Towards detection of SARS-CoV-2 RNA in human saliva: A paper-based cell-free toehold switch biosensor with a visual bioluminescent output

Split T7 switch-mediated cell-free protein synthesis system for detecting target nucleic acids

Cell-free protein synthesis (CFPS) reactions can be used to detect nucleic acids. However, most CFPS systems rely on a toehold switch and exhibit the following critical limitations: (i) off-target signals due to leaky translation in the absence of target nucleic acids, (ii) a suboptimal detection limit of approximately 30 nM without pre-amplification, and (iii) labor-intensive screening processes due to sequence constraints for the target nucleic acids. To overcome these shortcomings, we developed a new split T7 switch-mediated CFPS system in which the split T7 promoter was applied to a three-way junction structure to selectively initiate transcription-translation only in the presence of target nucleic acids. Both fluorescence and colorimetric detection systems were constructed by employing different reporter proteins. Notably, we introduced the self-complementation of split fluorescent proteins to streamline preparation of the proposed system, enabling versatile applications. Operation of this one-pot approach under isothermal conditions enabled the detection of target nucleic acids at concentrations as low as 10 pM, representing more than a thousand times improvement over previous toehold switch-based approaches. Furthermore, the proposed system demonstrated high specificity in detecting target nucleic acids and compatibility with various reporter proteins encoded in the expression region. By eliminating issues associated with the previous toehold switch system, our split T7 switch-mediated CFPS system could become a core platform for detecting various target nucleic acids.

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.

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.

Toehold switch plus signal amplification enables rapid detection

Recent world events have led to an increased interest in developing rapid and inexpensive clinical diagnostic platforms for viral detection. Here, the development of a cell-free toehold switch-based biosensor, which does not require upstream amplification of target RNA, is described for the detection of RNA viruses. Toehold switches were designed to avoid interfering secondary structure in the viral RNA binding region, mutational hotspots, and cross-reacting sequences of other coronaviruses. Using these design criteria, toehold switches were targeted to a low mutation region of the SARS-CoV-2 genome nonstructural protein 2 (nsp2). The designs were tested in a cell-free system using trigger RNA based on the viral genome and a highly sensitive fluorescent reporter gene, mNeonGreen. The detection sensitivity of our best toehold design, CSU 08, was in the low picomolar range of target (trigger) RNA. To increase the sensitivity of our cell-free biosensor to a clinically relevant level, we developed a modular downstream amplification system that utilizes toehold switch activation of tobacco etch virus (TEV) protease expression. The TEV protease cleaves a quenched fluorescent reporter, both increasing the signal fold change between control and sample and increasing the sensitivity to a clinically relevant low femtomolar range for target RNA detection.

Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes

Nucleic acid assays are not typically deployable in point-of-care settings because they require costly and sophisticated equipment for the control of the reaction temperature and for the detection of the signal. Here we report an instrument-free assay for the accurate and multiplexed detection of nucleic acids at ambient temperature. The assay, which we named INSPECTR (for internal splint-pairing expression-cassette translation reaction), leverages the target-specific splinted ligation of DNA probes to generate expression cassettes that can be flexibly designed for the cell-free synthesis of reporter proteins, with enzymatic reporters allowing for a linear detection range spanning four orders of magnitude and peptide reporters (which can be mapped to unique targets) enabling highly multiplexed visual detection. We used INSPECTR to detect a panel of five respiratory viral targets in a single reaction via a lateral-flow readout and ~4,000 copies of viral RNA via additional ambient-temperature rolling circle amplification of the expression cassette. Leveraging synthetic biology to simplify workflows for nucleic acid diagnostics may facilitate their broader applicability at the point of care.

Harnessing synthetic biology for advancing RNA therapeutics and vaccine design

Recent global events have drawn into focus the diversity of options for combatting disease across a spectrum of prophylactic and therapeutic approaches. The recent success of the mRNA-based COVID-19 vaccines has paved the way for RNA-based treatments to revolutionize the pharmaceutical industry. However, historical treatment options are continuously updated and reimagined in the context of novel technical developments, such as those facilitated through the application of synthetic biology. When it comes to the development of genetic forms of therapies and vaccines, synthetic biology offers diverse tools and approaches to influence the content, dosage, and breadth of treatment with the prospect of economic advantage provided in time and cost benefits. This can be achieved by utilizing the broad tools within this discipline to enhance the functionality and efficacy of pharmaceutical agent sequences. This review will describe how synthetic biology principles can augment RNA-based treatments through optimizing not only the vaccine antigen, therapeutic construct, therapeutic activity, and delivery vector. The enhancement of RNA vaccine technology through implementing synthetic biology has the potential to shape the next generation of vaccines and therapeutics.

