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Molecular Beacons With and Without Quenchers

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Handbook of Chemical Biology of Nucleic Acids

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Abstract

Modified nucleic acids have a wide range of applications in many areas of biochemistry. In particular, fluorescence-based nucleic acid systems have been studied extensively for their implementation in molecular biology as platforms for disease diagnosis. A hybridization probe is a fluorescent oligonucleotide used in DNA analysis, operating through sequence-specific complementary binding of a short synthetic oligonucleotide containing a fluorescent tag. Such fluorescent oligonucleotides play important roles in single-nucleotide polymorphism (SNP) typing, allowing both quantitative and qualitative analyses. Among them, stem–loop oligonucleotide probes have been developed to improve the specificity and selectivity toward target DNA. A molecular beacon (MB), a representative oligonucleotide probe having a stem–loop structure containing fluorescent and quencher units, is a probe used in biomolecular recognition. MB-based assays are fast, simple, and inexpensive and they enable real-time monitoring of nucleic acid responses in vivo and in vitro. Modifications of the structures and functions of MBs can lead to improved performance. For example, quencher-free molecular beacons (QF-MBs) are MBs, in which the quenching agent has been removed. Despite the absence of a quencher, QF-MBs can also identify specific target DNAs with high selectivity and sensitivity. MB and QF-MB probes have been applied widely in various fields, including SNP typing, monitoring of polymerase chain reactions (PCR), real-time detection of DNA–RNA hybridization in living cells, DNA mutation analysis, and disease diagnosis, including point-of-care (POC) testing.

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Authors and Affiliations

  1. Bioneer, Daejeon, Republic of Korea

    SueJin Lee & Byeang Hyean Kim

Authors
  1. SueJin Lee
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  2. Byeang Hyean Kim
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Correspondence to Byeang Hyean Kim .

Editor information

Editors and Affiliations

  1. Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan

    Naoki Sugimoto

Section Editor information

  1. Xiamen University, Xiamen, China

    Chaoyong Yang

  2. Institute of Molecular Medicine, Shanghai Jiao Tong University, Shanghai, China

    Chaoyong Yang

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Lee, S., Kim, B.H. (2022). Molecular Beacons With and Without Quenchers. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids. Springer, Singapore. https://doi.org/10.1007/978-981-16-1313-5_59-1

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  • DOI: https://doi.org/10.1007/978-981-16-1313-5_59-1

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  • Print ISBN: 978-981-16-1313-5

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