Engineering modular and tunable single-molecule sensors by decoupling sensing from sign output

Engineering modular and tunable single-molecule sensors by decoupling sensing from sign output


  • Abdelfattah, A. S. et al. Shiny and photostable chemigenetic indicators for prolonged in vivo voltage imaging. Science 365, 699–704 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, Y.-N., Cartwright, H. N. & Ho, C.-H. In vivo visualization of nitrate dynamics utilizing a genetically encoded fluorescent biosensor. Sci. Adv. 8, eabq4915 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cambronne, X. A. et al. Biosensor reveals a number of sources for mitochondrial NAD. Science 352, 1474–1477 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xue, L. et al. Probing coenzyme A homeostasis with semisynthetic biosensors. Nat. Chem. Biol. 19, 346–355 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Olsen, R. H. J. et al. TRUPATH, an open-source biosensor platform for interrogating the GPCR transducerome. Nat. Chem. Biol. 16, 841–849 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marvin, J. S. et al. A genetically encoded fluorescent sensor for in vivo imaging of GABA. Nat. Strategies 16, 763–770 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ino, D., Tanaka, Y., Hibino, H. & Nishiyama, M. A fluorescent sensor for real-time measurement of extracellular oxytocin dynamics within the mind. Nat. Strategies 19, 1286–1294 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brun, M. A., Tan, Okay.-T., Nakata, E., Hinner, M. J. & Johnsson, Okay. Semisynthetic fluorescent sensor proteins primarily based on self-labeling protein tags. J. Am. Chem. Soc. 131, 5873–5884 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Griss, R. et al. Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nat. Chem. Biol. 10, 598–603 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xue, L., Prifti, E. & Johnsson, Okay. A normal technique for the semisynthesis of ratiometric fluorescent sensor proteins with elevated dynamic vary. J. Am. Chem. Soc. 138, 5258–5261 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yu, Q. et al. Semisynthetic sensor proteins allow metabolic assays on the level of care. Science 361, 1122–1126 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Vecchia, M. D. et al. Spectrally tunable Forster resonance power transfer-based biosensors utilizing natural dye grafting. ACS Sens. 7, 2920–2927 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hellweg, L. et al. A normal methodology for the event of multicolor biosensors with massive dynamic ranges. Nat. Chem. Biol. 19, 1147–1157 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Beltrán, J. et al. Speedy biosensor improvement utilizing plant hormone receptors as reprogrammable scaffolds. Nat. Biotechnol. 40, 1855–1861 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Glasgow, A. A. et al. Computational design of a modular protein sense-response system. Science 366, 1024–1028 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Quijano-Rubio, A. et al. De novo design of modular and tunable protein biosensors. Nature 591, 482–487 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Feng, J. et al. A normal technique to assemble small molecule biosensors in eukaryotes. eLife 4, e10606 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tucker, C. L. & Fields, S. A yeast sensor of ligand binding. Nat. Biotechnol. 19, 1042–1046 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ricci, F., Vallée-Bélisle, A., Simon, A. J., Porchetta, A. & Plaxco, Okay. W. Utilizing nature’s “tips” to rationally tune the binding properties of biomolecular receptors. Acc. Chem. Res. 49, 1884–1892 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Choi, B. et al. Synthetic allosteric management of maltose binding protein. Phys. Rev. Lett. 94, 038103 (2005).

