Abdelfattah, A. S. et al. Bright and photostable chemigenetic indicators for extended in vivo voltage imaging. Science 365, 699–704 (2019).
Chen, Y.-N., Cartwright, H. N. & Ho, C.-H. In vivo visualization of nitrate dynamics using a genetically encoded fluorescent biosensor. Sci. Adv. 8, eabq4915 (2022).
Cambronne, X. A. et al. Biosensor reveals multiple sources for mitochondrial NAD. Science 352, 1474–1477 (2016).
Xue, L. et al. Probing coenzyme A homeostasis with semisynthetic biosensors. Nat. Chem. Biol. 19, 346–355 (2023).
Olsen, R. H. J. et al. TRUPATH, an open-source biosensor platform for interrogating the GPCR transducerome. Nat. Chem. Biol. 16, 841–849 (2020).
Marvin, J. S. et al. A genetically encoded fluorescent sensor for in vivo imaging of GABA. Nat. Methods 16, 763–770 (2019).
Ino, D., Tanaka, Y., Hibino, H. & Nishiyama, M. A fluorescent sensor for real-time measurement of extracellular oxytocin dynamics in the brain. Nat. Methods 19, 1286–1294 (2022).
Brun, M. A., Tan, K.-T., Nakata, E., Hinner, M. J. & Johnsson, K. Semisynthetic fluorescent sensor proteins based on self-labeling protein tags. J. Am. Chem. Soc. 131, 5873–5884 (2009).
Griss, R. et al. Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nat. Chem. Biol. 10, 598–603 (2014).
Xue, L., Prifti, E. & Johnsson, K. A general strategy for the semisynthesis of ratiometric fluorescent sensor proteins with increased dynamic range. J. Am. Chem. Soc. 138, 5258–5261 (2016).
Yu, Q. et al. Semisynthetic sensor proteins enable metabolic assays at the point of care. Science 361, 1122–1126 (2018).
Vecchia, M. D. et al. Spectrally tunable Forster resonance energy transfer-based biosensors using organic dye grafting. ACS Sens. 7, 2920–2927 (2022).
Hellweg, L. et al. A general method for the development of multicolor biosensors with large dynamic ranges. Nat. Chem. Biol. 19, 1147–1157 (2023).
Beltrán, J. et al. Rapid biosensor development using plant hormone receptors as reprogrammable scaffolds. Nat. Biotechnol. 40, 1855–1861 (2022).
Glasgow, A. A. et al. Computational design of a modular protein sense-response system. Science 366, 1024–1028 (2019).
Quijano-Rubio, A. et al. De novo design of modular and tunable protein biosensors. Nature 591, 482–487 (2021).
Feng, J. et al. A general strategy to construct small molecule biosensors in eukaryotes. eLife 4, e10606 (2015).
Tucker, C. L. & Fields, S. A yeast sensor of ligand binding. Nat. Biotechnol. 19, 1042–1046 (2001).
Ricci, F., Vallée-Bélisle, A., Simon, A. J., Porchetta, A. & Plaxco, K. W. Using nature’s “tricks” to rationally tune the binding properties of biomolecular receptors. Acc. Chem. Res. 49, 1884–1892 (2016).
Choi, B. et al. Artificial allosteric control of maltose binding protein. Phys. Rev. Lett. 94, 038103 (2005).
Vallée-Bélisle, A., Ricci, F. & Plaxco, K. W. Engineering biosensors with extended, narrowed, or arbitrarily edited dynamic range. J. Am. Chem. Soc. 134, 2876–2879 (2012).
Porchetta, A., Vallee-Belisle, A., Plaxco, K. W. & Ricci, F. Using distal-site mutations and allosteric inhibition to tune, extend, and narrow the useful dynamic range of aptamer-based sensors. J. Am. Chem. Soc. 134, 20601–20604 (2012).
Hariri, A. A. et al. Modular aptamer switches for the continuous optical detection of small-molecule analytes in complex media. Adv. Mater. 36, e2304410 (2024).
Chamorro-Garcia, A. et al. The sequestration mechanism as a generalizable approach to improve the sensitivity of biosensors and bioassays. Chem. Sci. 13, 12219–12228 (2022).
Dueber, J. E., Mirsky, E. A. & Lim, W. A. Engineering synthetic signaling proteins with ultrasensitive input/output control. Nat. Biotechnol. 25, 660–662 (2007).
Simon, A. J., Vallee-Belisle, A., Ricci, F. & Plaxco, K. W. Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors. Proc. Natl Acad. Sci. USA 111, 15048–15053 (2014).
Ortega, G. et al. Rational design to control the trade-off between receptor affinity and cooperativity. Proc. Natl Acad. Sci. USA 117, 19136–19140 (2020).
Ortega, G., Chamorro-Garcia, A., Ricci, F. & Plaxco, K. W. On the rational design of cooperative receptors. Annu. Rev. Biophys. 52, 319–337 (2023).
