Molecular beacon strategies for sensing purpose

Bidar, Negar; Amini, Mohammad; Oroojalian, Fatemeh; Baradaran, Behzad; Hosseini, Seyed Samad; Shahbazi, Mohammad‐Ali; Hashemzaei, Mahmoud; Mokhtarzadeh, Ahad; Hamblin, Michael R.; Guárdia, Miguel de la

doi:10.1016/j.trac.2020.116143

Cited by 45 publications

(34 citation statements)

References 147 publications

(176 reference statements)

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“…Various signalling labels are available to obtain MBs producing high signal-to-background ratios. These include inorganic materials, organic compounds [43], nanomaterials, metal complexes, conjugated polymers, superquenchers (SQs), and other materials exhibiting superior photophysical properties for sensing purpose [43][44][45].…”

Section: Molecular Beacon Design and Mechanismsmentioning

confidence: 99%

“…The application of the conventional stem-loop hairpin structure of MB probes, including fluorophore/quencher signalling pair, allows for measuring an instantaneous signal emission directly in solution, without removing unreacted MB molecules, in one single "mix-and-measure" step. MBbased sensing approaches can operate in the open-to signal or close-to signal configurations, depending on the design and the conformation of the MB probe [43]. The open-to signal configuration enables detecting the fluorescent signal related to the target molecule after linearising the stem-loop hairpin MB structure, thus defining turn-on biosensors.…”

Section: Molecular Beacons and Dna Origami In Biosensing: A Comparison And Peculiar Applicationsmentioning

confidence: 99%

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Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

2021

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Nucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

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Section: Molecular Beacon Design and Mechanismsmentioning

confidence: 99%

Section: Molecular Beacons and Dna Origami In Biosensing: A Comparison And Peculiar Applicationsmentioning

confidence: 99%

Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

2021

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“…Some of them show breakthrough detection ability. Most of these applications are focused on increasing the sensitivity itself, such as amplifying the target or amplifying the signal [ 3 , 4 , 5 , 6 , 7 ]. In particular, molecular beacons, consisting of DNA hairpins with a fluorescent label at one end and quenchers at the other end, are widely used because they obviate the requirement to label the target molecule.…”

Section: Introductionmentioning

confidence: 99%

Bead-Immobilized Multimodal Molecular Beacon-Equipped DNA Machinery for Specific RNA Target Detection: A Prototypical Molecular Nanobiosensor

Kim

Ahn

2021

Nanomaterials

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A variety of nanostructured diagnostic tools have been developed for the precise detection of known genetic variants. Molecular beacon systems are very promising tools due to their specific selectivity coupled with relatively lower cost and time requirements than existing molecular detection tools such as next generation sequencing or real-time PCR (polymerase chain reaction). However, they are prone to errors induced by secondary structure responses to environmental fluctuations, such as temperature and pH. Herein, we report a temperature-insensitive, bead-immobilized, molecular beacon-equipped novel DNA nanostructure for detection of cancer miRNA variants with the consideration of thermodynamics. This system consists of three parts: a molecular beacon for cancer-specific RNA capture, a stem body as a core template, and a single bead for solid-support. This DNA system was selectively bound to nanosized beads using avidin–biotin chemistry. Synthetic DNA nanostructures, designed based on the principle of fluorescence-resonance enhanced transfer, were effectively applied for in vitro cancer-specific RNA detection. Several parameters were optimized for higher performance, with a focus on thermodynamic stability. Theoretical issues regarding the secondary structure of a single molecular beacon and its combinatory forms were also studied. This study provides design guidelines for new sensing systems of miRNA variation for next-generation biotechnological applications.

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“…The fluorophore–quencher system has been widely used in biosensing fields, especially in target oligonucleotide detection [ 16 , 17 ]. The fluorophore is quenched internally at the beginning and is later restored when recognized and bound to its target molecule.…”

Section: Introductionmentioning

confidence: 99%

DNAzyme-Amplified Label-Free Biosensor for the Simple and Sensitive Detection of Pyrophosphatase

et al. 2021

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The level of pyrophosphatase (PPase) expression has been suggested as a potential biomarker of various cancers, and its prognostic value has been evaluated in patients suffering from lung cancer, colorectal cancer, and hyperthyroidism. However, the detection of PPase usually needs specific materials that require complicated, time-consuming reactions with restricted linear range and sensitivity, limiting their application in early clinical diagnosis. Herein, we developed a DNAzyme-based biosensor for the detection of PPase. In the presence of PPase, pyrophosphate (PPi) and Cu2+ ions released from the PPi–Cu2+–PPi complex induce the cleavage of the DNAzyme and the corresponding substrate. An apurinic/apyrimidinic (AP) site was elaborately designed within substrates that could encase the fluorophore 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND). The fluorescence of ATMND was initially quenched but restored when the DNAzyme/substrate complex was hydrolyzed with the release of ATMND. In this way, the PPase activity can be estimated by detecting the increased fluorescence of the released ATMND. Under optimized conditions, the activity of PPase could be analyzed at concentrations from 0.5 to 1000 mU, with the lowest detectable concentration being 0.5 mU. This work lays a foundation for developing a DNAzyme-amplified fluorescent biosensor with a high sensitivity, a wide linear range, and single-step operation for use as an easy diagnostic for PPase analysis.

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Molecular beacon strategies for sensing purpose

Cited by 45 publications

References 147 publications

Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

Bead-Immobilized Multimodal Molecular Beacon-Equipped DNA Machinery for Specific RNA Target Detection: A Prototypical Molecular Nanobiosensor

DNAzyme-Amplified Label-Free Biosensor for the Simple and Sensitive Detection of Pyrophosphatase

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