An efficient localized catalytic hairpin assembly-based DNA nanomachine for miRNA-21 imaging in living cells. 2021

Juan Wu, and Yonghui Tian, and Lu He, and Jing Zhang, and Zhijun Huang, and Zewei Luo, and Yixiang Duan
Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, Shaanxi, P.R. China. zwluo@nwu.edu.cn yduan@nwu.edu.cn.

As an enzyme-free isothermal amplification strategy, catalytic hairpin assembly (CHA) is a very promising method for cell imaging. However, the practical application of CHA on intracellular miRNA imaging is limited by slow kinetics, insufficient amplification efficiency and strong interference in living cells. Herein, a localized catalytic hairpin assembly-based DNA nanomachine (LCHA nanomachine) was developed for the rapid, efficient and reliable fluorescence resonance energy transformation (FRET) imaging of miRNA-21 in living cells. The nanomachine was simply constructed by a one-step self-assembly process of a stator strand, a pair of hairpin probes from CHA and an AS1411 aptamer. Benefiting from the spatial-confinement effect, a pair of hairpin probes with high collision frequency was rapidly and efficiently assembled using miRNA-21 as the catalyst on a stator strand in every nanomachine. Compared with the free-CHA nanomachine, the LCHA nanomachine shortened the reaction time by 4.5-fold for reaching a plateau and significant improved the sensitivity by 7.6-fold for miRNA-21 detection in vitro. Importantly, the nanomachine was successfully applied for miRNA-21 imaging in living cells. With the assistance of an AS1411 aptamer and stator strand, the pair of hairpin probes with the ratio of 1 : 1 synchronously transported into a co-site of the cytoplasm, which ensures efficient imaging of trace miRNA-21. The signal output of the ratio of 6-carboxy-fluorescein (FAM) to tetramethyl rhodamine (TAMRA) intensities guaranteed reliability through avoiding the interference from different amounts of the nanomachine that enters into cells. Notably, the nanomachine can distinguish the miRNA-21 expression level in different kinds of cancer cells. By virtue of the advantages of simplicity, efficiency and reliability, the proposed strategy provides a powerful method for exploring the functions of miRNA and diagnosis of disease.

UI MeSH Term Description Entries
D002384 Catalysis The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction. Catalyses
D015203 Reproducibility of Results The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results. Reliability and Validity,Reliability of Result,Reproducibility Of Result,Reproducibility of Finding,Validity of Result,Validity of Results,Face Validity,Reliability (Epidemiology),Reliability of Results,Reproducibility of Findings,Test-Retest Reliability,Validity (Epidemiology),Finding Reproducibilities,Finding Reproducibility,Of Result, Reproducibility,Of Results, Reproducibility,Reliabilities, Test-Retest,Reliability, Test-Retest,Result Reliabilities,Result Reliability,Result Validities,Result Validity,Result, Reproducibility Of,Results, Reproducibility Of,Test Retest Reliability,Validity and Reliability,Validity, Face
D015374 Biosensing Techniques Any of a variety of procedures which use biomolecular probes to measure the presence or concentration of biological molecules, biological structures, microorganisms, etc., by translating a biochemical interaction at the probe surface into a quantifiable physical signal. Bioprobes,Biosensors,Electrodes, Enzyme,Biosensing Technics,Bioprobe,Biosensing Technic,Biosensing Technique,Biosensor,Electrode, Enzyme,Enzyme Electrode,Enzyme Electrodes,Technic, Biosensing,Technics, Biosensing,Technique, Biosensing,Techniques, Biosensing
D021881 DNA, Catalytic Molecules of DNA that possess enzymatic activity. Catalytic DNA,Deoxyribozymes,DNAzyme,DNAzymes,Deoxyribozyme
D035683 MicroRNAs Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing. RNA, Small Temporal,Small Temporal RNA,miRNA,stRNA,Micro RNA,MicroRNA,Primary MicroRNA,Primary miRNA,miRNAs,pre-miRNA,pri-miRNA,MicroRNA, Primary,RNA, Micro,Temporal RNA, Small,miRNA, Primary,pre miRNA,pri miRNA

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