A polycation-chaperoned in-stem molecular beacon system

Asanuma, Hiroyuki; Osawa, Takuya; Kashida, Hiromu; Fujii, Tomoyuki; Liang, Xingguo; Niwa, Kosuke; Yoshida, Yasuko; Shimada, Noritomo; Maruyama, Atsushi

doi:10.1039/c2cc16812j

Cited by 32 publications

(24 citation statements)

References 30 publications

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“…The probe, however, was able to produce an S/N ratio of only ~40%. Asanuma et al improved the in-stem MB probe by incorporating three fluorophore/quencher pairs in stem portion of an MB probe [139]. In the presence of poly(L-lysine)-graft-dextran, an impressive S/N ratio of 570 was achieved.…”

Section: Recent Variations Of Mb Probesmentioning

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: Recent Variations Of Mb Probesmentioning

confidence: 99%

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Kolpashchikov

2012

Scientifica

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“…Encouraged by efficient fluorescence quenching observed for the PH/PN pair, which can potentially serve as a good combination of fluorophore and quencher molecules, we designed MB probes with the PH/PN pair in the stem region (Figure a) . The MB probes containing PH/PN were prepared through enzymatic ligation between one strand containing PH and the other strand containing PN in the presence of a template strand (see the Supporting Information).…”

Section: Resultsmentioning

confidence: 99%

“…PH was introduced into the oligopyrimidine sequence of the 6‐mer stem region to avoid electron‐transfer quenching by the purine bases in an open form . In a closed form of the MB probe, very weak fluorescence was detected (Figure b) . Upon addition of the 16‐mer target oligonucleotide strand, which was complementary to the loop regions of the MB probe, fluorescence signal recovery was observed; this means that the conformation of the MB probe was converted from closed to open, and the PH/PN pair could indeed serve as the fluorophore and quencher pair.…”

Section: Resultsmentioning

confidence: 99%

“…As for the quenching mechanism, temporal separation between the fluorophore and quencher by end‐fraying, and a change in the relative orientation of these molecules can cause less quenching; this results in an increased background emission. To overcome these negative influences, in‐stem MBs, in which the fluorophore and quencher molecules were embedded in a stem region to limit movement of the molecules and force the molecules close together, was developed . The improvement of the signal enhancement from a closed to an open form, through the appropriate use of highly emissive fluorophores and efficient quencher molecules, is essential and there is still room for improving the intrinsic fluorescence response.…”

Section: Introductionmentioning

confidence: 99%

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Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex

Takada

Ishino

Takata

et al. 2018

Chemistry A European J

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The preparation of homo- and heterocomplexes composed of the parent perylene diimide (PH) and pyrrolidine-substituted perylene diimide (PN) in DNA and rapid electron transfer in these complexes, which has been analyzed by steady-state fluorescence and femtosecond transient absorption measurements, have been demonstrated. The DNA molecules possessing PH and PN were prepared through a recently developed method that involved the reaction of enzymatically generated abasic sites with the amino groups of the perylene diimide molecules, through which these molecules can be incorporated as base surrogates within the DNA base stack. Melting temperature analysis showed that the PH and PN monomers, and their homo- and heterodimers, contribute to the stabilization of the DNA duplex, and is comparable to that of natural base pairs. Fluorescence measurements showed that PH in a single-stranded oligopyrimidine showed a strong fluorescence, whereas the fluorescence of PH was completely quenched upon pairing with PN (PH/PN) through duplex formation. The transient absorption measurements showed that a rapid electron-transfer reaction in the stacked PH/PN heterodimer occurred on a sub-picosecond timescale, which allowed highly efficient fluorescence quenching. The PH/PN pair, which served as a fluorophore and quencher, were utilized to design molecular beacon probes with a high signal/noise ratio. The PH/PN pair was also capable of forming a stable, stacked dimer structure and induced rapid electron transfer that could serve as a good signal reporter for fluorescent nucleic acid detection.

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“…The S/B ratio drastically improves as the number of E-Q is increased; the ISMB with three E-Q pairs has an S/B ratio of as high as over 500 in the presence of cationic graft copolymer (PLL-g-Dex) as shown in Figure 4B. 23 This ISMB design can be applied to other fluorophores. For example, we have synthesized an ISMB tethering Cy3 (Y 4 and Y D in Figure 3A).…”

mentioning

confidence: 93%

Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions

Kashida

Asanuma

2016

Bulletin of the Chemical Society of Japan

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. Currently his research interests are focused on the development of functional artificial oligonucleotides with acyclic scaffolds, such as, 1) photoregulation of DNA and RNA functions, 2) design of new XNAs, 3) new fluorescent probes for practical applications, 4) design of nucleic acid-based drugs, and 5) assembled functional molecules. AbstractThe authors have developed various kinds of pseudo base pairs using a D-threoninol scaffold. Although the chemical structures of the pseudo base pairs are much different from natural nucleobases, they can mimic supramolecular properties of natural base pairs. Moreover, modified DNA can possess various functions that cannot be achieved by natural nucleic acids, such as fluorescent switchability, photocrosslinking, insulating and emission color change. These pseudo base pairs can be used to prepare various functional nanomaterials. In the present account, we summarize our recent work on pseudo base pairs, focusing on molecular designs and functions.

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A polycation-chaperoned in-stem molecular beacon system

Cited by 32 publications

References 30 publications

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex

Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions

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