Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

Detection of TuMV by a toehold switch sensor coupled with NASBA amplification in Pseudostellaria heterophylla

Pseudostellaria heterophylla (P. heterophylla) is a perennial herb that has been used as a medicinal food for hundreds of years in China. Viral infections during the production of P. heterophylla severely reduce the yield and quality. Turnip mosaic virus (TuMV) is a common and highly variable viral pathogen in P. heterophylla plants. A high-efficiency diagnostic system is urgently needed to control and alleviate TuMV infection. However, the current detection methods still have various deficiencies that limit their field application. Here, a cell-free expression system relying on nucleic acid sequence-based amplification (NASBA) with toehold switch sensors and a visual reporter for color change was developed and introduced for TuMV detection in P. heterophylla. After designing and screening the approach, the selected sensitive sensor was able to detect 1 pM TuMV RNA fragments within 40 min, and the detection limit was less than 10 fM if the time was extended to 90 min. The sensor exhibited high specificity, with no cross-reactivity detected when tested against cucumber mosaic virus, another prevalent viral pathogen in P. heterophylla. In addition, in in-field samples, TuMV was successfully detected directly from both purified and crude RNA extracts in approximately 3 h. This cell-free synthetic biology tool is rapid, sensitive, specific and field-applicable and provides high-capacity and low-cost diagnostics for TuMV in P. heterophylla, as well as various viruses in herbs and other host plants.

A cell-free biosensor signal amplification circuit with polymerase strand recycling

Cell-free systems are powerful synthetic biology technologies that can recapitulate gene expression and sensing without the complications of living cells. Cell-free systems can perform more advanced functions when genetic circuits are incorporated. Here we expand cell-free biosensing by engineering a highly specific isothermal amplification circuit called polymerase strand recycling (PSR), which leverages T7 RNA polymerase off-target transcription to recycle nucleic acid inputs within DNA strand displacement circuits. We first construct simple PSR circuits to detect different RNA targets with high specificity. We then interface PSR circuits to amplify signals from allosteric transcription factor-based biosensors for small molecule detection. A double equilibrium model of transcription factor-DNA/ligand binding predicts that PSR can improve biosensor sensitivity, which we confirm experimentally by improving the limits of detection by 10-fold to submicromolar levels for two biosensors. We believe this work expands the capabilities of cell-free circuits and demonstrates PSR's potential for diverse applications in biotechnology.

Simple and Cost-effective Fluoride Riboswitch-Based Whole-Cell Biosensor for the Determination of Fluoride in Drinking Water

Fluoride in drinking water poses health risks when exceeding WHO-recommended limits, necessitating accurate detection methods. This study developed a highly selective fluoride riboswitch (FRS)-based whole-cell biosensor using an E. coli mutant with a recombinant plasmid carrying the FRS fused to the lacZ reporter gene. Fluoride binding to the FRS aptamer triggers β-galactosidase expression, enabling fluoride quantification by a colorimetric assay. Using a calibration curve (R2 > 0.9), fluoride concentrations in Sri Lankan water samples were determined (0.15-0.90 ppm). Minimal interference from common ions (Cl⁻, OH⁻, Na⁺, K⁺, Ca2⁺, CO₃2⁻, HCO₃⁻, and NO₃⁻) confirmed the biosensor's narrow specificity and high selectivity towards fluoride.

Scalable Cell-Free Production of Active T7 RNA Polymerase

The SARS-CoV-2 pandemic highlighted the urgent need for biomanufacturing paradigms that are robust and fast. Here, we demonstrate the rapid process development and scalable cell-free production of T7 RNA polymerase, a critical component in mRNA vaccine synthesis. We carry out a 1-L cell-free gene expression (CFE) reaction that achieves over 90% purity, low endotoxin levels, and enhanced activity relative to commercial T7 RNA polymerase. To achieve this demonstration, we implement rolling circle amplification to circumvent difficulties in DNA template generation, and tune cell-free reaction conditions, such as temperature, additives, purification tags, and agitation, to boost yields. We achieve production of a similar quality and titer of T7 RNA polymerase over more than four orders of magnitude in reaction volume. This proof of principle positions CFE as a viable solution for decentralized biotherapeutic manufacturing, enhancing preparedness for future public health crises or emergent threats.

PET-derived heteroatom-doped carbon quantum dots as color-modulated solid-state fluorescent materials

Plastic waste was transformed into high-performance quantum dots (QDs), combining technological innovation with a focus on environmental sustainability. The excellent fluorescence properties of the synthesized quantum dots were utilized to detect Fe3+ and F- ions with high sensitivity and selectivity in an "on-off-on" dual-mode fashion. Additionally, the synthesized quantum dots exhibited stable solid-state fluorescence, enabling their use in solid-phase applications without the typical fluorescence loss observed in other materials. The versatility and tunability of the synthesized materials were demonstrated by producing three different emission colors, achieved through the incorporation of various heteroatoms during the synthesis process. This solid-state fluorescent material provides a pathway for sensing and optoelectronic applications, as well as advanced optical devices with customizable designs in the future.