    Article 
    PubMed 

    Google Scholar
     

  • Vallée-Bélisle, A., Ricci, F. & Plaxco, Okay. W. Engineering biosensors with prolonged, narrowed, or arbitrarily edited dynamic vary. J. Am. Chem. Soc. 134, 2876–2879 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Porchetta, A., Vallee-Belisle, A., Plaxco, Okay. W. & Ricci, F. Utilizing distal-site mutations and allosteric inhibition to tune, prolong, and slender the helpful dynamic vary of aptamer-based sensors. J. Am. Chem. Soc. 134, 20601–20604 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hariri, A. A. et al. Modular aptamer switches for the continual optical detection of small-molecule analytes in advanced media. Adv. Mater. 36, e2304410 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Chamorro-Garcia, A. et al. The sequestration mechanism as a generalizable method to enhance the sensitivity of biosensors and bioassays. Chem. Sci. 13, 12219–12228 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dueber, J. E., Mirsky, E. A. & Lim, W. A. Engineering artificial signaling proteins with ultrasensitive enter/output management. Nat. Biotechnol. 25, 660–662 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Simon, A. J., Vallee-Belisle, A., Ricci, F. & Plaxco, Okay. W. Intrinsic dysfunction as a generalizable technique for the rational design of extremely responsive, allosterically cooperative receptors. Proc. Natl Acad. Sci. USA 111, 15048–15053 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ortega, G. et al. Rational design to regulate the trade-off between receptor affinity and cooperativity. Proc. Natl Acad. Sci. USA 117, 19136–19140 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ortega, G., Chamorro-Garcia, A., Ricci, F. & Plaxco, Okay. W. On the rational design of cooperative receptors. Annu. Rev. Biophys. 52, 319–337 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Simon, A. J., Vallée-Bélisle, A., Ricci, F., Watkins, H. M. & Plaxco, Okay. W. Utilizing the population-shift mechanism to rationally introduce “Hill-type” cooperativity right into a usually non-cooperative receptor. Angew. Chem. Int. Ed. 53, 9471–9475 (2014).

    Article 
    CAS 

    Google Scholar
     

  • Marras, A. E., Zhou, L., Su, H. J. & Castro, C. E. Programmable movement of DNA origami mechanisms. Proc. Natl Acad. Sci. USA 112, 713–718 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marras, A. E. et al. Cation-activated avidity for speedy reconfiguration of DNA nanodevices. ACS Nano 12, 9484–9494 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shi, Z. & Arya, G. Free power panorama of salt-actuated reconfigurable DNA nanodevices. Nucleic Acids Res. 48, 548–560 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Funke, J. J. & Dietz, H. Putting molecules with Bohr radius decision utilizing DNA origami. Nat. Nanotechnol. 11, 47–52 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Funke, J. J. et al. Uncovering the forces between nucleosomes utilizing DNA origami. Sci. Adv. 2, e1600974 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sulc, P. et al. Sequence-dependent thermodynamics of a coarse-grained DNA mannequin. J. Chem. Phys. 137, 135101 (2012).

    Article 
    PubMed 

    Google Scholar
     

  • Smock, R. G. & Gierasch, L. M. Sending indicators dynamically. Science 324, 198–203 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Darcy, M. et al. Excessive-force software by a nanoscale DNA pressure spectrometer. ACS Nano 16, 5682–5695 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zadeh, J. N. et al. NUPACK: evaluation and design of nucleic acid methods. J. Comput. Chem. 32, 170–173 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shaw, A. et al. Binding to nanopatterned antigens is dominated by the spatial tolerance of antibodies. Nat. Nanotechnol. 14, 184–190 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pfeiffer, M. et al. Single antibody detection in a DNA origami nanoantenna. iScience 24, 103072 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fang, X., Sen, A., Vicens, M. & Tan, W. Artificial DNA aptamers to detect protein molecular variants in a high-throughput fluorescence quenching assay. ChemBioChem 4, 829–834 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lai, R. Y., Plaxco, Okay. W. & Heeger, A. J. Aptamer-based electrochemical detection of picomolar platelet-derived development issue straight in blood serum. Anal. Chem. 79, 229–233 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Andrae, J., Gallini, R. & Betsholtz, C. Function of platelet-derived development elements in physiology and drugs. Genes Dev. 22, 1276–1312 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Leitzel, Okay. et al. Elevated plasma platelet-derived development issue B-chain ranges in most cancers sufferers. Most cancers Res. 51, 4149–4154 (1991).