Signal Amplification for Cell-Free Biosensors, an Analog-to-Digital Converter

Toehold switches are biosensors useful for the detection of endogenous and environmental RNAs. They have been successfully engineered to detect virus RNAs in cell-free gene expression reactions. Their inherent sequence programmability makes engineering a fast and predictable process. Despite improvements in the design, toehold switches suffer from leaky translation in the OFF state, which compromises the fold change and sensitivity of the biosensor. To address this, we constructed and tested signal amplification circuits for three toehold switches triggered by Dengue and SARS-CoV-2 RNAs and an artificial RNA. The serine integrase circuit efficiently contained leakage, boosted the expression fold change from OFF to ON, and decreased the detection limit of the switches by 3-4 orders of magnitude. Ultimately, the integrase circuit converted the analog switches' signals into digital-like output. The circuit is broadly useful for biosensors and eliminates the hard work of designing and testing multiple switches to find the best possible performer.

Detection of Bile Acids in Complex Matrices Using a Transcription Factor-Based Biosensor

Bile acids play an important role in digestion and human health, are found throughout the gastrointestinal tract, and are excreted in feces. Therefore, bile acids are promising biomarkers for monitoring health and detecting fecal contamination in water sources. Here, we engineered a bile acid sensor by expressing the transcription factor BreR, a TetR-like repressor from Vibrio cholorae, in Escherichia coli. The sensor was further optimized by screening a promoter library. To further characterize the BreR sensor and increase its utility, we moved expression to a cell-free expression (CFE) system, resulting in an approximately 3 orders of magnitude increase in deoxycholic acid sensitivity. We next optimized this sensor to detect bile acids in fecal water, wastewater, and serum and transferred the CFE sensor to a paper-based assay to enhance fieldability.

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.

Paper-based analytical devices for point-of-need applications

Paper-based analytical devices (PADs) are powerful platforms for point-of-need testing since they are inexpensive devices fabricated in different shapes and miniaturized sizes, ensuring better portability. Additionally, the readout and detection systems can be accomplished with portable devices, allying with the features of both systems. These devices have been introduced as promising analytical platforms to meet critical demands involving rapid, reliable, and simple testing. They have been applied to monitor species related to environmental, health, and food issues. Herein, an outline of chronological events involving PADs is first reported. This work also introduces insights into fundamental parameters to engineer new analytical platforms, including the paper type and device operation. The discussions involve the main analytical techniques used as detection systems, such as colorimetry, fluorescence, and electrochemistry. It also showed recent advances involving PADs, especially combining optical and electrochemical detection into a single device. Dual/combined detection systems can overcome individual barriers of the analytical techniques, making possible simultaneous determinations, or enhancing the devices' sensitivity and/or selectivity. In addition, this review reports on distance-based detection, which is also considered a trend in analytical chemistry. Distance-based detection offers instrument-free analyses and avoids user interpretation errors, which are outstanding features for analyses at the point of need, especially for resource-limited regions. Finally, this review provides a critical overview of the practical specifications of the recent analytical platforms involving PADs, demonstrating their challenges. Therefore, this work can be a highly useful reference for new research and innovation.

Short Activators and Repressors of RNA Toehold Switches

RNA toehold switches are a widely used class of molecule to detect specific RNA "trigger" sequences, but their design, intended function, and characterization to date leave it unclear whether they can function properly with triggers shorter than 36 nucleotides. Here, we explore the feasibility of using standard toehold switches with 23-nucleotide truncated triggers. We assess the crosstalk of different triggers with significant homology and identify a highly sensitive trigger region where just one mutation from the consensus trigger sequence can reduce switch activation by 98.6%. However, we also find that triggers with as many as seven mutations outside of this region can still lead to 5-fold induction of the switch. We also present a new approach using 18- to 22-nucleotide triggers as translational repressors for toehold switches and assess the off-target regulation for this strategy as well. The development and characterization of these strategies could help enable applications like microRNA sensors, where well-characterized crosstalk between sensors and detection of short target sequences are critical.

Biosensors for saliva biomarkers

The analysis of salivary biomarkers has gained interest and is advantageous for simple, safe, and non-invasive testing in diagnosis as well as treatment. This chapter explores the importance of saliva biomarkers and summarizes recent advances in biosensor fabrication. The identification of diagnostic, prognostic and therapeutic markers in this matrix enables more rapid and frequent testing when combined with the use of biosensor technology. Challenges and future goals are highlighted and examined.