Cell-free synthesis system: An accessible platform from biosensing to biomanufacturing

The fundamental aspect of cell-free synthesis systems is the in vitro transcription-translation process. By artificially providing the components required for protein expression, in vitro protein production alleviates various limitations tied to in vivo production, such as oxygen supply and nutrient constraints, thus showcasing substantial potential in engineering applications. This article presents a comprehensive review of cell-free synthesis systems, with a primary focus on biosensing and biomanufacturing. In terms of biosensing, it summarizes the recognition-response mechanisms and key advantages of cell-free biosensors. Moreover, it examines the strategies for the cell-free production of intricate proteins, including membrane proteins and glycoproteins. Additionally, the integration of cell-free metabolic engineering approaches with cell-free synthesis systems in biomanufacturing is thoroughly discussed, with the expectation that biotechnology will embrace greater prosperity.

Semiautomated Production of Cell-Free Biosensors

Cell-free synthetic biology biosensors have potential as effective in vitro diagnostic technologies for the detection of chemical compounds, such as toxins and human health biomarkers. They have several advantages over conventional laboratory-based diagnostic approaches, including the ability to be assembled, freeze-dried, distributed, and then used at the point of need. This makes them an attractive platform for cheap and rapid chemical detection across the globe. Though promising, a major challenge is scaling up biosensor manufacturing to meet the needs of their multiple uses. Currently, cell-free biosensor assembly during lab-scale development is mostly performed manually by the operator, leading to quality control and performance variability issues. Here we explore the use of liquid-handling robotics to manufacture cell-free biosensor reactions. We compare both manual and semiautomated reaction assembly approaches using the Opentrons OT-2 liquid handling platform on two different cell-free gene expression assay systems that constitutively produce colorimetric (LacZ) or fluorescent (GFP) signals. We test the designed protocol by constructing an entire 384-well plate of fluoride-sensing cell-free biosensors and demonstrate that they perform close to expected detection outcomes.

Cell-Free Expression of Soluble Leafhopper Proteins from Brochosomes

Brochosomes are proteinaceous nanostructures produced by leafhopper insects with superhydrophobic and antireflective properties. Unfortunately, the production and study of brochosome-based materials has been limited by poor understanding of their major constituent subunit proteins, known as brochosomins, as well as their sensitivity to redox conditions due to essential disulfide bonds. Here, we used cell-free gene expression (CFE) to achieve recombinant production and analysis of brochosomin proteins. Through the optimization of redox environment, reaction temperature, and disulfide bond isomerase concentration, we achieved soluble brochosomin yields of up to 341 ± 30 μg/mL. Analysis using dynamic light scattering and transmission electron microscopy revealed distinct aggregation patterns among cell-free mixtures with different expressed brochosomins. We anticipate that the CFE methods developed here will accelerate the ability to change the geometries and properties of natural and modified brochosomes, as well as facilitate the expression and structural analysis of other poorly understood protein complexes.

Design Principles for Polymerase Strand Recycling Circuits

Cell-free biosensing systems are being engineered as versatile and programmable diagnostic technologies. A core component of cell-free biosensors are programmable molecular circuits that improve biosensor speed, sensitivity and specificity by performing molecular computations such as logic evaluation and signal amplification. In previous work, we developed one such circuit system called Polymerase Strand Recycling (PSR) which amplifies cell-free molecular circuits by using T7 RNA polymerase off-target transcription to recycle nucleic acid inputs. We showed that PSR circuits can be configured to detect RNA target inputs as well as be interfaced with allosteric transcription factor-based biosensors to amplify signal and enhance sensitivity. Here we expand the development of PSR circuit design principles to generalize the platform for detecting a diverse set of model microRNA inputs. We show that PSR circuit function can be enhanced through engineering T7 RNAP, and present troubleshooting strategies to optimize PSR circuit performance.

Molecules Targeting EriCF1 Increase Streptococcus mutans Fluoride Sensitivity

Dental caries, as one of the prevalent oral infectious diseases worldwide, constitutes a considerable disease burden. Fluoride has been widely used to prevent dental caries for decades. However, fluoride alone may not always be sufficient. The major cariogenic bacterial species, Streptococcus mutans, has not been effectively controlled by daily fluoride exposure, possibly because it has a detoxification mechanism. Studies have shown that most microorganisms have fluoride exporters dedicated to exporting fluoride ions (F-). S. mutans possesses 2 homologous genes, eriCF1 and eriCF2, which encode fluoride exporters, but their function has not been fully clarified. In this work, we constructed the markerless gene deletion mutants, overexpression, and complemented strains of S. mutans UA159. Assessing fluoride sensitivity, intracellular F- levels, and cell membrane permeability revealed that EriCF1 was the major functional unit of the fluoride exporter in S. mutans. To further enhance the antibacterial efficiency of fluoride, we identified 3 diphenylurea derivatives that might target EriCF1 by molecular docking, which significantly enhanced the antibacterial effect of sodium fluoride (NaF) by synergistically impeding fluoride efflux, as demonstrated by chequerboard broth microdilution assays. Moreover, these compounds combined with 1 mM NaF impaired the cariogenicity of S. mutans significantly in vivo and with good biocompatibility, especially compounds 9 and 15. Collectively, these findings suggest that fluoride exporters in S. mutans could serve as a potential target for caries prevention, and the diphenylurea derivatives identified for targeting EriCF1 could be a valuable therapeutic approach when combined with fluoride, providing promising measures for dental caries prevention.

