Notomi, T. et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28, e63–e63 (2000).
Piepenburg, O., Williams, C. H., Stemple, D. L. & Armes, N. A. DNA detection using recombination proteins. PLoS Biol. 4, e204 (2006).
Fozouni, P. et al. Amplification-free detection of SARS-CoV-2 with CRISPR–Cas13a and mobile phone microscopy. Cell 184, 323–333 (2021).
Chen, J. S. et al. CRISPR–Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360, 436–439 (2018).
Gootenberg, J. S. et al. Nucleic acid detection with CRISPR–Cas13a/C2c2. Science 356, 438–442 (2017).
Holland, P. M., Abramson, R. D., Watson, R. & Gelfand, D. H. Detection of specific polymerase chain reaction product by utilizing the 5′–3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl Acad. Sci. USA 88, 7276–7280 (1991).
Broughton, J. P. et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 38, 870–874 (2020).
Marras, S. A., Kramer, F. R. & Tyagi, S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 30, e122–e122 (2002).
Yeh, H.-C., Sharma, J., Han, J. J., Martinez, J. S. & Werner, J. H. A. DNA–silver nanocluster probe that fluoresces upon hybridization. Nano Lett. 10, 3106–3110 (2010).
O’Neill, P. R., Gwinn, E. G. & Fygenson, D. K. UV excitation of DNA stabilized Ag cluster fluorescence via the DNA bases. J. Phys. Chem. C 115, 24061–24066 (2011).
Petty, J. T., Zheng, J., Hud, N. V. & Dickson, R. M. DNA-templated Ag nanocluster formation. J. Am. Chem. Soc. 126, 5207–5212 (2004).
Yeh, H.-C. et al. A fluorescence light-up Ag nanocluster probe that discriminates single-nucleotide variants by emission color. J. Am. Chem. Soc. 134, 11550–11558 (2012).
Blevins, M. S. et al. Footprints of nanoscale DNA–silver cluster chromophores via activated-electron photodetachment mass spectrometry. ACS Nano 13, 14070–14079 (2019).
Copp, S. M. et al. Magic numbers in DNA-stabilized fluorescent silver clusters lead to magic colors. J. Phys. Chem. Lett. 5, 959–963 (2014).
He, C., Goodwin, P. M., Yunus, A. I., Dickson, R. M. & Petty, J. T. A split DNA scaffold for a green fluorescent silver cluster. J. Phys. Chem. C 123, 17588–17597 (2019).
Schultz, D. et al. Evidence for rod-shaped DNA-stabilized silver nanocluster emitters. Adv. Mater. 25, 2797–2803 (2013).
Petty, J. T. et al. Optical sensing by transforming chromophoric silver clusters in DNA nanoreactors. Anal. Chem. 84, 356–364 (2012).
Chen, J. et al. CRISPR/Cas precisely regulated DNA-templated silver nanocluster fluorescence sensor for meat adulteration detection. J. Agric. Food Chem. 70, 14296–14303 (2022).
Lee, C. Y., Park, K. S., Jung, Y. K. & Park, H. G. A label-free fluorescent assay for deoxyribonuclease I activity based on DNA-templated silver nanocluster/graphene oxide nanocomposite. Biosens. Bioelectron. 93, 293–297 (2017).
Kuo, Y. A. et al. Massively parallel selection of nanocluster beacons. Adv. Mater. 34, e2204957 (2022).
Chen, Y.-A. et al. Nanocluster beacons enable detection of a single N6-methyladenine. J. Am. Chem. Soc. 137, 10476–10479 (2015).
Obliosca, J. M. et al. A complementary palette of nanocluster beacons. ACS Nano 8, 10150–10160 (2014).
Cerretani, C., Kanazawa, H., Vosch, T. & Kondo, J. Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster. Angew. Chem. Int. Ed. 58, 17153–17157 (2019).
Petty, J. T. et al. A DNA-encapsulated silver cluster and the roles of its nucleobase ligands. J. Phys. Chem. C 122, 28382–28392 (2018).
Koszinowski, K. & Ballweg, K. A highly charged Ag64+ core in a DNA‐encapsulated silver nanocluster. Chem. Eur. J. 16, 3285–3290 (2010).
Gonzalez-Rosell, A. et al. Chloride ligands on DNA-stabilized silver nanoclusters. J. Am. Chem. Soc. 145, 10721–10729 (2023).
Huard, D. J. et al. Atomic structure of a fluorescent Ag8 cluster templated by a multistranded DNA scaffold. J. Am. Chem. Soc. 141, 11465–11470 (2018).
Markham, N. R. & Zuker, M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol. 453, 3–31 (2008).
Cong, X. et al. Determining membrane protein–lipid binding thermodynamics using native mass spectrometry. J. Am. Chem. Soc. 138, 4346–4349 (2016).
McCabe, J. W. et al. Variable-temperature electrospray ionization for temperature-dependent folding/refolding reactions of proteins and ligand binding. Anal. Chem. 93, 6924–6931 (2021).
Ramachandran, A. & Santiago, J. G. CRISPR enzyme kinetics for molecular diagnostics. Anal. Chem. 93, 7456–7464 (2021).
Nguyen, L. T., Smith, B. M. & Jain, P. K. Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection. Nat. Commun. 11, 4906 (2020).
Nalefski, E. A. et al. Kinetic analysis of Cas12a and Cas13a RNA-guided nucleases for development of improved CRISPR-based diagnostics. iScience 24, 102996 (2021).
Yeh, H.-C., Sharma, J., Han, J. J., Martinez, J. S. & Werner, J. H. A beacon of light. IEEE Nanotechnol. Mag. 5, 28–33 (2011).
Juul, S. et al. Nanocluster beacons as reporter probes in rolling circle enhanced enzyme activity detection. Nanoscale 7, 8332–8337 (2015).
Ge, L., Sun, X., Hong, Q. & Li, F. Ratiometric nanocluster beacon: a label-free and sensitive fluorescent DNA detection platform. ACS Appl. Mater. Interfaces 9, 13102–13110 (2017).
Suo, T. et al. A versatile turn-on fluorometric biosensing profile based on split aptamers-involved assembly of nanocluster beacon sandwich. Sens. Actuators B 324, 128586 (2020).
Gwinn, E., Schultz, D., Copp, S. M. & Swasey, S. DNA-protected silver clusters for nanophotonics. Nanomaterials 5, 180–207 (2015).
Zou, X., Kang, X. & Zhu, M. Recent developments in the investigation of driving forces for transforming coinage metal nanoclusters. Chem. Soc. Rev. 52, 5892–5967 (2023).
Leytus, S. P., Melhado, L. L. & Mangel, W. F. Rhodamine-based compounds as fluorogenic substrates for serine proteinases. Biochem. J. 209, 299–307 (1983).
Broto, M. et al. Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs. Nat. Nanotechnol. 17, 1120–1126 (2022).
Hu, Q. et al. DNAzyme-based faithful probing and pulldown to identify candidate biomarkers of low abundance. Nat. Chem. 16, 122–131 (2023).
Fort, K. L. et al. Implementation of ultraviolet photodissociation on a benchtop Q exactive mass spectrometer and its application to phosphoproteomics. Anal. Chem. 88, 2303–2310 (2016).
Sanders, J. D. et al. Enhanced ion mobility separation and characterization of isomeric phosphatidylcholines using absorption mode Fourier transform multiplexing and ultraviolet photodissociation mass spectrometry. Anal. Chem. 94, 4252–4259 (2022).
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