Preloader

Nucleic acid-based fluorescent sensor systems: a review

  • Butler JE. Enzyme-linked immunosorbent assay. J Immunoass. 2000;21:165–209.

    CAS 

    Google Scholar 

  • Buchwalow IB, Minin EA, Boecker W. A multicolor fluorescence immunostaining technique for simultaneous antigen targeting. Acta Histochemica. 2005;107:143–8.

    CAS 
    PubMed 

    Google Scholar 

  • Kubista M, Andrade JM, Bengtsson M, Forootan A, Jonák J, Lind K, et al. The real-time polymerase chain reaction. Mol Asp Med. 2006;27:95–125.

    CAS 

    Google Scholar 

  • Min T. FISH Techniques. Methods Mol Biol. 2003;220:193–212.

    CAS 
    PubMed 

    Google Scholar 

  • Chi X, Gatti P, Papoian T. Safety of antisense oligonucleotide and siRNA-based therapeutics. Drug Disco Today. 2017;22:823–33.

    CAS 

    Google Scholar 

  • Seeman NC, Sleiman HF. DNA nanotechnology. Nat Rev Mater. 2018;3:17068.

    CAS 

    Google Scholar 

  • Kuzuya A, Ohya Y. DNA nanostructures as scaffolds for metal nanoparticles. Polym J. 2012;44:452–60.

    CAS 

    Google Scholar 

  • Madsen M, Gothelf KV. Chemistries for DNA nanotechnology. Chem Rev. 2019;119:6384–458.

    CAS 
    PubMed 

    Google Scholar 

  • Yuan Y, Gu Z, Yao C, Luo D, Yang D. Nucleic acid–based functional nanomaterials as advanced cancer therapeutics. Small. 2019;15:1900172.

    Google Scholar 

  • Tan X, Jiab F, Wang P, Zhang K. Nucleic acid-based drug delivery strategies. J Control Release. 2020;323:240–52.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stephanopoulos N. Hybrid nanostructures from the self-assembly of proteins and DNA. Chem. 2020;6:364–405.

    CAS 

    Google Scholar 

  • Hamada S, Luo D. Enzyme-based fabrication of physical DNA hydrogels: new materials and applications. Polym J. 2020;52:891–8.

    CAS 

    Google Scholar 

  • Zhou W, Saran R, Liu J. Metal Sensing by DNA. Chem Rev. 2017;117:8272–325.

    CAS 
    PubMed 

    Google Scholar 

  • Peng H, Newbigging AM, Wang Z, Tao J, Deng W, Le XC, et al. DNAzyme-mediated assays for amplified detection of nucleic acids and proteins. Anal Chem. 2018;90:190–207.

    CAS 
    PubMed 

    Google Scholar 

  • Samanta D, Ebrahimi SB, Mirkin CA. Nucleic-acid structures as intracellular probes for live cells. Adv Mater. 2020;32:1901743.

    CAS 

    Google Scholar 

  • Tyagi S, Kramer FR. Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol. 1996;14:303–8.

    CAS 
    PubMed 

    Google Scholar 

  • Pisa MD, Seitz O. Nucleic acid templated reactions for chemical biology. ChemMedChem. 2017;12:872–82.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Tomoike F, Abe H. RNA imaging by chemical probes. Adv Drug Deliv Rev. 2019;147:44–58.

    CAS 
    PubMed 

    Google Scholar 

  • Santangelo P, Nitin N, Bao G. Nanostructured probes for RNA detection in living cells. Ann Biomed Eng. 2006;34:39–50.

    PubMed 

    Google Scholar 

  • Zhao D, Yang Y, Qu N, Chen M, Ma Z, Krueger CJ, et al. Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2’-O-methyl RNA molecular beacons. Biomaterials. 2016;100:172–83.

    CAS 
    PubMed 

    Google Scholar 

  • Bohländer PR, Abba ML, Bestvater F, Allgayer H, Wagenknecht HA. Two wavelength-shifting molecular beacons for simultaneous and selective imaging of vesicular miRNA-21 and miRNA-31 in living cancer cells. Org Biomol Chem. 2016;14:5001–6.