Ultrasensitive Water Contaminant Detection with Transcription Factor Interfaced Microcantilevers

Water contamination by harmful chemicals is a growing global concern, creating a need to develop technologies that can detect a range of target compounds at the required concentrations. Here, we address this need by merging biological allosteric transcription factors with DNA-coated nanomechanical microcantilevers to detect chemicals in water with a digital readout. After proof-of-concept demonstration and optimization to detect anhydrotetracycline with the TetR transcription factor, we use the CadC transcription factor to detect Pb2+ and Cd2+ in water at concentrations down to 2 and 1 ppb, respectively, in less than 15 min. A computational model suggests this improvement in sensitivity could be achieved by the DNA-coated microcantilever surface changing the transcription factor binding properties. Our findings demonstrate a promising approach for water quality monitoring with fast, highly sensitive, digital readout.

Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation

Precise and tunable gene expression is crucial for various biotechnological applications, including protein overexpression, fine-tuned metabolic pathway engineering, and dynamic gene regulation. Untranslated regions (UTRs) of mRNAs have emerged as key regulatory elements that modulate transcription and translation. In this review, we explore recent advances in UTR engineering strategies for bacterial gene expression optimization. We discuss approaches for enhancing protein expression through AU-rich elements, RG4 structures, and synthetic dual UTRs, as well as ProQC systems that improve translation fidelity. Additionally, we examine strategies for fine-tuning gene expression using UTR libraries and synthetic terminators that balance metabolic flux. Finally, we highlight riboswitches and toehold switches, which enable dynamic gene regulation in response to environmental or metabolic cues. The integration of these UTR-based regulatory tools provides a versatile and modular framework for optimizing bacterial gene expression, enhancing metabolic engineering, and advancing synthetic biology applications.

A modular cell-free protein biosensor platform using split T7 RNA polymerase

Conventional laboratory protein detection techniques are not suitable for point-of-care (POC) use because they require expensive equipment and laborious protocols, and existing POC assays suffer from long development timescales. Here, we describe a modular cell-free biosensing platform for generalizable protein detection that we call TLISA (T7 RNA polymerase-linked immunosensing assay), designed for extreme flexibility and equipment-free use. TLISA uses a split T7 RNA polymerase fused to affinity domains against a protein. The target antigen drives polymerase reassembly, inducing reporter expression. We characterize the platform and then demonstrate its modularity by using 16 affinity domains against four different antigens with minimal protocol optimization. We show that TLISA is suitable for POC use by sensing human biomarkers in serum and saliva with a colorimetric readout within 1 hour and by demonstrating functionality after lyophilization. Altogether, this technology has the potential to enable truly rapid, reconfigurable, modular, and equipment-free detection of diverse classes of proteins.

Illuminating anions in biology with genetically encoded fluorescent biosensors

Anions are critical to all life forms. Anions can be absorbed as nutrients or biosynthesized. Anions shape a spectrum of fundamental biological processes at the organismal, cellular, and subcellular scales. Genetically encoded fluorescent biosensors can capture anions in action across time and space dimensions with microscopy. The firsts of such technologies were reported more than 20 years for monoatomic chloride and polyatomic cAMP anions. However, the recent boom of anion biosensors illuminates the unknowns and opportunities that remain for toolmakers and end users to meet across the aisle to spur innovations in biosensor designs and applications for discovery anion biology. In this review, we will canvas progress made over the last three years for biologically relevant anions that are classified as halides, oxyanions, carboxylates, and nucleotides.

RNA folding kinetics control riboswitch sensitivity in vivo

Riboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity to ligand (EC50) is controlled is critical to explain how highly conserved aptamer domains are deployed in a variety of contexts with different sensitivity demands. Here we uncover roles by which RNA folding dynamics control riboswitch sensitivity in cells. By investigating the Clostridium beijerinckii pfl ZTP riboswitch, we identify multiple mechanistic routes of altering expression platform sequence and structure to slow RNA folding, all of which enhance riboswitch sensitivity. Applying these methods to riboswitches with diverse aptamer architectures and regulatory mechanisms demonstrates the generality of our findings, indicating that any riboswitch that operates in a kinetic regime can be sensitized by slowing expression platform folding. Our results add to the growing suite of knowledge and approaches that can be used to rationally program cotranscriptional RNA folding for biotechnology applications, and suggest general RNA folding principles for understanding dynamic RNA systems in other areas of biology.

Ligand-Responsive Artificial Protein-Protein Communication for Field-Deployable Cell-Free Biosensing

Natural protein-protein communications, such as those between transcription factors (TFs) and RNA polymerases/ribosomes, underpin cell-free biosensing systems operating on the transcription/translation (TXTL) paradigm. However, their deployment in field analysis is hampered by the delayed response (hour-level) and the complex composition of in vitro TXTL systems. For this purpose, we present a de novo-designed ligand-responsive artificial protein-protein communication (LIRAC) by redefining the connection between TFs and non-interacting CRISPR/Cas enzymes. By rationally designing a chimeric DNA adaptor and precisely regulating its binding affinities to both proteins, LIRAC immediately transduces target-induced TF allostery into rapid CRISPR/Cas enzyme activation within a homogeneous system. Consequently, LIRAC obviates the need for RNA/protein biosynthesis inherent to conventional TXTL-based cell-free systems, substantially reducing reaction complexity and time (from hours to 10 minutes) with improved sensitivity and tunable dynamic range. Moreover, LIRAC exhibits excellent versatility and programmability for rapidly and sensitively detecting diverse contaminants, including antibiotics, heavy metal ions, and preservatives. It also enables the creation of a multi-protein communication-based tristate logic for the intelligent detection of multiple contaminants. Integrated with portable devices, LIRAC has been proven effective in the field analysis of environmental samples and personal care products, showcasing its potential for environmental and health monitoring.

