Long Non-Coding RNA Detection Based on Multi-Probe-Induced Rolling Circle Amplification for Hepatocellular Carcinoma Early Diagnosis

Yao, Yanheng; Duan, Chengjie; Chen, Yan; Hou, Zhiqiang; Cheng, Wenting; Li, Dayong; Wang, Zhongyun; Xiang, Yang

doi:10.1021/acs.analchem.2c04594

Cited by 10 publications

(15 citation statements)

References 24 publications

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“…Polymerization and isomerization cyclic amplification (PICA) is an intramolecular polymerization that integrates primer with template within one single-strand DNA and fulfills the self-expansion in an autonomous manner with repetitive sequences. , Compared with traditional DNA amplification approaches, such as polymerase chain reaction (PCR), rolling circle amplification (RCA), and hybridization chain reaction (HCR), the PICA avoids the stoichiometric ratio between template and primer and false cascading amplification, holding a simple-designed way to generate long ssDNA for decorating substantial signal probes and providing a possibility to combine with other amplifying technologies for constructing a highly effective target conversion efficiency detection system.…”

Section: Introductionmentioning

confidence: 99%

Metal Porphyrin Complex Combined with Polymerization and Isomerization Cyclic Amplification for a Sensitive Photoelectrochemical Assay

et al. 2023

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5,10,15,-21H,23H-porphine (TPAPP) possesses good light-harvesting ability and photoelectrochemical (PEC) cathode response signal; however, the disadvantages of easy stacking and weak hydrophilicity limit its application as a signal probe in PEC biosensors. Based on these, we prepared a Fe 3+ and Cu 2+ co-coordinating photoactive material (TPAPP-Fe/Cu) with horseradish peroxidase (HRP)-like activity. The metal ions in the porphyrin center not only enabled the directional flow of photogenerated electrons between electron-rich porphyrin and positive metal ions within inner-/intermolecular layers but also accelerated electron transfer through a synergistic redox reaction of Fe(III)/Fe(II) and Cu(II)/Cu(I) as well as rapid generation of superoxide anion radicals (O 2 −• ) by mimicking catalytically produced and dissolved oxygen, thereby providing the desired cathode photoactive material with extremely high photoelectric conversion efficiency. Accordingly, by combining with toehold-mediated strand displacement (TSD)-induced single cycle and polymerization and isomerization cyclic amplification (PICA), an ultrasensitive PEC biosensor was constructed for the detection of colon cancer-related miRNA-182-5p. The ultratrace target could be converted to abundant output DNA by TSD possessing the desirable amplifying ability to trigger PICA for forming long ssDNA with repetitive sequences, thus decorating substantial TPAPP-Fe/Cu-labeled DNA signal probes for producing high PEC photocurrent. Meanwhile, the Mn(III) mesotetraphenylporphine chloride (MnPP) was embedded in dsDNA to further exhibit a sensitization effect toward TPAPP-Fe/Cu and an acceleration effect analogous to that of metal ions in the porphyrin center above. As a result, the proposed biosensor displayed a detection limit as low as 0.2 fM, facilitating the development of high-performance biosensors and showing great potential in early clinical diagnosis.

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Section: Introductionmentioning

confidence: 99%

Metal Porphyrin Complex Combined with Polymerization and Isomerization Cyclic Amplification for a Sensitive Photoelectrochemical Assay

et al. 2023

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“…POCT methods typically employ isothermal amplification to eliminate the need for complex thermal cycling procedures. , This includes techniques such as rolling circle amplification (RCA), − strand displacement amplification (SDA), , recombinase polymerase amplification (RPA), and loop-mediated isothermal amplification (LAMP). − Direct staining of isothermally amplified products with dyes is sufficiently sensitive but may fall short on specificity due to the nonspecific nature of dye staining on nucleic acids. , Numerous reports have combined isothermal amplification with CRISPR/Cas to implement high sensitivity and specificity simultaneously by harvesting the sequence-specific capability of Cas endonuclease, which, however, necessitates the introduction of additional enzymes, increasing the cost and complexity. − …”

Section: Introductionmentioning

confidence: 99%

Precise Detection of Viral RNA by Programming Multiplex Rolling Circle Amplification and Strand Displacement

Wang,

Ma,

et al. 2023

Anal. Chem.

