Abdelfattah, A. S. et al. Vivid and photostable chemigenetic indicators for prolonged in vivo voltage imaging. Science 365, 699–704 (2019).
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).
Cambronne, X. A. et al. Biosensor reveals a number of 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. Strategies 16, 763–770 (2019).
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).
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).
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, Okay. A basic technique for the semisynthesis of ratiometric fluorescent sensor proteins with elevated dynamic vary. J. Am. Chem. Soc. 138, 5258–5261 (2016).
Yu, Q. et al. Semisynthetic sensor proteins allow metabolic assays on the level of care. Science 361, 1122–1126 (2018).
Vecchia, M. D. et al. Spectrally tunable Forster resonance vitality transfer-based biosensors utilizing natural dye grafting. ACS Sens. 7, 2920–2927 (2022).
Hellweg, L. et al. A basic methodology for the event of multicolor biosensors with massive dynamic ranges. Nat. Chem. Biol. 19, 1147–1157 (2023).
Beltrán, J. et al. Fast biosensor growth utilizing 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 basic technique to assemble 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, Okay. W. Utilizing nature’s “methods” to rationally tune the binding properties of biomolecular receptors. Acc. Chem. Res. 49, 1884–1892 (2016).
Choi, B. et al. Synthetic allosteric management of maltose binding protein. Phys. Rev. Lett. 94, 038103 (2005).
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).
Porchetta, A., Vallee-Belisle, A., Plaxco, Okay. W. & Ricci, F. Utilizing distal-site mutations and allosteric inhibition to tune, prolong, and slim the helpful dynamic vary of aptamer-based sensors. J. Am. Chem. Soc. 134, 20601–20604 (2012).
Hariri, A. A. et al. Modular aptamer switches for the continual optical detection of small-molecule analytes in complicated media. Adv. Mater. 36, e2304410 (2024).
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).
Dueber, J. E., Mirsky, E. A. & Lim, W. A. Engineering artificial signaling proteins with ultrasensitive enter/output management. Nat. Biotechnol. 25, 660–662 (2007).
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).
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).
Ortega, G., Chamorro-Garcia, A., Ricci, F. & Plaxco, Okay. 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, 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).
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).
Marras, A. E. et al. Cation-activated avidity for fast reconfiguration of DNA nanodevices. ACS Nano 12, 9484–9494 (2018).
Shi, Z. & Arya, G. Free vitality panorama of salt-actuated reconfigurable DNA nanodevices. Nucleic Acids Res. 48, 548–560 (2020).
Funke, J. J. & Dietz, H. Inserting molecules with Bohr radius decision utilizing DNA origami. Nat. Nanotechnol. 11, 47–52 (2016).
Funke, J. J. et al. Uncovering the forces between nucleosomes utilizing DNA origami. Sci. Adv. 2, e1600974 (2016).
Sulc, P. et al. Sequence-dependent thermodynamics of a coarse-grained DNA mannequin. J. Chem. Phys. 137, 135101 (2012).
Smock, R. G. & Gierasch, L. M. Sending alerts dynamically. Science 324, 198–203 (2009).
Darcy, M. et al. Excessive-force software by a nanoscale DNA power spectrometer. ACS Nano 16, 5682–5695 (2022).
Zadeh, J. N. et al. NUPACK: evaluation and design of nucleic acid techniques. 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. Artificial DNA aptamers to detect protein molecular variants in a high-throughput fluorescence quenching assay. ChemBioChem 4, 829–834 (2003).
Lai, R. Y., Plaxco, Okay. W. & Heeger, A. J. Aptamer-based electrochemical detection of picomolar platelet-derived progress issue immediately in blood serum. Anal. Chem. 79, 229–233 (2007).
Andrae, J., Gallini, R. & Betsholtz, C. Position of platelet-derived progress components in physiology and drugs. Genes Dev. 22, 1276–1312 (2008).
Leitzel, Okay. et al. Elevated plasma platelet-derived progress issue B-chain ranges in most cancers sufferers. Most cancers Res. 51, 4149–4154 (1991).
Jiao, C. et al. Noncanonical crRNAs derived from host transcripts allow 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 measurement dedication with single-molecule FRET readout. ACS Nano 17, 3088–3097 (2023).
Domljanovic, I. et al. DNA origami e 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 moveable 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).
Gopinath, A. et al. Absolute and arbitrary orientation of single-molecule shapes. Science 371, eabd6179 (2021).
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).
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. Fast prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).
Trofymchuk, Okay. et al. Addressable nanoantennas with cleared hotspots for single-molecule detection on a conveyable 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 mannequin. J. Chem. Phys. 134, 085101 (2011).
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).
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).
Suma, A. et al. TacoxDNA: A user-friendly internet server for simulations of complicated DNA constructions, from single strands to origami. J. Comput. Chem. 40, 2586–2595 (2019).
Poppleton, E. et al. Design, optimization and evaluation of enormous DNA and RNA nanostructures by means of interactive visualization, modifying 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 built-in evaluation of imaging, single-molecule, and ensemble fluorescence knowledge. Biophys. J. 114, 1518–1528 (2018).
Grabenhorst, L. et al. Supply knowledge—engineering modular and tunable single molecule sensors by decoupling sensing from sign output. Zenodo https://doi.org/10.5281/zenodo.12168537 (2024).