Combining padlock exponential rolling circle amplification with CoFe2O4 magnetic nanoparticles for microRNA detection by nanoelectrocatalysis without a substrate

Yu, Nan; Wang, Zhen; Wang, Chaochen; Han, Jing; Bu, Huaiyu

doi:10.1016/j.aca.2017.01.069

Cited by 51 publications

(15 citation statements)

References 43 publications

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“…By contrast, T4Rnl2 rarely sealed the RNA-splinted padlock probe regardless of the ATP concentration (Fig. 2A,B ), contrary to previous reports 17 – 20 . In addition, the yield of the circularized padlock probe (10 µM, 11.53 ± 1.6%; 400 µM, 8.06 ± 1.2%; and 1 mM, 8.17 ± 1.1%; Fig.…”

Section: Resultscontrasting

confidence: 92%

“…In our strategy, both the detection sensitivity and specificity depend on the sealing efficiency of the RNA-splinted padlock probe. Therefore, we first examined whether SplintR ligase can more efficiently seal an RNA-splinted padlock probe than T4Dnl and T4Rnl2, which were used previously 10 – 15 , 17 – 20 .…”

Section: Resultsmentioning

confidence: 99%

“…By contrast, T4Dnl and SplintR ligase could seal RNA-splinted padlock probes, and SplintR ligase was more suitable for this process. Therefore, we speculated that the results of previous reports using T4Rnl2 17 – 20 for RPRCA reflected background DNA synthesis from non-circularized padlock probes or contaminating DNA in the reaction, which frequently occurs in both RCA and WGA using phi29 DNA polymerase 3 , 25 , 31 . Incidentally, we could not perform the ligation experiment in the presence of 400–500 mM ATP as described previously 18 , 19 because ATP was not dissolved in the buffer at these concentrations.…”

Section: Discussionmentioning

confidence: 97%

“…T4Dnl can recognize an RNA-splinted padlock probe as a substrate by reducing the adenosine triphosphate (ATP) concentration in the reaction mixture to 10 µM 10 – 15 , although the sealing efficiency of T4Dnl is significantly lower for RNA-splinted padlock probes than for ‘DNA-splinted padlock probes’ 5 , 16 . T4Rnl2 can also efficiently recognize an RNA-splinted padlock probe as a substrate 17 – 20 . However, its activity has not been confirmed by other research groups 5 , 16 , 21 – 23 ; thus, the sealing activity of T4Rnl2 regarding RNA-splinted padlock probes remains controversial.…”

Section: Introductionmentioning

confidence: 99%

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RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection

Takahashi

Ohkawachi

Horio

et al. 2018

Sci Rep

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RNA-primed rolling circle amplification (RPRCA) is a useful laboratory method for RNA detection; however, the detection of RNA is limited by the lack of information on 3′-terminal sequences. We uncovered that conventional RPRCA using pre-circularized probes could potentially detect the internal sequence of target RNA molecules in combination with RNase H. However, the specificity for mRNA detection was low, presumably due to non-specific hybridization of non-target RNA with the circular probe. To overcome this technical problem, we developed a method for detecting a sequence of interest in target RNA molecules via RNase H-assisted RPRCA using padlocked probes. When padlock probes are hybridized to the target RNA molecule, they are converted to the circular form by SplintR ligase. Subsequently, RNase H creates nick sites only in the hybridized RNA sequence, and single-stranded DNA is finally synthesized from the nick site by phi29 DNA polymerase. This method could specifically detect at least 10 fmol of the target RNA molecule without reverse transcription. Moreover, this method detected GFP mRNA present in 10 ng of total RNA isolated from Escherichia coli without background DNA amplification. Therefore, this method can potentially detect almost all types of RNA molecules without reverse transcription and reveal full-length sequence information.