"Just add small molecules" cell-free protein synthesis: Combining DNA template and cell extract preparation into a single fermentation

Cell-free protein synthesis (CFPS) is a versatile biotechnology platform enabling a broad range of applications including clinical diagnostics, large-scale production of officinal therapeutics, small-scale on-demand production of personal magistral therapeutics, and exploratory research. The shelf stability and scalability of CFPS systems also have the potential to overcome cost and infrastructure challenges for distributing and using essential medical tests at home in both high- and low-income countries. However, CFPS systems are often more time-consuming and expensive to prepare than traditional in vivo systems, limiting their broader use. Much work has been done to lower CFPS costs by optimizing cell extract preparation, small molecule reagent recipes, and DNA template preparation. In order to further reduce reagent cost and preparation time, this work presents a CFPS system that does not require separately purified DNA template. Instead, a DNA plasmid encoding the recombinant protein is transformed into the cells used to make the extract, and the extract preparation process is modified to allow enough DNA to withstand homogenization-induced shearing. The finished extract contains sufficient levels of intact DNA plasmid for the CFPS system to operate. For a 10 mL scale CFPS system expressing recombinant sfGFP protein for a biosensor, this new system reduces reagent cost by more than half. This system is applied to a proof-of-concept glutamine sensor compatible with smartphone quantification to demonstrate its viability for further cost reduction and use in low-resource settings.

Engineering At-Home Dilution and Filtration Methods to Enable Paper-Based Colorimetric Biosensing in Human Blood with Cell-Free Protein Synthesis

Diagnostic blood tests can guide the administration of healthcare to save and improve lives. Most clinical biosensing blood tests require a trained technician and specialized equipment to process samples and interpret results, which greatly limits test accessibility. Colorimetric paper-based diagnostics have an equipment-free readout, but raw blood obscures a colorimetric response which has motivated diverse efforts to develop blood sample processing techniques. This work uses inexpensive readily-available materials to engineer user-friendly dilution and filtration methods for blood sample collection and processing to enable a proof-of-concept colorimetric biosensor that is responsive to glutamine in 50 µL blood drop samples in less than 30 min. Paper-based user-friendly blood sample collection and processing combined with CFPS biosensing technology represents important progress towards the development of at-home biosensors that could be broadly applicable to personalized healthcare.

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.

Solid-Phase Cell-Free Protein Synthesis and Its Applications in Biotechnology

Cell-free systems for the in vitro production of proteins have revolutionized the synthetic biology field. In the last decade, this technology is gaining momentum in molecular biology, biotechnology, biomedicine and even education. Materials science has burst into the field of in vitro protein synthesis to empower the value of existing tools and expand its applications. In this sense, the combination of solid materials (normally functionalized with different biomacromolecules) together with cell-free components has made this technology more versatile and robust. In this chapter, we discuss the combination of solid materials with DNA and transcription-translation machinery to synthesize proteins within compartments, to immobilize and purify in situ the nascent protein, to transcribe and transduce DNAs immobilized on solid surfaces, and the combination of all or some of these strategies.

Rapid and Finely-Tuned Expression for Deployable Sensing Applications

Organisms from across the tree of life have evolved highly efficient mechanisms for sensing molecules of interest using biomolecular machinery that can in turn be quite valuable for the development of biosensors. However, purification of such machinery for use in in vitro biosensors is costly, while the use of whole cells as in vivo biosensors often leads to long sensor response times and unacceptable sensitivity to the chemical makeup of the sample. Cell-free expression systems overcome these weaknesses by removing the requirements associated with maintaining living sensor cells, allowing for increased function in toxic environments and rapid sensor readout at a production cost that is often more reasonable than purification. Here, we focus on the challenge of implementing cell-free protein expression systems that meet the stringent criteria required for them to serve as the basis for field-deployable biosensors. Fine-tuning expression to meet these requirements can be achieved through careful selection of the sensing and output elements, as well as through optimization of reaction conditions via tuning of DNA/RNA concentrations, lysate preparation methods, and buffer conditions. Through careful sensor engineering, cell-free systems can continue to be successfully used for the production of tightly regulated, rapidly expressing genetic circuits for biosensors.

Promising instrument-free detections of various analytes using smartphones with Spotxel® Reader

In consideration of the problems related to food safety, environmental pollution, and the spread of infected diseases nowadays, we urgently need testing methods that can be easily performed by common people. Smartphone-based detections are promising for general applications. However, some of these analytical strategies require a combination of accessories and instruments, such as portable electrochemical workstations, mini multi-mode microplate readers, and complex temperature control devices, etc., which are small but still expensive. Herein, we comprehensively introduce a free app (Spotxel^® Reader) that can provide accurate data analysis for microplate or parallel-format test sensors without an instrument. By simulating the optical signal of the test samples through a smartphone, the sensing results can be obtained for free. We discuss the detection strategies involved in the reported smartphone-based analyses using Spotxel^® Reader. Prospects for the development of this free app for future detection applications are presented. This review aims to popularize free analysis software, so that ordinary people may realize convenient tests.

Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens

Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.