Long-Term Protein Synthesis with PURE in a Mesoscale Dialysis System

Cell-free systems are powerful tools in synthetic biology with versatile and wide-ranging applications. However, a significant bottleneck for these systems, particularly the PURE cell-free system, is their limited reaction lifespan and yield. Dialysis offers a promising approach to prolong reaction lifetimes and increase yields, yet most custom dialysis systems require access to sophisticated equipment like 3D printers or microfabrication tools. In this study, we utilized an easy-to-assemble, medium-scale dialysis system for cell-free reactions using commercially available components. By employing dialysis with periodic exchange of the feeding solution, we achieved a protein yield of 1.16 mg/mL GFP in the PURE system and extended protein synthesis for at least 12.5 consecutive days, demonstrating the system's excellent stability.

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

Confronting PFAS persistence: enzymes catalyzing C-F bond cleavage

Studies of enzymes catalyzing carbon-fluorine (C-F) bond cleavage have focused largely on a limited number of native microbial hydrolases that are reactive with the natural product fluoroacetate. Driven by widespread interest in biodegrading commercial fluorinated compounds, many of which are known as per- and polyfluorinated alkyl substances (PFAS), it is necessary to identify and engineer new enzymes. For example, some hydrolases react with -CF2- moieties, a common functionality in PFAS. Additional enzymatic C-F cleaving mechanisms catalyzed by reductases, lyases, and oxygenases have been identified via screening. Screening and evolving PFAS defluorination in bacteria is inhibited by the obligate release of toxic fluoride from C-F cleavage. Engineering greater fluoride tolerance in bacteria is a problem that must be solved in tandem with enzyme improvement.

Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking

Transition metals function as structural and catalytic cofactors for a large diversity of proteins and enzymes that collectively comprise the metalloproteome. Metallostasis considers all cellular processes, notably metal sensing, metalloproteome remodeling, and trafficking (or allocation) of metals that collectively ensure the functional integrity and adaptability of the metalloproteome. Bacteria employ both protein and RNA-based mechanisms that sense intracellular transition metal bioavailability and orchestrate systems-level outputs that maintain metallostasis. In this review, we contextualize metallostasis by briefly discussing the metalloproteome and specialized roles that metals play in biology. We then offer a comprehensive perspective on the diversity of metalloregulatory proteins and metal-sensing riboswitches, defining general principles within each sensor superfamily that capture how specificity is encoded in the sequence, and how selectivity can be leveraged in downstream synthetic biology and biotechnology applications. This is followed by a discussion of recent work that highlights selected metalloregulatory outputs, including metalloproteome remodeling and metal allocation by metallochaperones to both client proteins and compartments. We close by briefly discussing places where more work is needed to fill in gaps in our understanding of metallostasis.

Microbial biosensors for diagnostics, surveillance and epidemiology: Today's achievements and tomorrow's prospects

Microbial biosensors hold great promise for engineering high-performance, field-deployable and affordable detection devices for medical and environmental applications. This review explores recent advances in the field, highlighting new sensing strategies and modalities for whole-cell biosensors as well as the remarkable expansion of microbial cell-free systems. We also discuss improvements in robustness that have enhanced the ability of biosensors to withstand the challenging conditions found in biological samples. However, limitations remain in expanding the detection repertoire, particularly for proteins. We anticipate that the AI-powered revolution in protein design will streamline the engineering of custom-made sensing modules and unlock the full potential of microbial biosensors.

Engineering a PbrR-Based Biosensor for Cell-Free Detection of Lead at the Legal Limit

Industrialization and failing infrastructure have led to a growing number of irreversible health conditions resulting from chronic lead exposure. While state-of-the-art analytical chemistry methods provide accurate and sensitive detection of lead, they are too slow, expensive, and centralized to be accessible to many. Cell-free biosensors based on allosteric transcription factors (aTFs) can address the need for accessible, on-demand lead detection at the point of use. However, known aTFs, such as PbrR, are unable to detect lead at concentrations regulated by the Environmental Protection Agency (24-72 nM). Here, we develop a rapid cell-free platform for engineering aTF biosensors with improved sensitivity, selectivity, and dynamic range characteristics. We apply this platform to engineer PbrR mutants for a shift in limit of detection from 10 μM to 50 nM lead and demonstrate use of PbrR as a cell-free biosensor. We envision that our workflow could be applied to engineer any aTF.

Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives

Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.

A modular cell-free protein biosensor platform using split T7 RNA polymerase

Conventional laboratory protein detection techniques are not suitable for point-of-care (POC) use because they require expensive equipment and laborious protocols, and existing POC assays suffer from long development timescales. Here, we describe a modular cell-free biosensing platform for generalizable protein detection that we call TLISA (T7 RNA polymerase-Linked ImmunoSensing Assay), designed for extreme flexibility and equipment-free use. TLISA uses a split T7 RNA polymerase fused to affinity domains against a protein. The target antigen drives polymerase reassembly, inducing reporter expression. We characterize the platform, then demonstrate its modularity by using 16 affinity domains against four different antigens with minimal protocol optimization. We show TLISA is suitable for POC use by sensing human biomarkers in serum and saliva with a colorimetric readout within one hour and by demonstrating functionality after lyophilization. Altogether, this technology could have potentially revolutionary impacts, enabling truly rapid, reconfigurable, equipment-free detection of virtually any protein.

