Modularized synthetic biology enabled intelligent biosensors

• Dai Y.
• Liu C.C.

Recent advances on electrochemical biosensing strategies toward universal point-of-care systems.

Angew. Chem. Int. Edit. 2019; 58: 12355-12368

• Krämer J.
• et al.

Molecular probes, chemosensors, and nanosensors for optical detection of biorelevant molecules and ions in aqueous media and biofluids.

Chem. Rev. 2022; 122: 3459-3636

• Grubaugh N.D.
• et al.

Tracking virus outbreaks in the twenty-first century.

Nat. Microbiol. 2019; 4: 10-19

• Pantel K.
• Alix-Panabières C.

Liquid biopsy and minimal residual disease-latest advances and implications for cure.

Nat. Rev. Clin. Oncol. 2019; 16: 409-424

• Nwokolo O.A.
• et al.

Rational design of memory-based sensors: the case of molecular calorimeters.

Angew. Chem. Int. Edit. 2021; 60: 1610-1614

• Liu A.P.
• et al.

The living interface between synthetic biology and biomaterial design.

Nat. Mater. 2022; 21: 390-397

• Zhang C.
• et al.

Synthetic biology-powered biosensors based on CRISPR/Cas mediated cascade signal amplification for precise RNA detection.

Chem. Eng. J. 2022; 446136864

• Amalfitano E.
• Pardee K.

Logic invades cell-free biosensing.

Nat. Chem. Biol. 2022; 18: 356-358

• Sheth R.U.
• Wang H.H.

DNA-based memory devices for recording cellular events.

Nat. Rev. Genet. 2018; 19: 718-732

• Greco F.V.
• et al.

Harnessing the central dogma for stringent multi-level control of gene expression.

Nat. Commun. 2021; 12: 1738

• Brooks S.M.
• Alper H.S.

Applications, challenges, and needs for employing synthetic biology beyond the lab.

Nat. Commun. 2021; 12: 1390

• Svetlicic E.
• et al.

Genomic characterization and assessment of pathogenic potential of Legionella spp. isolates from environmental monitoring.

Front. Microbiol. 2023; 131091964

• Boyd M.A.
• Kamat N.P.

Designing artificial cells towards a new generation of biosensors.

Trends Biotechnol. 2021; 39: 927-939

• Sedlmayer F.
• et al.

Synthetic gene circuits for the detection, elimination and prevention of disease.

Nat. Biomed. Eng. 2018; 2: 399-415

• Bereza-Malcolm L.T.
• et al.

Environmental sensing of heavy metals through whole cell microbial biosensors: a synthetic biology approach.

ACS Synth. Biol. 2015; 4: 535-546

• Guo M.
• et al.

Third generation whole-cell sensing systems: synthetic biology inside, nanomaterial outside.

Trends Biotechnol. 2021; 39: 550-559

• Wu M.R.
• et al.

Engineering advanced cancer therapies with synthetic biology.

Nat. Rev. Cancer. 2019; 19: 187-195

• Ba F.
• et al.

SYMBIOSIS: synthetic manipulable biobricks via orthogonal serine integrase systems.

Nucleic Acids Res. 2022; 50: 2973-2985

• Malcı K.
• et al.

Standardization of synthetic biology tools and assembly methods for saccharomyces cerevisiae and emerging yeast species.

ACS Synth. Biol. 2022; 11: 2527-2547

• Courbet A.
• et al.

Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates.

Sci. Transl. Med. 2015; 7289ra283

• Ren W.
• et al.

Design of an adaptive boost energy-saving fuzzy control system driven by the finite state machine.

Math. Probl. Eng. 2021; 2021: 1-12

• Choe J.H.
• et al.

SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma.

Sci. Transl. Med. 2021; 13eabe7378

• Wang F.
• et al.

Precise molecular profiling of circulating exosomes using a metal-organic framework-based sensing interface and an enzyme-based electrochemical logic platform.

Anal. Chem. 2022; 2: 875-883

• Du P.
• et al.

De novo design of an intercellular signaling toolbox for multi-channel cell-cell communication and biological computation.

Nat. Commun. 2020; 11: 4226

• Zah E.
• et al.

T cells expressing CD19/CD20 bispecific chimeric antigen receptors prevent antigen escape by malignant B cells.

Cancer Immunol. Res. 2016; 4: 498-508

• Jung J.K.
• et al.

Programming cell-free biosensors with DNA strand displacement circuits.

Nat. Chem. Biol. 2022; 18: 385-393

• Roquet N.
• et al.

Synthetic recombinase-based state machines in living cells.

Science. 2016; 353aad8559

• Weinberg B.H.
• et al.

Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells.

Nat. Biotechnol. 2017; 35: 453-462

• Xie M.
• Fussenegger M.

Designing cell function: assembly of synthetic gene circuits for cell biology applications.

Nat. Rev. Mol. Cell Biol. 2018; 19: 507-525

• Sheth R.U.
• et al.

Multiplex recording of cellular events over time on CRISPR biological tape.

