing resemblance between cellular reaction networks and ecosystems.

Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling

One-step purification of a multi-enzyme complex was developed based on a mixture of cell extracts containing three dockerin-containing enzymes and one family 3 cellulose-binding module (CBM3)-containing scaffoldin through high-affinity adsorption on low-cost solid regenerated amorphous cellulose (RAC). The three-enzyme complex, called synthetic metabolon, was self-assembled through the high-affinity interaction between the dockerin in each enzyme and three cohesins in the synthetic scaffoldin. The metabolons were either immobilized on the external surface of RAC or free when the scaffoldin contained an intein between the CBM3 and three cohesins. The immobilized and free metabolons containing triosephosphate isomerase, aldolase, and fructose 1,6-biphosphatase exhibited initial reaction rates 48 and 38 times, respectively, that of the non-complexed three-enzyme mixture at the same enzyme loading. Such reaction rate enhancements indicated strong substrate channeling among synthetic metabolons due to the close spatial organization among cascade enzymes. These results suggested that the construction of synthetic metabolons by using cohesins, dockerins, and cellulose-binding modules from cellulosomes not only decreased protein purification labor and cost for in vitro synthetic biology projects but also accelerated reaction rates by 1 order of magnitude compared to non-complexed enzymes. Synthetic metabolons would be an important biocatalytic module for in vitro and in vivo synthetic biology projects.

Bottom-up construction of in vitro switchable memories

Reaction networks displaying bistability provide a chemical mechanism for long-term memory storage in cells, as exemplified by many epigenetic switches. These biological systems are not only bistable but switchable, in the sense that they can be flipped from one state to the other by application of specific molecular stimuli. We have reproduced such functions through the rational assembly of dynamic reaction networks based on basic DNA biochemistry. Rather than rewiring genetic systems as synthetic biology does in vivo, our strategy consists of building simplified dynamic analogs in vitro, in an artificial, well-controlled milieu. We report successively a bistable system, a two-input switchable memory element, and a single-input push-push memory circuit. These results suggest that it is possible to build complex time-responsive molecular circuits by following a modular approach to the design of dynamic in vitro behaviors. Our approach thus provides an unmatched opportunity to study topology/function relationships within dynamic reaction networks.