    PubMed 

    Google Scholar 

  • Park YK, Jung WY, Park MG, Song SK, Lee YS, Heo H, et al. Bioimaging of multiple piRNAs in a single breast cancer cell using molecular beacons. Med Chem Commun. 2017;8:2228–32.

    CAS 

    Google Scholar 

  • Maksimenko A, Ishchenko AA, Sanz G, Laval J, Elder RH, Saparbaev MK. A molecular beacon assay for measuring base excision repair activities. Biochem Biophys Res Commun. 2004;319:240–6.

    CAS 
    PubMed 

    Google Scholar 

  • Matsumoto N, Toga T, Hayashi R, Sugasawa K, Katayanagi K, Ide H, et al. Fluorescent probes for the analysis of DNA strand scission in base excision repair. Nucl Acids Res. 2010;8:e101.

    Google Scholar 

  • Toga T, Kuraoka I, Yasui A, Iwai S. A transfection reporter for the prevention of false-negative results in molecular beacon experiments. Anal Biochem. 2013;440:9–11.

    CAS 
    PubMed 

    Google Scholar 

  • Mirbahai L, Kershaw RM, Green RM, Hayden RE, Meldrum RA, Hodges NJ. Use of a molecular beacon to track the activity of base excision repair protein OGG1 in live cells. DNA Repair. 2010;9:144–52.

    CAS 
    PubMed 

    Google Scholar 

  • Wang L, Yang CJ, Medley CD, Benner SA, Tan W. Locked nucleic acid molecular beacons. J Am Chem Soc. 2005;127:15664–5.

    CAS 
    PubMed 

    Google Scholar 

  • Vilaivan T. Fluorogenic PNA probes. Beilstein J Org Chem. 2018;14:253–81.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Murayama K, Kamiya Y, Kashida H, Asanuma H. Ultrasensitive molecular beacon designed with totally serinol nucleic acid (SNA) for monitoring mRNA in cells. ChemBioChem. 2015;16:1298–301.

    CAS 
    PubMed 

    Google Scholar 

  • Asanuma H, Murayama K, Kamiya Y, Kashida H. Design of photofunctional oligonucleotides by copolymerization of natural nucleobases with base surrogates prepared from acyclic scaffolds. Polym J. 2017;49:279–89.

    CAS 

    Google Scholar 

  • Kashida H, Takatsu T, Fujii T, Sekiguchi K, Liang X, Niwa K, et al. In-stem molecular beacon containing a pseudo base pair of threoninol nucleotides for the removal of background emission. Angew Chem Int Ed. 2009;48:7044–7.

    CAS 

    Google Scholar 

  • Berndl S, Wagenknecht HA. Fluorescent color readout of DNA hybridization with thiazole orange as an artificial DNA base. Angew Chem Int Ed. 2009;48:2418–21.

    CAS 

    Google Scholar 

  • Saito Y, Shinohara Y, Bag SS, Takeuchi Y, Matsumoto K, Saito I. Ends free and self-quenched molecular beacon with pyrene labeled pyrrolocytidine in the middle of the stem. Tetrahedron. 2009;65:934–9.

    CAS 

    Google Scholar 

  • Häner R, Biner SM, Langenegger SM, Meng T, Malinovskii VL. A highly sensitive, excimer-controlled molecular beacon. Angew Chem Int Ed. 2010;49:1227–30.

    Google Scholar 

  • Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole orange dimers in DNA: fluorescent base substitutions with hybridization readout. Chem Eur J. 2016;22:2386–95.

    CAS 
    PubMed 

    Google Scholar 

  • Miyoshi Y, Ohtsuki T, Kashida H, Asanuma H, Watanabe K. In-stem molecular beacon targeted to a 5’-region of tRNA inclusive of the D arm that detects mature tRNA with high sensitivity. PLoS ONE. 2019;14:e0211505.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pan W, Yang H, Li N, Yang L, Tang B. Simultaneous visualization of multiple mRNAs and matrix metalloproteinases in living cells using a fluorescence nanoprobe. Chem Eur J. 2015;21:6070–3.