Expanding luciferase reporter systems for cell-free protein expression

Luciferases are often used as a sensitive, versatile reporter in cell-free transcription-translation (TXTL) systems, for research and practical applications such as engineering genetic parts, validating genetic circuits, and biosensor outputs. Currently, only two luciferases (Firefly and Renilla) are commonly used without substrate cross-talk. Here we demonstrate the expansion of the cell-free luciferase reporter system, with two orthogonal luciferase reporters: N. nambi luciferase (Luz) and LuxAB. These luciferases do not have cross-reactivity with the Firefly and Renilla substrates. We also demonstrate a substrate regeneration pathway for one of the new luciferases, enabling long-term time courses of protein expression monitoring in the cell-free system. Furthermore, we reduced the number of genes required in TXTL expression, by engineering a cell extract containing part of the luciferase enzymes. Our findings lead to an expanded platform with multiple orthogonal luminescence translation readouts for in vitro protein expression.

Transcription Factor-Based Biosensors for Detecting Pathogens

Microorganisms are omnipresent and inseparable from our life. Many of them are beneficial to humans, while some are not. Importantly, foods and beverages are susceptible to microbial contamination, with their toxins causing illnesses and even death in some cases. Therefore, monitoring and detecting harmful microorganisms are critical to ensuring human health and safety. For several decades, many methods have been developed to detect and monitor microorganisms and their toxicants. Conventionally, nucleic acid analysis and antibody-based analysis were used to detect pathogens. Additionally, diverse chromatographic methods were employed to detect toxins based on their chemical and structural properties. However, conventional techniques have several disadvantages concerning analysis time, sensitivity, and expense. With the advances in biotechnology, new approaches to detect pathogens and toxins have been reported to compensate for the disadvantages of conventional analysis from different research fields, including electrochemistry, nanotechnology, and molecular biology. Among them, we focused on the recent studies of transcription factor (TF)-based biosensors to detect microorganisms and discuss their perspectives and applications. Additionally, the other biosensors for detecting microorganisms reported in recent studies were also introduced in this review.

Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria

RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.

Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima

Nucleic acid sensing is a 3 decades old but still challenging area of application for different biological sub-domains, from pathogen detection to single cell transcriptomics analysis. The many applications of nucleic acid detection and identification are mostly carried out by PCR techniques, sequencing, and their derivatives used at large scale. However, these methods’ limitations on speed, cost, complexity and specificity have motivated the development of innovative detection methods among which nucleic acid biosensing technologies seem promising. Toehold switches are a particular class of RNA sensing devices relying on a conformational switch of secondary structure induced by the pairing of the detected trigger RNA with a de novo designed synthetic sensing mRNA molecule. Here we describe a streamlined methodology enabling the development of such a sensor for the RNA-mediated detection of an endangered plant species in a cell-free reaction system. We applied this methodology to help identify the rosewood Dalbergia maritima, a highly trafficked wood, whose protection is limited by the capacity of the authorities to distinguish protected logs from other unprotected but related species. The streamlined pipeline presented in this work is a versatile framework enabling cheap and rapid development of new sensors for custom RNA detection.

Advances, Challenges and Future Trends of Cell-Free Transcription-Translation Biosensors

In recent years, the application of cell-free protein synthesis systems in biosensing has been developing rapidly. Cell-free synthetic biology, with its advantages of high biosafety, fast material transport, and high sensitivity, has overcome many defects of cell-based biosensors and provided an abiotic substitute for biosensors. In addition, the application of freeze-drying technology has improved the stability of such systems, making it possible to realize point-of-care application of field detection and broadening the application prospects of cell-free biosensors. However, despite these advancements, challenges such as the risk of sample interference due to the lack of physical barriers, maintenance of activity during storage, and poor robustness still need to be addressed before the full potential of cell-free biosensors can be realized on a larger scale. In this review, current strategies and research results for improving the performance of cell-free biosensors are summarized, including a comprehensive discussion of the existing challenges, future trends, and potential investments needed for improvement.

Update on the Development of Toehold Switch-Based Approach for Molecular Diagnostic Tests of COVID-19

A high volume of diagnostic tests is needed during the coronavirus disease 2019 (COVID-19) pandemic to obtain representative results. These results can help to design and implement effective policies to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis using current gold standard methods, i.e., real-time quantitative PCR (RT-qPCR), is challenging, especially in areas with limited trained personnel and health-related infrastructure. The toehold switch-based diagnostic system is a promising alternative method for detecting SARS-CoV-2 that has advantages such as inexpensive cost per testing, rapid, and highly sensitive and specific analysis. Moreover, the system can be applied to paper-based platforms, simplifying the distribution and utilization in low-resource settings. This review provides insight into the development of toehold switch-based diagnostic devices as the most recent methods for detecting SARS-CoV-2.