Target‐Induced Catalytic Assembly of Y‐Shaped DNA and Its Application for In Situ Imaging of MicroRNAs

Xue, Chang; Zhang, Shuxin; Ouyang, Changhe; Chang, Dingran; Salena, Bruno J.; Li, Yingfu; Wu, Zai‐Sheng

doi:10.1002/ange.201804741

Cited by 19 publications

(12 citation statements)

References 67 publications

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“…Though these methods have made some progress, they failed the selective and accurate biosensing for some biological targets in a specific situation where the properties of targets and analogues (such as nucleic acids sequences) are too similar to be distinguished. For example, although a number of intracellular microRNAs (miRNAs) biosensors have been developed based on sequence complementarity of miRNAs and nucleic acid probes [8][9][10][11][12][13][14] , their detection accuracy for mature miRNAs is affected by the presence of its precursor (precursor microRNAs, abbreviated as pre-miRNAs) since the sequence of mature miR-NAs is also present in the precursors. Alternatively, considering the different length of mature miRNAs (19-23 nt) and pre-miRNAs (60-70 nt) 15 , a size-selective molecular strategy based on the size difference between targets and non-targets is promising.…”

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confidence: 99%

Size-selective molecular recognition based on a confined DNA molecular sieve using cavity-tunable framework nucleic acids

Peng

et al. 2020

Nat Commun

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Size selectivity is an important mechanism for molecular recognition based on the size difference between targets and non-targets. However, rational design of an artificial sizeselective molecular recognition system for biological targets in living cells remains challenging. Herein, we construct a DNA molecular sieve for size-selective molecular recognition to improve the biosensing selectivity in living cells. The system consists of functional nucleic acid probes (e.g., DNAzymes, aptamers and molecular beacons) encapsulated into the inner cavity of framework nucleic acid. Thus, small target molecules are able to enter the cavity for efficient molecular recognition, while large molecules are prohibited. The system not only effectively protect probes from nuclease degradation and nonspecific proteins binding, but also successfully realize size-selective discrimination between mature microRNA and precursor microRNA in living cells. Therefore, the DNA molecular sieve provides a simple, general, efficient and controllable approach for size-selective molecular recognition in biomedical studies and clinical diagnoses.

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confidence: 99%

Size-selective molecular recognition based on a confined DNA molecular sieve using cavity-tunable framework nucleic acids

Peng

et al. 2020

Nat Commun

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“…To date, many analytical methods have been reported for sensitive miRNA detection. − However, most of these methods are only suitable for the detection of miRNAs in buffer or extracted RNA samples. For direct visualization of intracellular miRNA, in situ imaging (ISI) technology and those methods derived from this technique are the most common pathways. − Because of the low target miRNA expression level, various amplification strategies based on enzymatic reactions, such as rolling circle amplification (RCA) − and strand displacement amplification (SDA), have been established for sensitive detection of intracellular miRNAs. In these methods, the cells are generally pretreated with paraformaldehyde to increase the penetration of the cell membrane, enabling enzymes and DNA probes to enter the cytoplasm.…”

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confidence: 99%

Biomineralized Metal–Organic Framework Nanoparticles Enable Enzymatic Rolling Circle Amplification in Living Cells for Ultrasensitive MicroRNA Imaging

Zhang

Nie

et al. 2019

Anal. Chem.

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The enzymatic amplification strategy in living cells faces challenges of highly efficient intracellular codelivery of amplification reagents including DNA polymerase. In this work, we develop biomineralized metal−organic framework nanoparticles (MOF NPs) as a carrier system for intracellular codelivery of ϕ29 DNA polymerase (ϕ29DP) and nucleic acid probes and realize a polymerization amplification reaction in living cells. A pH-sensitive biodegradable MOF NP of zeolitic imidazolate framework-8 (ZIF-8) is utilized to encapsulate ϕ29DP and adsorb nucleic acid probes. After uptake into cells, the encapsulated ϕ29DP and surface-adsorbed DNA probes are released and escaped from endolysosomes. In the presence of ϕ29DP and deoxyribonucleotide triphosphates (dNTPs), the intracellular miRNA-21 triggers a rolling circle amplification (RCA) reaction and the autonomous synthesized Mg 2+ -dependent DNAzyme cleaves the fluorogenic substrate, providing a readout fluorescence signal for the monitoring of miRNA-21. This is the first example of the intracellular RCA reaction in living cells. Therefore, the proposed method provides new opportunities for achieving enzymatic amplification reaction in living cells.

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“…The enzymatic amplification in ClickerFISH is based on rolling circle replication of short DNA circles (24,27,28,36). Three sets of clickable barcode primers and corresponding padlock probes (Supplementary Table S1) were designed to minimize non-specific complementarity using the NCBI’s BLAST Human transcripts program.…”

Section: Resultsmentioning

confidence: 99%

“…Among them, these RNA imaging included mRNA, microRNA and even base modification analysis, and provided the spatial location information in single cells. Additionally, some in situ imaging technologies such as single-molecule fluorescence in situ hybridization (smFISH) (22,23) and enzymatic DNA amplification-assisted FISH (24–29) have achieved single-molecule sensitivity based on signal amplification, and determined spatially resolved RNA copies in single cells. Despite the effectiveness, these methods can only detect RNA sequence of interest due to hybridization-assisted target recognition.…”

Section: Introductionmentioning

confidence: 99%

Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures

Chen

Bai

Cao

et al. 2019

Nucleic Acids Research

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Spatially resolved visualization of RNA processing and structures is important for better studying single-cell RNA function and landscape. However, currently available RNA imaging methods are limited to sequence analysis, and not capable of identifying RNA processing events and structures. Here, we developed click-encoded rolling FISH (ClickerFISH) for visualizing RNA polyadenylation and structures in single cells. In ClickerFISH, RNA 3′ polyadenylation tails, single-stranded and duplex regions are chemically labeled with different clickable DNA barcodes. These barcodes then initiate DNA rolling amplification, generating repetitive templates for FISH to image their subcellular distributions. Combined with single-molecule FISH, the proposed strategy can also obtain quantitative information of RNA of interest. Finally, we found that RNA poly(A) tailing and higher-order structures are spatially organized in a cell type-specific style with cell-to-cell heterogeneity. We also explored their spatiotemporal patterns during cell cycle stages, and revealed the highly dynamic organization especially in S phase. This method will help clarify the spatiotemporal architecture of RNA polyadenylation and structures.

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Target‐Induced Catalytic Assembly of Y‐Shaped DNA and Its Application for In Situ Imaging of MicroRNAs

Abstract: Supportinginformation and the ORCID identification number(s) for the author(s) of this article can be found under: https://doi.

Cited by 19 publications

References 67 publications

Size-selective molecular recognition based on a confined DNA molecular sieve using cavity-tunable framework nucleic acids

Size-selective molecular recognition based on a confined DNA molecular sieve using cavity-tunable framework nucleic acids

Biomineralized Metal–Organic Framework Nanoparticles Enable Enzymatic Rolling Circle Amplification in Living Cells for Ultrasensitive MicroRNA Imaging

Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures

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