    CAS 
    PubMed 

    Google Scholar 

  • Ishiguro T, Saitoh J, Yawata H, Otsuka M, Inoue T, Sugiura Y. Fluorescence detection of specific sequence of nucleic acids by oxazole yellow-linked oligonucleotides. Homogeneous quantitative monitoring of in vitro transcription. Nucl Acids Res. 1996;24:4992–7.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hövelmann F, Gaspar I, Ephrussi A, Seitz O. Brightness enhanced DNA FIT-probes for wash-free RNA imaging in tissue. J Am Chem Soc. 2013;135:19025–32.

    PubMed 

    Google Scholar 

  • Svanvik N, Westman G, Wang D, Kubista M. Light-up probes: thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution. Anal Biochem. 2000;281:26–35.

    CAS 
    PubMed 

    Google Scholar 

  • Köhler O, Seitz O. Thiazole orange as fluorescent universal base in peptide nucleic acids. Chem Commun. 2003:2938–9.

  • Köhler O, Jarikote DV, Seitz O. Forced intercalation probes (FIT Probes): thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous single-nucleotide-polymorphism detection. ChemBioChem. 2005;6:69–77.

    PubMed 

    Google Scholar 

  • Socher E, Jarikote DV, Knoll A, Röglin L, Burmeister J, Seitz O. FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery. Anal Biochem. 2008;375:318–30.

    CAS 
    PubMed 

    Google Scholar 

  • Bethge L, Singh I, Seitz O. Designed thiazole orange nucleotides for the synthesis of single labelled oligonucleotides that fluoresce upon matched hybridization. Org Biomol Chem. 2010;8:2439–48.

    CAS 
    PubMed 

    Google Scholar 

  • Knoll A, Kankowski S, Schöllkopf S, Meier JC, Seitz O. Chemo-biological mRNA imaging with single nucleotide specificity. Chem Commun. 2019;55:14817–20.

    CAS 

    Google Scholar 

  • Tepper O, Zheng H, Appella DH, Yavin E. Cyclopentane FIT-PNAs: bright RNA sensors. Chem Commun. 2021;57:540–3.

    CAS 

    Google Scholar 

  • Sato T, Sato Y, Nishizawa S. Triplex-forming peptide nucleic acid probe having thiazole orange as a base surrogate for fluorescence sensing of double-stranded RNA. J Am Chem Soc. 2016;138:9397–400.

    CAS 
    PubMed 

    Google Scholar 

  • Sato T, Sato Y, Nishizawa S. Optimization of the alkyl linker of TO base surrogate in triplex-forming PNA for enhanced binding to double-stranded RNA. Chem Eur J. 2017;23:4079–88.

    CAS 
    PubMed 

    Google Scholar 

  • Tanabe T, Sato T, Sato Y, Nishizawa S. Design of a fluorogenic PNA probe capable of simultaneous recognition of 3’-overhang and double-stranded sequences of small interfering RNAs. RSC Adv. 2018;8:42095–9.

    CAS 

    Google Scholar 

  • Ikeda S, Okamoto A. Hybridization-Sensitive On–off DNA probe: application of the exciton coupling effect to effective fluorescence quenching. Chem Asian J. 2008;3:958–68.

    CAS 
    PubMed 

    Google Scholar 

  • Ikeda S, Kubota T, Kino K, Okamoto A. Sequence dependence of fluorescence emission and quenching of doubly thiazole orange labeled DNA: effective design of a hybridization-sensitive probe. Bioconjugate Chem. 2008;19:1719–25.

    CAS 

    Google Scholar 

  • Kubota T, Ikeda S, Yanagisawa H, Yuki M, Okamoto A. Hybridization-sensitive fluorescent probe for long-term monitoring of intracellular RNA. Bioconjugate Chem. 2009;20:1256–61.

    CAS 

    Google Scholar 

  • Ikeda S, Kubota T, Yuki M, Okamoto A. Exciton-controlled hybridization-sensitive fluorescent probes: multicolor detection of nucleic acids. Angew Chem Int Ed. 2009;48:6480–4.

    CAS 

    Google Scholar 

  • Kubota T, Ikeda S, Okamoto A. Doubly thiazole orange-labeled DNA for live cell RNA imaging. Bull Chem Soc Jpn. 2009;82:110–7.

