Fluorescence quenching properties of multiple pyrene-modified RNAs

Maie, Kenji; Nakamura, Mitsunobu; Takada, Tadao; Yamana, Kazushige

doi:10.1016/j.bmc.2009.05.074

Cited by 11 publications

(3 citation statements)

References 46 publications

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“…The quantum yield of P6x / P6y involving six pyrenes stacked with each other was 0.05, which was 17-fold greater than pyrene monomer emission from an interstrand-wedged motif. This quantum yield is almost comparable with those of pyrene cluster reported by other groups. , Thus, it can be concluded that the cluster motif is suitable for the maximization of excimer emission of pyrene.…”

Section: Resultssupporting

confidence: 88%

Accumulation of Fluorophores into DNA Duplexes To Mimic the Properties of Quantum Dots

et al. 2010

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By using perylene and pyrene as fluorophores, we have designed various fluorophore assemblies that mimic inorganic quantum dots in showing a high emission intensity, a large Stokes' shift, and a modulated emission maximum. For this purpose, we utilized two kinds of duplex motifs with D-threoninols as scaffolds: cluster and interstrand-wedged motifs. In the cluster motif, fluorophores are introduced into both strands to produce tentative pseudo-"base-pairs", in which the dyes strongly interact with each other and form dimers, trimers, or hexamers. In the interstrand-wedged motif, a base-pair is inserted between the fluorophores to suppress their direct interaction. These two motifs were applied to accumulate dyes within a DNA duplex, depending on their emission properties. Since pyrene exhibits strong excimer emission, the emission at 500 nm of a pyrene cluster motif strongly increased as the number of accumulated dyes increased, whereas the interstrand-wedged motif quenched pyrene monomer emission. In contrast, assembled perylenes, which are mostly quenched by dimerization, showed intense monomer emission in the interstrand-wedged motif, whereas perylene cluster motifs strongly suppressed perylene emission. These two motifs were then applied to the heteroassembly of pyrenes and perylenes. Both a large Stokes' shift and a modulation of the emission maximum, which are also characteristics of inorganic quantum dots, were successfully realized using fluorescent resonance energy transfer (FRET) and exciplex formation. These fluorophore assemblies thus obtained could be enzymatically ligated to longer DNA, demonstrating that this technique has the potential to be a versatile labeling agent for biomolecules.

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Section: Resultssupporting

confidence: 88%

Accumulation of Fluorophores into DNA Duplexes To Mimic the Properties of Quantum Dots

et al. 2010

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“…On the other hand, the pyrene attached to oligo-DNA duplexes in the same manner was intercalated into the B-form double helixes without fluorescence. Additionally, when multiple pyrenes are consecutively incorporated into an RNA strand, the RNA showed pyrene excimer fluorescence and circular dichroism signals due to the exciton coupling of the pyrenes upon hybridization with a complement (Nakamura et al, 2005b(Nakamura et al, , 2007Maie et al, 2009). Recently, we reported that complementary 15-mer or 21-mer RNAs having five 2 -O-pyrene attached nucleosides, which were separated by one nucleoside from each other, could form a duplex without any loss of thermal stability.…”

Section: Commentary Background Informationmentioning

confidence: 99%

Highly Ordered Pyrene π‐Stacks on an RNA Duplex

Nakamura

Takada

Yamana

2015

CP Nucleic Acid Chemistry

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The syntheses of 2'-O-(pyren-1-ylmethyl)uridine phosphoramidite, 2'-O-(pyren-1-ylmethyl)adenosine phosphoramidite, and multiple pyrene-attached oligo-RNAs are described in this unit. The 2'-O-(pyren-1-ylmethyl)nucleosides are converted into the corresponding 2'-O-(pyren-1-ylmethyl)nucleoside 3'-phosphoramidites, which can be incorporated into the specific position of oligo-RNAs by solid-phase oligonucleotide synthesis. The multiple pyrene-attached oligo-RNA forms an A-form duplex with a complementary multiple pyrene-attached oligo-RNA; the pyrenes are associated with π-stacking along the outside of the duplex.

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“…[30][31][32] However, some disadvantages such as dye aggregation, poor solubility in aqueous solution and relatively short excitation/emission wavelength limit their application to some extent. 22,33,34 Herein, to solve these problems mentioned above, we designed a near infrared (NIR) mitochondrial dye, 4-1-pyrenyl-vinyl-N-ethylquinolinium chloride (PQ, Scheme 1b), by introducing a hydrophilic cation moiety N-ethylquinolinium and established a supramolecular approach to enhance the solubility, photostability and uorescence quantum yield in staining mitochondria by forming the host-guest inclusion complex PQ@CB [8] with the water soluble macrocyclic host CB [8]. The result demonstrated that the CB [8] host forms a stable complex with PQ and prevents PQ aggregation in aqueous solution, resulting in a dramatic increase in uorescence intensity, and the photostability of this complex was greatly improved compared with that of the PQ dye alone.…”

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confidence: 99%