Cell-Free Translation Quantification via a Fluorescent Minihelix

Cell-free gene expression systems are used in numerous applications, including medicine making, diagnostics, and educational kits. Accurate quantification of nonfluorescent proteins in these systems remains a challenge. To address this challenge, we report the adaptation and use of an optimized tetra-cysteine minihelix both as a fusion protein and as a standalone reporter with the FlAsH dye. The fluorescent reporter helix is short enough to be encoded on a primer pair to tag any protein of interest via PCR. Both the tagged protein and the standalone reporter can be detected quantitatively in real time or at the end of cell-free expression reactions with standard 96/384-well plate readers, an RT-qPCR system, or gel electrophoresis without the need for staining. The fluorescent signal is stable and correlates linearly with the protein concentration, enabling product quantification. We modified the reporter to study cell-free expression dynamics and engineered ribosome activity. We anticipate that the fluorescent minihelix reporter will facilitate efforts in engineering in vitro transcription and translation systems.

Cell-Free Biosensors Based on Modular Eukaryotic Riboswitches That Function in One Pot at Ambient Temperature

Artificial riboswitches responsive to user-defined analytes can be constructed by successfully inserting in vitro selected aptamers, which bind to the analytes, into untranslated regions of mRNA. Among them, eukaryotic riboswitches are more promising as biosensors than bacterial ones because they function well at ambient temperature. In addition, cell-free expression systems allow the broader use of these riboswitches as cell-free biosensors in an environmentally friendly manner without cellular limitations. The current best cell-free eukaryotic riboswitch regulates eukaryotic canonical translation initiation through self-cleavage mediated by an implanted analyte-responsive ribozyme (i.e., an aptazyme, an aptamer-ribozyme fusion). However, it has critical flaws as a sensor: due to the less-active ribozyme used, self-cleavage and translation reactions must be conducted separately and sequentially, and a different aptazyme has to be selected to change the analyte specificity, even if an aptamer for the next analyte is available. We here stepwise engineered novel types of cell-free eukaryotic riboswitches that harness highly active self-cleavage and thus require no reaction partitioning. Despite the single-step and one-pot reaction, these riboswitches showed higher analyte dose dependency and sensitivities than the current best cell-free eukaryotic riboswitch requiring multistep reactions. In addition, the analyte specificity can be changed in an extremely facile way, simply by aptamer substitution (and the subsequent simple fine-tuning for giant aptamers). Given that cell-free systems can be lyophilized for storage and transport, the present one-pot and thus easy-to-handle cell-free biosensors utilizing eukaryotic riboswitches are expected to be widely used for on-the-spot sensing of analytes at ambient temperature.

The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch

A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of Escherichia coli RNA polymerase in vitro transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants. We showed that only variants containing the mesophilic pseudoknot function at 37°C. We next systematically varied the pseudoknot sequence and found that a single wobble base pair is critical for function. Characterizing thermophilic variants at 65°C through Thermus aquaticus RNA polymerase in vitro transcription showed the importance of this wobble pair for function even at elevated temperatures. Finally, we performed all-atom molecular dynamics simulations which supported the experimental findings, visualized the RNA structure switching process, and provided insight into the important role of magnesium ions. Together these studies provide deeper insights into the role of riboswitch sequence in influencing folding and function that will be important for understanding of RNA-based gene regulation and for synthetic biology applications.

Engineering a cell-free biosensor signal amplification circuit with polymerase strand recycling

Cell-free systems are powerful synthetic biology technologies because of their ability to recapitulate sensing and gene expression without the complications of living cells. Cell-free systems can perform even more advanced functions when genetic circuits are incorporated as information processing components. Here we expand cell-free biosensing by engineering a highly specific isothermal signal amplification circuit called polymerase strand recycling (PSR) that leverages T7 RNA polymerase off-target transcription to recycle nucleic acid inputs within DNA strand displacement circuits. We develop design rules for PSR circuit components and use these rules to construct modular biosensors that can directly sense different RNA targets with limits of detection in the nM range and high specificity. We then use PSR for signal amplification within allosteric transcription factor-based biosensors for small molecule detection. We use a double equilibrium model of transcription factor:DNA and transcription factor:ligand binding interactions to predict biosensor sensitivity enhancement by PSR, and then demonstrate this approach experimentally by achieving 3.6-4.6-fold decreases in biosensor EC50 to sub micromolar ranges. We believe this work expands the current capabilities of cell-free circuits by incorporating PSR, which we anticipate will have a wide range of uses within biotechnology.

Direct fluoride monitoring using a fluorogenic RNA-based biosensor

Fluorinated compounds, whether naturally occurring or from anthropogenic origin, have been extensively exploited in the last century. Degradation of these compounds by physical or biochemical processes is expected to result in the release of fluoride. Several fluoride detection mechanisms have been previously described. However, most of these methods are not compatible with high- and ultrahigh-throughput screening technologies, lack the ability to real-time monitor the increase of fluoride concentration in solution, or rely on costly reagents (such as cell-free expression systems). Our group recently developed "FluorMango" as the first completely RNA-based and direct fluoride-specific fluorogenic biosensor. To do so, we merged and engineered the Mango-III light-up RNA aptamer and the fluoride-specific aptamer derived from a riboswitch, crcB. In this chapter, we explain how this RNA-based biosensor can be produced in large scale before providing examples of how it can be used to quantitatively detect (end-point measurement) or monitor in real-time fluoride release in complex biological systems by translating it into measurable fluorescent signal.

Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy

Riboswitches have received significant attention over the last two decades for their multiple functionalities and great potential for applications in various fields. This article highlights and reviews the recent advances in biosensing and biotherapy. These fields involve a wide range of applications, such as food safety detection, environmental monitoring, metabolic engineering, live cell imaging, wearable biosensors, antibacterial drug targets, and gene therapy. The discovery, origin, and optimization of riboswitches are summarized to help readers better understand their multidimensional applications. Finally, this review discusses the multidimensional challenges and development of riboswitches in order to further expand their potential for novel applications.

Advances in ligand-specific biosensing for structurally similar molecules

The specificity of biological systems makes it possible to develop biosensors targeting specific metabolites, toxins, and pollutants in complex medical or environmental samples without interference from structurally similar compounds. For the last two decades, great efforts have been devoted to creating proteins or nucleic acids with novel properties through synthetic biology strategies. Beyond augmenting biocatalytic activity, expanding target substrate scopes, and enhancing enzymes' enantioselectivity and stability, an increasing research area is the enhancement of molecular specificity for genetically encoded biosensors. Here, we summarize recent advances in the development of highly specific biosensor systems and their essential applications. First, we describe the rational design principles required to create libraries containing potential mutants with less promiscuity or better specificity. Next, we review the emerging high-throughput screening techniques to engineer biosensing specificity for the desired target. Finally, we examine the computer-aided evaluation and prediction methods to facilitate the construction of ligand-specific biosensors.

Creation of Architecturally Minimal Transcriptionally Activating Riboswitches Responsive to Theophylline Reveals an Unconventional Design Strategy

Riboswitches are noncoding RNA switches that are largely utilized in bacteria and play a significant role in synthetic biology. Nonetheless, their natural counterparts possess lengthy sequences and intricate structures, posing challenges for their modular integration into complex gene circuits. Consequently, it is imperative to develop simplified synthetic riboswitches that can be effortlessly incorporated into gene circuits. The conventional approach to generate synthetic riboswitches entails tedious library construction and extensive screening, which frequently yields suboptimal performance. To overcome this obstacle, alternative methods are urgently needed. In this study, we created a novel approach to designing a diverse set of transcription-activating riboswitches that exhibit high performance and broad compatibility. The strategy involved starting with a synthetic theophylline RNA aptamer and designing an expression platform that forms a transcriptional terminator in its inactive state but switches to an antiterminator when it is activated. Several sequences were designed, constructed, and subjected to virtual screening, resulting in the identification of two transcription-activating riboswitches. These riboswitches were then engineered to reduce the basal leakage and increase the activation level through extending the hairpin region using a screened random sequence. These architecturally minimal synthetic riboswitches were highly adapted to different constitutive promoters in a modular manner, generating a differentially responsive output to theophylline. As a proof-of-principle, the synthetic riboswitches were applied to rewire a synthetic quorum-sensing circuit (QSC). The reprogrammed QSC successfully modulated the temporal responsive profile against the activation. This strategy is expected to expand the variety of high-performance riboswitches that are responsive to different ligands, thereby further facilitating the design of complex genetic circuits.

Rational design of eukaryotic riboswitches that up-regulate IRES-mediated translation initiation with high switching efficiency through a kinetic trapping mechanism in vitro

In general, riboswitches functioning through a cotranscriptional kinetic trapping mechanism (kt-riboswitches) show higher switching efficiencies in response to practical concentrations of their ligand molecules than eq-riboswitches, which function by an equilibrium mechanism. However, the former have been much more difficult to design due to their more complex mechanism. We here successfully developed a rational strategy for constructing eukaryotic kt-riboswitches that ligand-dependently enhance translation initiation mediated by an internal ribosome entry site (IRES). This was achieved both by utilizing some predicted structural features of a highly efficient bacterial kt-riboswitch identified through screening and by completely decoupling an aptamer domain from the IRES. Three kt-riboswitches optimized through this strategy, each responding to a different ligand, exhibited three- to sevenfold higher induction ratios (up to ∼90) than previously optimized eq-riboswitches regulating the same IRES-mediated translation in wheat germ extract. Because the IRES used functions well in various eukaryotic expression systems, these types of kt-riboswitches are expected to serve as major eukaryotic gene regulators based on RNA. In addition, the present strategy could be applied to the rational construction of other types of kt-riboswitches, including those functioning in bacterial expression systems.

Synthetic biology tools for environmental protection

Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.

At-Home, Cell-Free Synthetic Biology Education Modules for Transcriptional Regulation and Environmental Water Quality Monitoring

As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by simply adding water and DNA to freeze-dried crude extracts of non-pathogenic Escherichia coli. We introduce activities and supporting curricula to teach the structure and function of the lac operon, dose-responsive behavior, considerations for biosensor outputs, and a "build-your-own" activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high-school students in their classrooms─and at home─without professional laboratory equipment. This work promises to catalyze access to interactive synthetic biology education opportunities.

Enabling technology and core theory of synthetic biology

Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.