    CAS 

    Google Scholar 

  • Okamoto A. ECHO probes: a concept of fluorescence control for practical nucleic acid sensing. Chem Soc Rev. 2011;40:5815–28.

    CAS 
    PubMed 

    Google Scholar 

  • Ikeda S, Yanagisawa H, Nakamura A, Wang DO, Yukia M, Okamoto A. Hybridization-sensitive fluorescence control in the near-infrared wavelength range. Org Biomol Chem. 2011;9:4199–204.

    CAS 
    PubMed 

    Google Scholar 

  • Oomoto I, Suzuki-Hirano A, Umeshima H, Han YW, Yanagisawa H, Carlton P, et al. ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues. Nucl Acids Res. 2015;43:e126.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Chen J, Morihiro K, Fukui D, Guo L, Okamoto A. Live-cell sensing of telomerase activity by using hybridization-sensitive fluorescent oligonucleotide probes. ChemBioChem. 2020;21:1022–7.

    CAS 
    PubMed 

    Google Scholar 

  • Hrdlicka PJ, Babu BR, Sørensen MD, Harrit N, Wengel J. Multilabeled pyrene-functionalized 2’-amino-LNA probes for nucleic acid detection in homogeneous fluorescence assays. J Am Chem Soc. 2005;127:13293–9.

    CAS 
    PubMed 

    Google Scholar 

  • Asanuma H, Akahane M, Kondo N, Osawa T, Kato T, Kashida H. Quencher-free linear probe with multiple fluorophores on an acyclic scaffold. Chem Sci. 2012;3:3165–9.

    CAS 

    Google Scholar 

  • Ro JJ, Lee HJ, Kim BH. PyA-cluster system for the detection and imaging of miRNAs in living cells through double-three-way junction formation. Chem Commun. 2018;54:7471–4.

    CAS 

    Google Scholar 

  • Paige JS, Wu KY, Jaffrey SR. RNA mimics of green fluorescent protein. Science. 2011;333:642–6.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Paige JS, Nguyen-Duc T, Song W, Jaffrey SR. Fluorescence imaging of cellular metabolites with RNA. Science. 2012;335:1194.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Strack RL, Song W, Jaffrey SR. Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. Nat Protoc. 2014;9:146–55.

    CAS 
    PubMed 

    Google Scholar 

  • Song W, Strack RL, Jaffrey SR. Imaging bacterial protein expression using genetically encoded RNA sensors. Nat Methods. 2013;10:873–5.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kolpashchikov DM, Spelkov AA. Binary (split) light-up aptameric sensors. Angew Chem Int Ed. 2021;60:4988–99.

    CAS 

    Google Scholar 

  • Babendure JR, Adams SR, Tsien RY. Aptamers switch on fluorescence of triphenylmethane dyes. J Am Chem Soc. 2003;125:14716–17.

    CAS 
    PubMed 

    Google Scholar 

  • Sando S, Narita A, Hayami M, Aoyama Y. Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA. Chem Commun. 2008:3858–60.

  • Strack RL, Disney MD, Jaffrey SR. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat–containing RNA. Nat Methods. 2013;10:1219–24.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Filonov GS, Moon JD, Svensen N, Jaffrey SR. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J Am Chem Soc. 2014;136:16299–308.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dolgosheina EV, Jeng SCY, Panchapakesan SSS, Cojocaru R, Chen PSK, Wilson PD, et al. RNA Mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. ACS Chem Biol. 2014;9:2412–20.

    CAS 
    PubMed 

    Google Scholar 

  • Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, et al. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol. 2014;21:658–63.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Okuda M, Fourmy D, Yoshizawa S. Use of Baby Spinach and Broccoli for imaging of structured cellular RNAs. Nucl Acids Res. 2017;45:1404–15.

    CAS 
    PubMed 

    Google Scholar 

  • Autour A, Jeng SCY, Cawte AD, Abdolahzadeh A, Galli A, Panchapakesan SSS. David Rueda, Ryckelynck M, Unrau PJ. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells. Nat Commun. 2018;9:656.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Warner KD, Sjekloća L, Song W, Filonov GS, Jaffrey SR, Ferré-D’Amaré AR. A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nat Chem Biol. 2017;13:1195–201.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Song W, Filonov GS, Kim H, Hirsch M, Li X, Moon JD, et al. Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. Nat Chem Biol. 2017;13:1187–94.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yu Q, Shi J, Mudiyanselage APKKK, Wu R, Zhao B, Zhou M, et al. Genetically encoded RNA-based sensors for intracellular imaging of silver ions. Chem Commun. 2019;55:707–10.