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Detection of viral infections (e.g., SARS-CoV-2) with high precision is critical to disease control and treatment. There is an urgent need to develop point-of-care detection methods to complement the gold standard laboratory-based PCR assay with comparable sensitivity and specificity. Herein, we developed a method termed mCAD to achieve ultraspecific point-of-care detection of SARS-CoV-2 RNA while maintaining high sensitivity by programming multiplex rolling circle amplification and toehold-mediated strand displacement reactions. RCA offers sufficient amplification of RNA targets for subsequent detection. Most importantly, a multilayer of detection specificity is implemented into mCAD via sequence-specific hybridization of nucleic acids across serial steps of this protocol to fully eliminate potential false-positive detections. Using mCAD, we demonstrated a highly specific, sensitive, and convenient visual detection of SARS-CoV-2 RNA from both synthetic and clinical samples, exhibiting performance comparable to qPCR. We envision that mCAD will find its broad applications in clinical prospects for nucleic acid detections readily beyond SARS-CoV-2 RNA.

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“…10,11 LncRNAs have been recognized as both non-invasive cancer-ous biomarkers and promising therapeutic targets. 12,13 Accordingly, sensitive detection of lncRNA is of vital importance for early clinical diagnosis, lncRNA-targeted treatment, and prognosis monitoring of tumors.…”

mentioning

confidence: 99%

“…Long non-coding RNAs (lncRNAs) with a sequence of longer than 200 nt play vital regulatory functions in diverse cellular and physiological processes, including cell differentiation, chromatin remodeling, post-transcriptional regulation, and epigenetic control of gene expression. , Abnormal expression of lncRNAs is linked to various diseases, such as type-2 diabetes mellitus, cardiomyopathy, and cancers (e.g., hepatocellular carcinoma, breast, cervical, and prostate cancers). − In particular, lncRNAs act as key regulators involved in various biological processes of cancers, including tumor formation, progression, proliferation, invasion, metastasis, and drug resistance . For example, the lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) sequesters miRNAs by miRNA response elements (MREs) located in the MALAT1 sequence, alleviating the suppressive effect of tumor suppressor miRNAs (TSmiRs) on oncogenic targets to promote proliferation and invasion of tumor cells. , Moreover, lncRNAs exhibit good resistance to RNase digestion and circulate in body fluids with higher stability (e.g., half-life time of 9–12 h for MALAT1). , LncRNAs have been recognized as both non-invasive cancerous biomarkers and promising therapeutic targets. , Accordingly, sensitive detection of lncRNA is of vital importance for early clinical diagnosis, lncRNA-targeted treatment, and prognosis monitoring of tumors.…”

mentioning

confidence: 99%

Corn-Based Fluorescent Light-Up Biosensors with Improved Signal-to-Background Ratio for Label-Free Detection of Long Noncoding RNAs

et al. 2023

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Long noncoding RNAs (lncRNAs) play pivotal roles in multifarious physiological and pathological processes, and their aberrant expression may disturb the normal regulatory network of gene expression to induce diverse human diseases. Herein, we construct a fluorescent light-up biosensor with a low background for label-free detection of lncRNAs by coupling duplex-specific nuclease (DSN)-assisted target recycling amplification with transcription-driven synthesis of fluorogenic RNA aptamer-Corns. We design two linear probes, including a capture probe for initiating a cyclic cleavage reaction and a linear template for transcribing RNA aptamer-Corn. Target lncRNA is recognized by capture probes assembled on magnetic bead (MB) surfaces to trigger a DSN-assisted cyclic cleavage reaction, releasing abundant T7 promoter sequences. After magnetic separation, free T7 promoter hybridizes with a linear template to induce efficient transcription amplification with the assistance of T7 RNA polymerase, producing numerous fluorogenic RNA aptamer-Corns that can light up small-molecule fluorogens 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO). Notably, the introduction of MBs facilitates both the separation of cleaved capture probes and the enrichment/isolation of target lncRNAs from the complex biological matrix. Benefiting from the high efficiency of DSN/T7 RNA polymerase-mediated cascade amplification and high signal-to-background ratio of the Corn–DFHO complex, this biosensor is capable of sensitively quantifying lncRNA with a detection limit of 31.98 aM. Moreover, it can precisely quantify lncRNA at the single-cell level and even in complex biological samples, and it can differentiate tumor cells from normal cells. Importantly, this Corn-based biosensor is readily extended to detect other lncRNAs by altering capture probe sequences, opening a new avenue for molecular diagnosis.

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Long Non-Coding RNA Detection Based on Multi-Probe-Induced Rolling Circle Amplification for Hepatocellular Carcinoma Early Diagnosis

Cited by 10 publications

References 24 publications

Metal Porphyrin Complex Combined with Polymerization and Isomerization Cyclic Amplification for a Sensitive Photoelectrochemical Assay

Metal Porphyrin Complex Combined with Polymerization and Isomerization Cyclic Amplification for a Sensitive Photoelectrochemical Assay

Precise Detection of Viral RNA by Programming Multiplex Rolling Circle Amplification and Strand Displacement

Corn-Based Fluorescent Light-Up Biosensors with Improved Signal-to-Background Ratio for Label-Free Detection of Long Noncoding RNAs

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