Engineering transmembrane signal transduction in synthetic membranes using two-component systems

Cells use signal transduction across their membranes to sense and respond to a wide array of chemical and physical signals. Creating synthetic systems which can harness cellular signaling modalities promises to provide a powerful platform for biosensing and therapeutic applications. As a first step toward this goal, we investigated how bacterial two-component systems (TCSs) can be leveraged to enable transmembrane-signaling with synthetic membranes. Specifically, we demonstrate that a bacterial two-component nitrate-sensing system (NarX-NarL) can be reproduced outside of a cell using synthetic membranes and cell-free protein expression systems. We find that performance and sensitivity of the TCS can be tuned by altering the biophysical properties of the membrane in which the histidine kinase (NarX) is integrated. Through protein engineering efforts, we modify the sensing domain of NarX to generate sensors capable of detecting an array of ligands. Finally, we demonstrate that these systems can sense ligands in relevant sample environments. By leveraging membrane and protein design, this work helps reveal how transmembrane sensing can be recapitulated outside of the cell, adding to the arsenal of deployable cell-free systems primed for real world biosensing.

Automated design of protein-binding riboswitches for sensing human biomarkers in a cell-free expression system

Cell-free genetically encoded biosensors have been developed to detect small molecules and nucleic acids, but they have yet to be reliably engineered to detect proteins. Here we develop an automated platform to convert protein-binding RNA aptamers into riboswitch sensors that operate within low-cost cell-free assays. We demonstrate the platform by engineering 35 protein-sensing riboswitches for human monomeric C-reactive protein, human interleukin-32γ, and phage MS2 coat protein. The riboswitch sensors regulate output expression levels by up to 16-fold with input protein concentrations within the human serum range. We identify two distinct mechanisms governing riboswitch-mediated regulation of translation rates and leverage computational analysis to refine the protein-binding aptamer regions, improving design accuracy. Overall, we expand the cell-free sensor toolbox and demonstrate how computational design is used to develop protein-sensing riboswitches with future applications as low-cost medical diagnostics.

A massively parallel screening platform for converting aptamers into molecular switches

Aptamer-based molecular switches that undergo a binding-induced conformational change have proven valuable for a wide range of applications, such as imaging metabolites in cells, targeted drug delivery, and real-time detection of biomolecules. Since conventional aptamer selection methods do not typically produce aptamers with inherent structure-switching functionality, the aptamers must be converted to molecular switches in a post-selection process. Efforts to engineer such aptamer switches often use rational design approaches based on in silico secondary structure predictions. Unfortunately, existing software cannot accurately model three-dimensional oligonucleotide structures or non-canonical base-pairing, limiting the ability to identify appropriate sequence elements for targeted modification. Here, we describe a massively parallel screening-based strategy that enables the conversion of virtually any aptamer into a molecular switch without requiring any prior knowledge of aptamer structure. Using this approach, we generate multiple switches from a previously published ATP aptamer as well as a newly-selected boronic acid base-modified aptamer for glucose, which respectively undergo signal-on and signal-off switching upon binding their molecular targets with second-scale kinetics. Notably, our glucose-responsive switch achieves ~30-fold greater sensitivity than a previously-reported natural DNA-based switch. We believe our approach could offer a generalizable strategy for producing target-specific switches from a wide range of aptamers.

Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing

Cell-free synthetic biology enables rapid prototyping of biological parts and synthesis of proteins or metabolites in the absence of cell growth constraints. Cell-free systems are frequently made from crude cell extracts, where composition and activity can vary significantly based on source strain, preparation and processing, reagents, and other considerations. This variability can cause extracts to be treated as black boxes for which empirical observations guide practical laboratory practices, including a hesitance to use dated or previously thawed extracts. To better understand the robustness of cell extracts over time, we assessed the activity of cell-free metabolism during storage. As a model, we studied conversion of glucose to 2,3-butanediol. We found that cell extracts from Escherichia coli and Saccharomyces cerevisiae subjected to an 18-month storage period and repeated freeze-thaw cycles retain consistent metabolic activity. This work gives users of cell-free systems a better understanding of the impacts of storage on extract behavior.

FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride

Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid (RNA)-based biosensor specific for fluoride is introduced. The molecule consists of two RNA aptamer modules, a fluoride-specific sensor derived from the crcB riboswitch which changes its structure upon interaction with the target ion, and the light-up RNA Mango-III that emits fluorescence when complexed with a fluorogen. The two modules are connected by an optimized communication module identified by ultrahigh-throughput screening, which results in extremely high fluorescence of FluorMango in the presence of fluoride, and background fluorescence in its absence. The value and efficiency of this biosensor by direct monitoring of defluorinase activity in living bacterial cells is illustrated, and the use of this new tool in future screening campaigns aiming at discovering new defluorinase activities is discussed.

Synthetic biology-based bioreactor and its application in biochemical analysis

In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.

Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods

Cell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these systems is optimization of cell extract preparation methods. However, the applied nature of these optimizations often limits investigation into the complex nature of the extracts themselves, which contain thousands of proteins and reaction networks with hundreds of metabolites. Here, we sought to uncover the black box of proteins and metabolites in Escherichia coli cell-free reactions based on different extract preparation methods. We assess changes in transcription and translation activity from σ⁷⁰ promoters in extracts prepared with acetate or glutamate buffer and the common post-lysis processing steps of a runoff incubation and dialysis. We then utilize proteomic and metabolomic analyses to uncover potential mechanisms behind these changes in gene expression, highlighting the impact of cold shock-like proteins and the role of buffer composition.

Electrochemical Cell-Free Biosensors for Antibody Detection

We report here the development of an electrochemical cell-free biosensor for antibody detection directly in complex sample matrices with high sensitivity and specificity that is particularly suitable for point-of-care applications. The approach is based on the use of programmable antigen-conjugated gene circuits that, upon recognition of a specific target antibody, trigger the cell-free transcription of an RNA sequence that can be consequently detected using a redox-modified probe strand immobilized to a disposable electrode. The platform couples the features of high sensitivity and specificity of cell-free systems and the strength of cost-effectiveness and possible miniaturization provided by the electrochemical detection. We demonstrate the sensitive, specific, selective, and multiplexed detection of three different antibodies, including the clinically-relevant Anti-HA antibody.