Simon, A. J., Vallée-Bélisle, A., Ricci, F., Watkins, H. M. & Plaxco, K. W. Using the population-shift mechanism to rationally introduce “Hill-type” cooperativity into a normally non-cooperative receptor. Angew. Chem. Int. Ed. 53, 9471–9475 (2014).
Marras, A. E., Zhou, L., Su, H. J. & Castro, C. E. Programmable motion of DNA origami mechanisms. Proc. Natl Acad. Sci. USA 112, 713–718 (2015).
Marras, A. E. et al. Cation-activated avidity for rapid reconfiguration of DNA nanodevices. ACS Nano 12, 9484–9494 (2018).
Shi, Z. & Arya, G. Free energy landscape of salt-actuated reconfigurable DNA nanodevices. Nucleic Acids Res. 48, 548–560 (2020).
Funke, J. J. & Dietz, H. Placing molecules with Bohr radius resolution using DNA origami. Nat. Nanotechnol. 11, 47–52 (2016).
Funke, J. J. et al. Uncovering the forces between nucleosomes using DNA origami. Sci. Adv. 2, e1600974 (2016).
Sulc, P. et al. Sequence-dependent thermodynamics of a coarse-grained DNA model. J. Chem. Phys. 137, 135101 (2012).
Smock, R. G. & Gierasch, L. M. Sending signals dynamically. Science 324, 198–203 (2009).
Darcy, M. et al. High-force application by a nanoscale DNA force spectrometer. ACS Nano 16, 5682–5695 (2022).
Zadeh, J. N. et al. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170–173 (2011).
Shaw, A. et al. Binding to nanopatterned antigens is dominated by the spatial tolerance of antibodies. Nat. Nanotechnol. 14, 184–190 (2019).
Pfeiffer, M. et al. Single antibody detection in a DNA origami nanoantenna. iScience 24, 103072 (2021).
Fang, X., Sen, A., Vicens, M. & Tan, W. Synthetic DNA aptamers to detect protein molecular variants in a high-throughput fluorescence quenching assay. ChemBioChem 4, 829–834 (2003).
Lai, R. Y., Plaxco, K. W. & Heeger, A. J. Aptamer-based electrochemical detection of picomolar platelet-derived growth factor directly in blood serum. Anal. Chem. 79, 229–233 (2007).
Andrae, J., Gallini, R. & Betsholtz, C. Role of platelet-derived growth factors in physiology and medicine. Genes Dev. 22, 1276–1312 (2008).
Leitzel, K. et al. Elevated plasma platelet-derived growth factor B-chain levels in cancer patients. Cancer Res. 51, 4149–4154 (1991).
Jiao, C. et al. Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. Science 372, 941–948 (2021).
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).
Ochmann, S. E. et al. DNA origami voltage sensors for transmembrane potentials with single-molecule sensitivity. Nano Lett. 21, 8634–8641 (2021).
Büber, E. et al. DNA origami curvature sensors for nanoparticle and vesicle size determination with single-molecule FRET readout. ACS Nano 17, 3088–3097 (2023).
Domljanovic, I. et al. DNA origami book biosensor for multiplex detection of cancer-associated nucleic acids. Nanoscale 14, 15432–15441 (2022).
Loretan, M. et al. Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope. Preprint at bioRxiv https://doi.org/10.1101/2024.05.08.593103 (2024).
Praetorius, F. et al. Biotechnological mass production of DNA origami. Nature 552, 84–87 (2017).
Gopinath, A. et al. Absolute and arbitrary orientation of single-molecule shapes. Science 371, eabd6179 (2021).
Williamson, P., Ijas, H., Shen, B., Corrigan, D. K. & Linko, V. Probing the conformational states of a pH-sensitive DNA origami zipper via label-free electrochemical methods. Langmuir 37, 7801–7809 (2021).
Chandrasekaran, A. R. Nuclease resistance of DNA nanostructures. Nat. Rev. Chem. 5, 225–239 (2021).
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).
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).
Douglas, S. M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).
Trofymchuk, K. et al. Addressable nanoantennas with cleared hotspots for single-molecule detection on a portable smartphone microscope. Nat. Commun. 12, 950 (2021).
Ouldridge, T. E., Louis, A. A. & Doye, J. P. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J. Chem. Phys. 134, 085101 (2011).
Snodin, B. E. et al. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. J. Chem. Phys. 142, 234901 (2015).
Rovigatti, L., Sulc, P., Reguly, I. Z. & Romano, F. A comparison between parallelization approaches in molecular dynamics simulations on GPUs. J. Comput. Chem. 36, 1–8 (2015).
Suma, A. et al. TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami. J. Comput. Chem. 40, 2586–2595 (2019).
Poppleton, E. et al. Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation. Nucleic Acids Res. 48, e72 (2020).
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).
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).
Schrimpf, W., Barth, A., Hendrix, J. & Lamb, D. C. PAM: a framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data. Biophys. J. 114, 1518–1528 (2018).
Grabenhorst, L. et al. Source data—engineering modular and tunable single molecule sensors by decoupling sensing from signal output. Zenodo https://doi.org/10.5281/zenodo.12168537 (2024).
