Accelerating Cell-Free Biosensors by Entropy-Driven Assembly of Transcription Templates.

Due to its high efficiency and selectivity, cell-free biosynthesis has found broad utility in the fields of bioproduction, environment monitoring, and disease diagnostics. However, the practical application is limited by its low productivity. Here, we introduce the entropy-driven assembly of transcription templates as dynamic amplifying modules to accelerate the cell-free transcription process. The catalytic DNA circuit with high sensitivity and enzyme-free format contributes to the production of large amounts of transcription templates, drastically accelerating the as-designed cell-free transcription system without interference from multiple enzymes. The proposed approach was successfully applied to the ultrasensitive detection of SARS-CoV-2, improving the sensitivity by 3 orders of magnitude. Thanks to the high programmability and diverse light-up RNA pairs, the method can be adapted to multiplexing detection, successfully demonstrated by the analysis of two different sites of the SARS-CoV-2 gene in parallel. Further, the flexibility of the entropy-driven circuit enables a dynamic responding range by tuning the circuit layers, which is beneficial for responding to targets with different concentration ranges. The strategy was also applied to the analysis of clinical samples, providing an alternative for sensitively detecting the current SARS-CoV-2 RNA that quickly mutates.

[1]  D. Tang,et al.  Recent advances in heterogeneous single-atom nanomaterials: From engineered metal-support interaction to applications in sensors , 2023, Coordination Chemistry Reviews.

[2]  F. Ricci,et al.  Electrochemical cell-free biosensors for antibody detection. , 2022, Angewandte Chemie.

[3]  Joongoo Lee,et al.  Programmable Synthesis of Biobased Materials Using Cell‐Free Systems , 2022, Advances in Materials.

[4]  Qiaoqiao Kang,et al.  Simple Amplifier Coupled with a Lanthanide Labeling Strategy for Multiplexed and Specific Quantification of MicroRNAs. , 2022, Analytical chemistry.

[5]  B. Ye,et al.  An RNA-based catalytic hairpin assembly circuit coupled with CRISPR-Cas12a for one-step detection of microRNAs. , 2022, Biosensors & bioelectronics.

[6]  F. Ricci,et al.  Programmable Cell-Free Transcriptional Switches for Antibody Detection , 2021, Journal of the American Chemical Society.

[7]  A. Ren,et al.  Structure-based investigation of fluorogenic Pepper aptamer , 2021, Nature Chemical Biology.

[8]  R. Weiss,et al.  Synthetic neuromorphic computing in living cells , 2021, Nature Communications.

[9]  J. Gorodkin,et al.  A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA , 2021, Nature Communications.

[10]  N. Raouafi,et al.  Multiplexed Magnetofluorescent Bioplatform for the Sensitive Detection of SARS-CoV-2 Viral RNA without Nucleic Acid Amplification , 2021, Analytical chemistry.

[11]  Murat Alp Güngen,et al.  SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators , 2021, Analytical Chemistry.

[12]  Nicolaas M. Angenent-Mari,et al.  Wearable materials with embedded synthetic biology sensors for biomolecule detection , 2021, Nature Biotechnology.

[13]  Jufang Wang,et al.  Detection and differentiation of respiratory syncytial virus subgroups A and B with colorimetric toehold switch sensors in a paper-based cell-free system. , 2021, Biosensors & bioelectronics.

[14]  Sai Bi,et al.  Rolling Circle Replication for Biosensing, Bioimaging, and Biomedicine. , 2021, Trends in biotechnology.

[15]  Jeong Wook Lee,et al.  Sensitive fluorescence detection of SARS-CoV-2 RNA in clinical samples via one-pot isothermal ligation and transcription , 2020, Nature Biomedical Engineering.

[16]  V. Martin,et al.  A yeast platform for high-level synthesis of tetrahydroisoquinoline alkaloids , 2020, Nature Communications.

[17]  Jaeyoung K. Jung,et al.  Cell-free biosensors for rapid detection of water contaminants , 2020, Nature Biotechnology.

[18]  Z. Cui,et al.  RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 , 2020, Microbial biotechnology.

[19]  Kecheng Zhang,et al.  DNA Amplifier-Functionalized Metal-Organic Frameworks for Multiplexed Detection and Imaging of Intracellular mRNA. , 2020, ACS sensors.

[20]  Francesca Volpetti,et al.  Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals , 2019, Nature Chemical Biology.

[21]  Yan Feng,et al.  Bacterial Consortium-Based Sensing System for Detecting Organophosphorus Pesticides. , 2018, Analytical chemistry.

[22]  Jeffrey J. Tabor,et al.  Phosphatase activity tunes two-component system sensor detection threshold , 2018, Nature Communications.

[23]  J. Collins,et al.  Complex cellular logic computation using ribocomputing devices , 2017, Nature.

[24]  Martin Fussenegger,et al.  Synthetic Biology-The Synthesis of Biology. , 2017, Angewandte Chemie.

[25]  D. Di Carlo,et al.  Homogeneous Entropy-Driven Amplified Detection of Biomolecular Interactions. , 2016, ACS nano.

[26]  Guillaume Lambert,et al.  Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components , 2016, Cell.

[27]  Sang Jun Lee,et al.  Development of a highly specific and sensitive cadmium and lead microbial biosensor using synthetic CadC-T7 genetic circuitry. , 2016, Biosensors & bioelectronics.

[28]  J. Collins,et al.  Synthetic biology devices for in vitro and in vivo diagnostics , 2015, Proceedings of the National Academy of Sciences.

[29]  Mauricio Barahona,et al.  Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities , 2015, Nucleic acids research.

[30]  James J. Collins,et al.  Paper-Based Synthetic Gene Networks , 2014, Cell.

[31]  Mauricio Barahona,et al.  Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks , 2014, Nucleic acids research.

[32]  James J Collins,et al.  Programmable bacteria detect and record an environmental signal in the mammalian gut , 2014, Proceedings of the National Academy of Sciences.

[33]  V. Martin,et al.  Reconstitution of a 10-gene pathway for synthesis of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisiae , 2014, Nature Communications.

[34]  F. Lienert,et al.  Synthetic biology in mammalian cells: next generation research tools and therapeutics , 2014, Nature Reviews Molecular Cell Biology.

[35]  Mauricio Barahona,et al.  A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals , 2013, Biosensors & bioelectronics.

[36]  Amina A. Qutub,et al.  Multiplexed in situ immunofluorescence using dynamic DNA complexes. , 2012, Angewandte Chemie.

[37]  S. Jaffrey,et al.  RNA Mimics of Green Fluorescent Protein , 2011, Science.

[38]  Xi Chen,et al.  Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods , 2011, Nucleic acids research.

[39]  Wendell A. Lim,et al.  Designing customized cell signalling circuits , 2010, Nature Reviews Molecular Cell Biology.

[40]  Sergei A Kazakov,et al.  An RNA-aptamer-based assay for the detection and analysis of malachite green and leucomalachite green residues in fish tissue. , 2010, Analytical chemistry.

[41]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[42]  Robert M. Dirks,et al.  Triggered amplification by hybridization chain reaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  D. Richman,et al.  Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. , 1990, Proceedings of the National Academy of Sciences of the United States of America.