    CAS 

    Google Scholar 

  • Gu Y, Huang LJ, Zhao W, Zhang TT, Cui MR, Yang XJ, et al. Living-cell microRNA imaging with self-assembling fragments of fluorescent protein-mimic RNA aptamer. ACS Sens. 2021;6:2339–47.

    CAS 
    PubMed 

    Google Scholar 

  • Sando S, Narita A, Aoyama Y. Light-up Hoechst–DNA aptamer Pair: generation of an aptamer-selective fluorophore from a conventional DNA-staining dye. ChemBioChem. 2007;8:1795–803.

    CAS 
    PubMed 

    Google Scholar 

  • Kato T, Shimada I, Kimura R, Hyuga M. Light-up fluorophore–DNA aptamer pair for label-free turn-on aptamer sensors. Chem Commun. 2016;52:4041–4.

    CAS 

    Google Scholar 

  • Wang H, Wang J, Sun N, Cheng H, Chen H, Pei R. Selection and characterization of malachite green aptamers for the development of light–up probes. ChemistrySelect. 2016;1:1571–4.

    CAS 

    Google Scholar 

  • Wang H, Wang J, Wang Q, Chen X, Liu M, Chen H, et al. Selection and characterization of dimethylindole red DNA aptamers for the development of light-up fluorescent probes. Talanta 2017;168:217–21.

    CAS 
    PubMed 

    Google Scholar 

  • Connelly RP, Madalozzo PF, Mordeson JE, Pratt AD, Gerasimova YV. Promiscuous dye binding by a light-up aptamer: application for label-free multi-wavelength biosensing. Chem Commun. 2021;57:3672–5.

    CAS 

    Google Scholar 

  • Lin S, Gao W, Tian Z, Yang C, Lu L, Mergny JL, et al. Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe. Chem Sci. 2015;6:4284–90.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lin S, Lua L, Liu JB, Liu C, Kang TS, Yang C, et al. A G-quadruplex-selective luminescent iridium(III) complex and its application by long lifetime. Biochim Biophys Acta. 2017;1861:1448–54.

    CAS 

    Google Scholar 

  • Thoa TTT, Minagawa N, Aigaki T, Ito Y, Uzawa T. Regulation of photosensitization processes by an RNA aptamer. Sci Rep. 2017;7:43272.

    PubMed 
    PubMed Central 

    Google Scholar 

  • Min I, Uzawa T, Serizawa T, Ito Y. “One stroke drawing” of poly(ribonucleic acids) with different aptamer functions for sensing probes. Polym J. 2021;53:667–75.

    CAS 

    Google Scholar 

  • Jani MS, Zou J, Veetil AT, Krishnan Y. A DNA-based fluorescent probe maps NOS3 activity with subcellular spatial resolution. Nat Chem Biol. 2020;660:660–6.

    Google Scholar 

  • Dirks RM, Pierce NA. Triggered amplification by hybridization chain reaction. PNAS 2004;101:15275–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Choi HMT, Chang JY, Trinh LA, Padilla JE, Fraser SE, Pierce NA. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat Biotechnol. 2010;28:1208–12.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Marrasa SAE, Bushkina Y, Tyagi S. High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules. PNAS. 2019;116:13921–6.

    Google Scholar 

  • Cheglakov Z, Cronin TM, He C, Weizmann Y. Live cell microRNA imaging using cascade hybridization reaction. J Am Chem Soc. 2015;137:6116–9.

    CAS 
    PubMed 

    Google Scholar 

  • Chen J, Yang HH, Yin W, Zhang Y, Ma Y, Chen D, et al. Metastable dumbbell probe-based hybridization chain reaction for sensitive and accurate imaging of intracellular-specific microRNAs in situ in living cells. Anal Chem. 2019;91:4625–31.

