In‐Stem Molecular Beacon Containing a Pseudo Base Pair of Threoninol Nucleotides for the Removal of Background Emission

Kashida, Hiromu; Takatsu, Tomohiko; Fujii, Tomoyuki; Sekiguchi, Koji; Liang, Xingguo; Niwa, Kosuke; Takase, Tomokazu; Yoshida, Yasuko; Asanuma, Hiroyuki

doi:10.1002/anie.200902367

Cited by 70 publications

(32 citation statements)

References 41 publications

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“…A possible advantage of DMB design over conventional MB probe might be the close dislocation of a fluorophore and a quencher, which potentially may result in an even more efficient quenching. DMB design may appear to produce efficient quenching if it uses nucleotides with a fluorophore and a quencher directly attached to deoxyribose, such as developed earlier by Asanuma [110, 111] and colleagues for in-stem MB probes (see Figure 9(b) below). The hybridization kinetics of DMB probe, however, was slower than that of the traditional MB probe.…”

Section: Challengesmentioning

confidence: 99%

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Kolpashchikov

2012

Scientifica

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Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.

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Section: Challengesmentioning

confidence: 99%

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Kolpashchikov

2012

Scientifica

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“…DNA with intrastrand and interstrand dimers mainly of pyrene and perylene exhibit strong excimer fluorescence [11][12][13][14][15] and can also be applied in molecular beacons. [16][17][18][19] However, the excitation of pyrene requires highenergy UV light, a circumstance that limits the bioanalytic and imaging applications significantly. Recently, we reported that the excitation of perylene bisimide pairs at 505 nm yields an excimer-type shift of the fluorescence by ca.…”

Section: Introductionmentioning

confidence: 99%

Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging

et al. 2010

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The chromophore of thiazole orange (TO) and its derivative TO3 were incorporated synthetically as base surrogates into oligonucleotides using automated phosphoramidite chemistry. In comparison to TO, the TO3 chromophore contains an extended carbomethine bridge that shifts the absorption and emission significantly to the red. (S)-1-Aminopropane-2,3-diol served as an acyclic linker between the phosphodiesters. This linker was attached either to the quinoline or the thiazole nitrogen of the TO and TO3 dyes. The optical properties of TO and TO3 were studied in different DNA base environments and with different opposite bases. Both dyes as fluorescent DNA base substitutions show a brightness that is

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“…In this design, threoninol nucleotides attached to a fluorophore and a quencher are incorporated into the stem region as pseudo base pairs (Figure 5A). 71 In the absence of target DNA, the fluorophore and quencher are stacked together in the middle of the stem region of the closed beacon, and background fluorescence is greatly suppressed as a result of the close stacking. In contrast, the presence of target generates strong emission from the intercalated fluorophore.…”

Section: Rationally Designed Molecular Beaconsmentioning

confidence: 99%

Rationally designed molecular beacons for bioanalytical and biomedical applications

et al. 2015

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Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of target, dsDNA probes can report the presence of a specific target through hybridization or specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.

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In‐Stem Molecular Beacon Containing a Pseudo Base Pair of Threoninol Nucleotides for the Removal of Background Emission

Cited by 70 publications

References 41 publications

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging

Rationally designed molecular beacons for bioanalytical and biomedical applications

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