The accuracy and usability of point-of-use fluoride biosensors in rural Kenya

Geogenic fluoride contaminates the water of tens of millions of people. However, many are unaware of the fluoride content due in part to shortcomings of detection methods. Biosensor tests are a relatively new approach to water quality testing that address many of these shortcomings but have never been tested by non-experts in a "real-world" setting. We therefore sought to assess the accuracy and usability of a point-of-use fluoride biosensor using surveys and field tests in Nakuru County, Kenya. Biosensor tests accurately classified elevated fluoride (≥1.5 ppm) in 89.5% of the 57 samples tested. Usability was also high; all participants were able to use the test and correctly interpreted all but one sample. These data suggest that biosensor tests can provide accurate, meaningful water quality data that help non-experts make decisions about the water they consume. Further scaling of these technologies could provide new approaches to track global progress towards Sustainable Development Goal 6.

Discovering riboswitches: the past and the future

Riboswitches are structured noncoding RNA domains used by many bacteria to monitor the concentrations of target ligands and regulate gene expression accordingly. In the past 20 years over 55 distinct classes of natural riboswitches have been discovered that selectively sense small molecules or elemental ions, and thousands more are predicted to exist. Evidence suggests that some riboswitches might be direct descendants of the RNA-based sensors and switches that were likely present in ancient organisms before the evolutionary emergence of proteins. We provide an overview of the current state of riboswitch research, focusing primarily on the discovery of riboswitches, and speculate on the major challenges facing researchers in the field.

Facile Expansion of the Variety of Orthogonal Ligand/Aptamer Pairs for Artificial Riboswitches

An RNA aptamer that induces suitable conformational changes upon binding to a user-defined ligand allows us to artificially construct a riboswitch, a ligand-dependent and cis-acting gene regulatory RNA. Although such an aptamer can be obtained through in vitro selection, it is still challenging to rationally expand the variety of orthogonal ligand/aptamer (ligand/riboswitch) pairs. To achieve this in a facile, selection-free way, we herein focused on a specific type of ligand, 6-nt nanosized DNA (nDNA) and its aptamer that was previously selected to construct a eukaryotic artificial riboswitch. Specifically, we merely mutated one or more possible Watson-Crick base pairs in the nDNA/aptamer (nDNA/riboswitch) interactions into another base pair or pairs. Using two sets that each had 16 comprehensive mutations, we obtained three groups of several orthogonal nDNA/riboswitch pairs. These pairs could be used to create complex gene circuits, including multiple simultaneous and/or multistep cascading regulations in synthetic biology.

A Low-Cost, Thermostable, Cell-Free Protein Synthesis Platform for On-Demand Production of Conjugate Vaccines

Cell-free protein synthesis systems that can be lyophilized for long-term, non-refrigerated storage and transportation have the potential to enable decentralized biomanufacturing. However, increased thermostability and decreased reaction cost are necessary for further technology adoption. Here, we identify maltodextrin as an additive to cell-free reactions that can act as both a lyoprotectant to increase thermostability and a low-cost energy substrate. As a model, we apply optimized formulations to produce conjugate vaccines for ∼$0.50 per dose after storage at room temperature (∼22 °C) or 37 °C for up to 4 weeks, and ∼$1.00 per dose after storage at 50 °C for up to 4 weeks, with costs based on raw materials purchased at the laboratory scale. We show that these conjugate vaccines generate bactericidal antibodies against enterotoxigenic Escherichia coli (ETEC) O78 O-polysaccharide, a pathogen responsible for diarrheal disease, in immunized mice. We anticipate that our low-cost, thermostable cell-free glycoprotein synthesis system will enable new models of medicine biosynthesis and distribution that bypass cold-chain requirements.

At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring

As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by just-adding-water and DNA to freeze-dried crude extracts of Escherichia coli . We introduce activities and supporting curricula to teach the structure and function of the lac operon, dose-responsive behavior, considerations for biosensor outputs, and a 'build-your-own' activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high school students in their classrooms - and at home - without professional laboratory equipment or researcher oversight. This work promises to catalyze access to interactive synthetic biology education opportunities.

Robust and tunable performance of a cell-free biosensor encapsulated in lipid vesicles

Cell-free systems have enabled the development of genetically encoded biosensors to detect a range of environmental and biological targets. Encapsulation of these systems in synthetic membranes to form artificial cells can reintroduce features of the cellular membrane, including molecular containment and selective permeability, to modulate cell-free sensing capabilities. Here, we demonstrate robust and tunable performance of a transcriptionally regulated, cell-free riboswitch encapsulated in lipid membranes, allowing the detection of fluoride, an environmentally important molecule. Sensor response can be tuned by varying membrane composition, and encapsulation protects from sensor degradation, facilitating detection in real-world samples. These sensors can detect fluoride using two types of genetically encoded outputs, enabling detection of fluoride at the Environmental Protection Agency maximum contaminant level of 0.2 millimolars. This work demonstrates the capacity of bilayer membranes to confer tunable permeability to encapsulated, genetically encoded sensors and establishes the feasibility of artificial cell platforms to detect environmentally relevant small molecules.