    CAS 
    PubMed 

    Google Scholar 

  • Yin P, Choi HMT, Calvert CR, Pierce NA. Programming biomolecular self-assembly pathways. Nat. 2008;451:318–22.

    CAS 

    Google Scholar 

  • Li B, Ellington AD, Chen X. Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucl Acids Res. 2011;39:e110.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wu C, Zhang SCL, Teng IT, Qiu L, Li J, Liu Y, et al. A Nonenzymatic hairpin DNA cascade reaction provides high signal gain of mRNA imaging inside live cells. J Am Chem Soc. 2015;137:4900–3.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mudiyanselage APKKK, Yu Q, Leon-Duque MA, Zhao B, Wu R, You M. Genetically encoded catalytic hairpin assembly for sensitive RNA imaging in live cells. J Am Chem Soc. 2018;140:8739–45.

    Google Scholar 

  • Wu H, Zhou WJ, Liu L, Fan Z, Tang H, Yu RQ, et al. In vivo mRNA imaging based on tripartite DNA probe mediated catalyzed hairpin assembly. Chem Commun. 2020;56:8782–5.

    CAS 

    Google Scholar 

  • Breaker RR, Joyce GF. A DNA enzyme that cleaves RNA. Chem Biol. 1994;1:223–9.

    CAS 
    PubMed 

    Google Scholar 

  • Wu P, Hwang K, Lan T, Lu Y. A DNAzyme-gold nanoparticle probe for uranyl ion in living cells. J Am Chem Soc. 2013;135:5254–7.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Young DD, Lively MO, Deiters A. Activation and deactivation of DNAzyme and antisense function with light for the photochemical regulation of gene expression in mammalian cells. J Am Chem Soc. 2010;132:6183–93.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zhou M, Liang X, Mochizuki T, Asanuma H. A light-driven DNA nanomachine for the efficient photoswitching of RNA digestion. Angew Chem Int Ed. 2010;49:2167–70.

    CAS 

    Google Scholar 

  • Hwang K, Wu P, Kim T, Lei L, Wang Y, Lu Y. Photocaged DNAzymes as a general method for sensing metal ions in living cells. Angew Chem Int Ed. 2014;53:13798–802.

    CAS 

    Google Scholar 

  • Yang C, Yin X, Huan SY, Chen L, Hu XX, Xiong MY, et al. Two-photon DNAzyme−gold nanoparticle probe for imaging intracellular metal ions. Anal Chem. 2018;90:3118–23.

    CAS 
    PubMed 

    Google Scholar 

  • Watanabe Y, Fujimoto K. Complete Photochemical Regulation of 8–17 DNAzyme activity by using reversible DNA photo-crosslinking. ChemBioChem. 2020;21:3244–8.

    CAS 
    PubMed 

    Google Scholar 

  • Liu J, Lu Y. Rational design of “Turn-On” allosteric DNAzyme catalytic beacons for aqueous mercury ions with ultrahigh sensitivity and selectivity. Angew Chem Int Ed. 2007;46:7587–90.

    CAS 

    Google Scholar 

  • Shimron S, Elbaz J, Henning A, Willner I. Ion-induced DNAzyme switches. Chem Commun. 2010;46:3250–2.

    CAS 

    Google Scholar 

  • Takezawa Y, Nakama T, Shionoya M. Enzymatic synthesis of Cu(II)-responsive deoxyribozymes through polymerase incorporation of artificial ligand-type nucleotides. J Am Chem Soc. 2019;141:19342–50.

    CAS 
    PubMed 

    Google Scholar 

  • Takezawa Y, Hu L, Nakama T, Shionoya M. Sharp switching of DNAzyme activity through the formation of a CuII-mediated carboxyimidazole base pair. Angew Chem Int Ed. 2020;59:21488–92.

    CAS 

    Google Scholar 

  • Nakama T, Takezawa Y, Sasaki D, Shionoya M. Allosteric regulation of DNAzyme activities through intrastrand transformation induced by Cu(II)-mediated artificial base pairing. J Am Chem Soc. 2020;142:10153–62.

