Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly

Liu, Meng; Zhang, Wenqing; Zhang, Qiang; Brennan, John D.; Yingfu, Li

doi:10.1002/anie.201503182

Cited by 64 publications

(48 citation statements)

References 63 publications

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“…Moreover, Li et al. presented a tandem reaction‐coupled hyperbranched RCA using a DNA aptamer‐blocked preprimer for the detection of PDGF . The recognition of a target by an aptamer induces the release of preprimer, which can be digested by phi29 DNA polymerase into a mature primer for hyperbranched RCA.…”

Section: Rca With Functional Nucleic Acidsmentioning

confidence: 99%

Circular Nucleic Acids: Discovery, Functions and Applications

Mohammed-Elsabagh

Paczkowski

et al. 2020

ChemBioChem

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acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topologycontrolled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.[a] Dr.

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Section: Rca With Functional Nucleic Acidsmentioning

confidence: 99%

Circular Nucleic Acids: Discovery, Functions and Applications

Mohammed-Elsabagh

Paczkowski

et al. 2020

ChemBioChem

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“…It can be performed at room temperature, requires minimal reagents (a linear and circular primer and one processing enzyme) and is compatible with many types of assay outputs . Our groups have reported on several methods to modulate RCA using a protein target, including: integration of a protein‐binding aptamer into a circular template to modulate RCA; binding of a protein to release an aptamer‐primer conjugate from reduced graphene oxide (rGO) to initiate RCA; using an aptamer to inhibit a linear primer from being extended along a circular template until target binds to release the aptamer; and use of protein‐binding DNAzymes that can release a DNA primer upon catalytic cleavage of an embedded ribonucleic acid to initiate RCA . While such systems could often be integrated into paper‐based POC devices, the assays still required multiple steps and expensive reagents such as rGO or doubly‐labelled DNAzyme species, or addition of labile reagents such as hemin or peroxide to generate a signal.…”

Section: Introductionmentioning

confidence: 99%

Protein‐Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer‐Containing DNA Primer

Bialy

Ali

et al. 2020

Chemistry A European J

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We report am ethodt od etect proteins via suppression of rolling circle amplification (RCA) by using an appropriate aptamer as the linear primer (denoted as an aptaprimer) to initiate RCA. In the absence of ap rotein target, the aptaprimer is free to initiate RCA, which can produce long DNA products that are detected via binding of af luorescent intercalating dye. Introduction of at arget causes the primer region within the aptamer to become unavailable for binding to the circulart emplate, inhibiting RCA. Using SYBR Gold or QuantiFluor dyes as fluorescent probest ob ind to the RCA reaction product, it is possible to produce ag eneric protein-modulatedR CA assay system that does not require fluorophore-or biotin-modified DNA species, substantially reducing complexitya nd cost of reagents. Based on this modulation of RCA, we demonstrate the ability to produce both solution and paper-based assays for rapid and quantitative detection of proteins including platelet derived growth factor and thrombin.[a] R.

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“…According to previous reports 39 , it seems that the 3′ → 5′ exonuclease activity of Phi29 DNA polymerase can work on single-stranded DNA but not on double-stranded DNA. In practical applications, however, it is possible that the 3′-tail may self-fold into intramolecular stem-loop structures.…”

Section: Resultsmentioning

confidence: 84%

Dual functional Phi29 DNA polymerase-triggered exponential rolling circle amplification for sequence-specific detection of target DNA embedded in long-stranded genomic DNA

Zhang

et al. 2017

Sci Rep

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An exonucleolytic digestion-assisted exponential rolling circle amplification (RCA) strategy was developed for sensitive and sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Herein, Phi29 DNA polymerase plays two important roles as exonuclease and polymerase. Long-stranded genomic DNAs can be broken into small DNA fragments after ultrasonication. The fragments that contain target DNA, hybridize with a linear padlock probe to trigger the formation of a circular RCA template. The tails protruding from the 3′-end of the target DNA sequences are then digested by the 3′ → 5′ exonuclease activity of Phi29 DNA polymerase even if they fold into a double-stranded structure. The digested DNA fragments can then initiate subsequent RCA reaction. RCA products, which are designed to fold into G-quadruplex structures, exponentially accumulate when appropriate nicking endonuclease recognition sites are introduced rationally into the RCA template. This method is demonstrated to work well for real genomic DNA detection using human pathogen Cryptococcus neoformans as a model. In addition, this work has two other important discoveries: First, the presence of a 3′-tail can protect the RCA primer from degradation by Phi29 DNA polymerase. Second, 3′ → 5′ exonucleolytic activity of Phi29 DNA polymerase can work for both single- and double-stranded DNA.

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Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly

Cited by 64 publications

References 63 publications

Circular Nucleic Acids: Discovery, Functions and Applications

Circular Nucleic Acids: Discovery, Functions and Applications

Protein‐Mediated Suppression of Rolling Circle Amplification for Biosensing with an Aptamer‐Containing DNA Primer

Dual functional Phi29 DNA polymerase-triggered exponential rolling circle amplification for sequence-specific detection of target DNA embedded in long-stranded genomic DNA

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