Science. 2017; 358: 1457-1461

• Ceze L.
• et al.

Molecular digital data storage using DNA.

Nat. Rev. Genet. 2019; 20: 456-466

• Zhang R.
• et al.

Topology-dependent interference of synthetic gene circuit function by growth feedback.

Nat. Chem. Biol. 2020; 16: 695-701

• Bernabé-Orts J.M.
• et al.

A memory switch for plant synthetic biology based on the phage ϕC31 integration system.

Nucleic Acids Res. 2020; 48: 3379-3394

• Riglar D.T.
• et al.

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation.

Nat. Biotechnol. 2017; 35: 653-658

• Mishra D.
• et al.

An engineered protein-phosphorylation toggle network with implications for endogenous network discovery.

Science. 2021; 373eaav0780

The kill-switch for CRISPR that could make gene-editing safer.

Nature. 2020; 577: 308-310

• Mimee M.
• et al.

Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota.

Cell Syst. 2016; 2: 214

• Bonnet J.
• et al.

Rewritable digital data storage in live cells via engineered control of recombination directionality.

Proc. Natl. Acad. Sci. U. S. A. 2012; 109: 8884-8889

• Liu T.Y.
• et al.

Accelerated RNA detection using tandem CRISPR nucleases.

Nat. Chem. Biol. 2021; 17: 982-988

• Hu Y.
• et al.

CRISPR/Cas9-engineered universal CD19/CD22 dual-targeted CAR-T cell therapy for relapsed/refractory B-cell acute lymphoblastic leukemia.

Clin. Cancer Res. 2021; 27: 2764-2772

• Perli S.D.
• et al.

Continuous genetic recording with self-targeting CRISPR-Cas in human cells.

Science. 2016; 353aag0511

• Tang W.
• Liu D.R.

Rewritable multi-event analog recording in bacterial and mammalian cells.

Science. 2018; 360eaap8992

• Doricchi A.
• et al.

Emerging approaches to DNA data storage: challenges and prospects.

ACS Nano. 2022; 16: 17552-17571

• Ho J.M.L.
• et al.

A suppressor tRNA-mediated feedforward loop eliminates leaky gene expression in bacteria.

Nucleic Acids Res. 2020; 49: e25

• Jones R.D.
• et al.

Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles.

Nat. Commun. 2022; 13: 1720

• Jahnke K.
• et al.

Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells.

Nat. Commun. 2021; 12: 3967

• Shaw W.M.
• et al.

Engineering a model cell for rational tuning of GPCR signaling.

Cell. 2019; 177: 782-796.e727

• Masubuchi T.
• et al.

Construction of integrated gene logic-chip.

Nat. Nanotechnol. 2018; 13: 933-940

• Pardee K.
• et al.

Paper-based synthetic gene networks.

Cell. 2014; 159: 940-954

• Broughton J.P.
• et al.

CRISPR-Cas12-based detection of SARS-CoV-2.

Nat. Nanotechnol. 2020; 38: 870-874

• Graham G.
• et al.

Genome-scale transcriptional dynamics and environmental biosensing.

Proc. Natl. Acad. Sci. U. S. A. 2020; 117: 3301-3306

• Amalfitano E.
• et al.

A glucose meter interface for point-of-care gene circuit-based diagnostics.

Nat. Commun. 2021; 12: 724

• de Puig H.
• et al.

Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants.

Sci. Adv. 2021; 7: 32

• Wang W.
• et al.

Harnessing the hygroscopic and biofluorescent behaviors of genetically tractable microbial cells to design biohybrid wearables.

Sci. Adv. 2017; 3e1601984

• Fan W.
• et al.

Machine-knitted washable sensor array textile for precise epidermal physiological signal monitoring.

Sci. Adv. 2020; 6eaay2840

• Nguyen P.Q.
• et al.

Wearable materials with embedded synthetic biology sensors for biomolecule detection.

Nat. Biotechnol. 2021; 39: 1366-1374

• Liu X.
• et al.

3D Printing of living responsive materials and devices.

Adv. Mater. 2018; 301704821

• Atkinson J.T.
• et al.

Real-time bioelectronic sensing of environmental contaminants.

Nature. 2022; 611: 548-553

• Adiga R.
• et al.

Point-of-care production of therapeutic proteins of good-manufacturing-practice quality.

Nat. Biomed. Eng. 2018; 2: 675-686

• Naseri G.
• Koffas M.A.G.

Application of combinatorial optimization strategies in synthetic biology.

Nat. Commun. 2020; 11: 2446

• Nielsen A.A.K.
• Voigt C.A.

Deep learning to predict the lab-of-origin of engineered DNA.

Nat. Commun. 2018; 9: 3135

• Angenent-Mari N.M.
• et al.

A deep learning approach to programmable RNA switches.

Nat. Commun. 2020; 11: 5057

• Justus K.B.
• et al.

A biosensing soft robot: autonomous parsing of chemical signals through integrated organic and inorganic interfaces.

Sci. Robot. 2019; 4: 31