    CAS 
    PubMed 

    Google Scholar 

  • Sando S, Narita A, Sasaki T, Aoyama Y. Locked TASC probes for homogeneous sensing of nucleic acids and imaging of fixed E. coli cells. Org Biomol Chem. 2005;3:1002–7.

    CAS 
    PubMed 

    Google Scholar 

  • Kolpashchikov DM. A binary deoxyribozyme for nucleic acid analysis. ChemBioChem. 2007;8:2039–42.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mokany E, Bone SM, Young PE, Doan TB, Todd AV. MNAzymes, a versatile new class of nucleic acid enzymes that can function as biosensors and molecular switches. J Am Chem Soc. 2010;132:1051–9.

    CAS 
    PubMed 

    Google Scholar 

  • Gerasimova YV, Cornett E, Kolpashchikov DM. RNA-cleaving deoxyribozyme sensor for nucleic acid analysis: the limit of detection. ChemBioChem. 2010;11:811–7.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hanpanich O, Oyanagi T, Shimada N, Maruyama A. Cationic copolymer-chaperoned DNAzyme sensor for microRNA detection. Biomaterials. 2019;225:119535.

    CAS 
    PubMed 

    Google Scholar 

  • Hanpanich O, Maruyama A. Cationic comb-type copolymer as an artificial chaperone. Polym J. 2019;51:935–43.

    CAS 

    Google Scholar 

  • Peng H, Li XF, Zhang H, Le XC. A microRNA-initiated DNAzyme motor operating in living cells. Nat Comm. 2017;8:14378.

    Google Scholar 

  • Wu Y, Huang J, Yang X, Yang Y, Quan K, Xie N, et al. Gold nanoparticle loaded split-DNAzyme probe for amplified miRNA detection in living cells. Anal Chem. 2017;89:8377–83.

    CAS 
    PubMed 

    Google Scholar 

  • Bakshi SF, Guz N, Zakharchenko A, Deng H, Tumanov AV, Woodworth CD, et al. Magnetic field-activated sensing of mRNA in living cells. J Am Chem Soc. 2017;139:12117–20.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wei J, Wang H, Wu Q, Gong X, Ma K, Liu X, et al. A smart, autocatalytic, DNAzyme biocircuit for in vivo, Amplified, MicroRNA Imaging. Angew Chem Int Ed. 2020;59:5965–71.

    CAS 

    Google Scholar 

  • Wang H, Chen Y, Wang H, Liu X, Zhou X, Wang F. DNAzyme-Loaded Metal–Organic Frameworks (MOFs) for Self-Sufficient Gene Therapy. Angew Chem Int Ed. 2019;58:7380–4.

    CAS 

    Google Scholar 

  • Xiao L, Gu C, Xiang Y. Orthogonal activation of RNA-cleaving DNAzymes in live cells by reactive oxygen species. Angew Chem Int Ed. 2019;58:14167–72.

    CAS 

    Google Scholar 

  • Banno A, Higashi S, Shibata A, Ikeda M. A stimuli-responsive DNAzyme displaying Boolean logic-gate responses. Chem Commun. 2019;55:1959–62.

    Google Scholar 

  • Wang Q, Tan K, Wang H, Shang J, Wan Y, Liu X, et al. Orthogonal demethylase-activated deoxyribozyme for intracellular imaging and gene regulation. J Am Chem Soc. 2021;143:6895–904.

    CAS 
    PubMed 

    Google Scholar 

  • Ebrahimi SB, Samanta D, Mirkin CA. DNA-based nanostructures for live-cell analysis. J Am Chem Soc. 2020;142:11343–56.

    CAS 
    PubMed 

    Google Scholar 

  • Wang DX, Wang J, Wang YX, Du YC, Huang Y, Tang AN, et al. DNA nanostructure-based nucleic acid probes: construction and biological applications. Chem Sci. 2021;12:7602–22.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fisher TL, Terhorst T, Cao X, Wagner RW. Intracellular disposition and metabolism of fluorescently-labled unmodified and modified oligouncleotides microijjected into mammalian cells. Nucleic Acids Res. 1993;21:3857–65.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Dong Y, Siegwart DJ, Anderson DG. Strategies, design, and chemistry in siRNA delivery systems. Adv Drug Deliv Rev. 2019;144:133–47.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Source link