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Section: Resultscontrasting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection

Takahashi

Ohkawachi

Horio

et al. 2018

Sci Rep

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“…For example, miR-21, a potential biomarker of oral cancer [ 152 ], ovarian cancer [ 153 ], and other cancers can now be detected using nanozyme biosensors. An ultrasensitive electrochemical biosensor for miR-21 detection was designed based on a padlock exponential rolling circle amplification (P-ERCA) assay [ 154 ] and CoFe 2 O 4 magnetic nanoparticles (CoFe 2 O 4 MNPs) [ 155 ]. This assay is a highly specific and sensitive amplification method with a detection limit down to the zeptomole level designed with a padlock probe composed of a hybridization sequence to miRNA and a nicking target site for the endonuclease.…”

Section: Nanozymes and Their Potential Applications In Biosensingmentioning

confidence: 99%

Nanozymes—Hitting the Biosensing “Target”

Darland

Zhao

2021

Sensors

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Nanozymes are a class of artificial enzymes that have dimensions in the nanometer range and can be composed of simple metal and metal oxide nanoparticles, metal nanoclusters, dots (both quantum and carbon), nanotubes, nanowires, or multiple metal-organic frameworks (MOFs). They exhibit excellent catalytic activities with low cost, high operational robustness, and a stable shelf-life. More importantly, they are amenable to modifications that can change their surface structures and increase the range of their applications. There are three main classes of nanozymes including the peroxidase-like, the oxidase-like, and the antioxidant nanozymes. Each of these classes catalyzes a specific group of reactions. With the development of nanoscience and nanotechnology, the variety of applications for nanozymes in diverse fields has expanded dramatically, with the most popular applications in biosensing. Nanozyme-based novel biosensors have been designed to detect ions, small molecules, nucleic acids, proteins, and cancer cells. The current review focuses on the catalytic mechanism of nanozymes, their application in biosensing, and the identification of future directions for the field.

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Lawsone assisted preparation of carbon nanofibers for the selective detection of miRNA molecules

Sahtani

Aykut

Tanik

2021

J of Chemical Tech & Biotech

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BACKGROUND: microRNA (miRNA) molecules are considered as biomarkers and have promising future for early-stage cancer diagnosis. Lawsone (Law) enriched carbon nanofibers (CNFs) were prepared via electrospinning process for the selective miRNA detection. Anti-miRNA molecules were attached on the CNFs immobilized screen printed electrodes (SPE) and used for the detection of miRNA molecules by observing guanine oxidation signal via differential pulse voltammetry (DPV) method. Three different miRNA molecules including the target (miRNA), single-base mismatched (SM.miRNA) and non-complementary (NC. miRNA) were hybridized with the previously attached anti-miRNA molecules (with guanine [PolyT(G)] and without guanine [PolyT(I)]) on the CNFs immobilized SPE surfaces.RESULTS: Guanine oxidation signal decreased after the hybridization of miRNA with anti-miRNA molecules on CNF immobilized SPE surfaces. Guanine oxidation signal was not detected on the PolyT(I) attached samples, but the existence of guanine oxidation signal was clear detected after the addition of miRNA molecules on the previously attached PolyT(I). Because no hybridization of anti-miRNA molecules with the non-complementary miRNA (NC.miRNA) molecules occurred, the guanine oxidation signal was not significantly decreased after the interaction of NC.miRNA with the attached PolyT(G). Since there was no hybridization between the NC.miRNA molecules with the attached PolyT(I) on the SPEs, weak guanine peaks were detected at PolyT(I)-NC.miRNA samples as a result of the existence of residual NC.miRNA molecules on SPE after washing. CONCLUSIONS: The measurement results confirm the enhanced selectivity of the miRNA molecules by using CNFs with SPEs and the developed biosensory system could be used to detect the specific RNA molecules.

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Combining padlock exponential rolling circle amplification with CoFe2O4 magnetic nanoparticles for microRNA detection by nanoelectrocatalysis without a substrate

Cited by 51 publications

References 43 publications

RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection

RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection

Nanozymes—Hitting the Biosensing “Target”

Lawsone assisted preparation of carbon nanofibers for the selective detection of miRNA molecules

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