    CAS 
    PubMed 

    Google Scholar
     

  • Jiao, C. et al. Noncanonical crRNAs derived from host transcripts allow multiplexable RNA detection by Cas9. Science 372, 941–948 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Selnihhin, D., Sparvath, S. M., Preus, S., Birkedal, V. & Andersen, E. S. Multifluorophore DNA origami beacon as a biosensing platform. ACS Nano 12, 5699–5708 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ochmann, S. E. et al. DNA origami voltage sensors for transmembrane potentials with single-molecule sensitivity. Nano Lett. 21, 8634–8641 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Büber, E. et al. DNA origami curvature sensors for nanoparticle and vesicle dimension willpower with single-molecule FRET readout. ACS Nano 17, 3088–3097 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Domljanovic, I. et al. DNA origami e book biosensor for multiplex detection of cancer-associated nucleic acids. Nanoscale 14, 15432–15441 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Loretan, M. et al. Direct single-molecule detection and super-resolution imaging with a low-cost transportable smartphone-based microscope. Preprint at bioRxiv https://doi.org/10.1101/2024.05.08.593103 (2024).

  • Praetorius, F. et al. Biotechnological mass manufacturing of DNA origami. Nature 552, 84–87 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gopinath, A. et al. Absolute and arbitrary orientation of single-molecule shapes. Science 371, eabd6179 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Williamson, P., Ijas, H., Shen, B., Corrigan, D. Okay. & Linko, V. Probing the conformational states of a pH-sensitive DNA origami zipper through label-free electrochemical strategies. Langmuir 37, 7801–7809 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chandrasekaran, A. R. Nuclease resistance of DNA nanostructures. Nat. Rev. Chem. 5, 225–239 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Scheckenbach, M., Schubert, T., Forthmann, C., Glembockyte, V. & Tinnefeld, P. Self-regeneration and self-healing in DNA origami nanostructures. Angew. Chem. Int. Ed. 60, 4931–4938 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Wassermann, L. M., Scheckenbach, M., Baptist, A. V., Glembockyte, V. & Heuer-Jungemann, A. Full site-specific addressability in DNA origami-templated silica nanostructures. Adv. Mater. 35, e2212024 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Douglas, S. M. et al. Speedy prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Trofymchuk, Okay. et al. Addressable nanoantennas with cleared hotspots for single-molecule detection on a transportable smartphone microscope. Nat. Commun. 12, 950 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ouldridge, T. E., Louis, A. A. & Doye, J. P. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA mannequin. J. Chem. Phys. 134, 085101 (2011).

    Article 
    PubMed 

    Google Scholar
     

  • Snodin, B. E. et al. Introducing improved structural properties and salt dependence right into a coarse-grained mannequin of DNA. J. Chem. Phys. 142, 234901 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Rovigatti, L., Sulc, P., Reguly, I. Z. & Romano, F. A comparability between parallelization approaches in molecular dynamics simulations on GPUs. J. Comput. Chem. 36, 1–8 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Suma, A. et al. TacoxDNA: A user-friendly net server for simulations of advanced DNA buildings, from single strands to origami. J. Comput. Chem. 40, 2586–2595 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Poppleton, E. et al. Design, optimization and evaluation of huge DNA and RNA nanostructures by interactive visualization, modifying and molecular simulation. Nucleic Acids Res. 48, e72 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Poppleton, E., Romero, R., Mallya, A., Rovigatti, L. & Sulc, P. OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures. Nucleic Acids Res. 49, W491–W498 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schroder, T. et al. Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics. Proc. Natl Acad. Sci. USA 120, e2211896120 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schrimpf, W., Barth, A., Hendrix, J. & Lamb, D. C. PAM: a framework for built-in evaluation of imaging, single-molecule, and ensemble fluorescence information. Biophys. J. 114, 1518–1528 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grabenhorst, L. et al. Supply information—engineering modular and tunable single molecule sensors by decoupling sensing from sign output. Zenodo https://doi.org/10.5281/zenodo.12168537 (2024).

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