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

Abstract

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.

Insulator Base Pairs for Lighting‐up Perylenediimide in a DNA Duplex

“…We recently reported the assembly of fluorophores in DNA duplexes, in which the fluorophores and the natural base pairs were alternately introduced. [22] The "insulator base pairs" can also be utilized to assemble fluorophores without decreasing the quantum yield.…”

Highly Sensitive and Robust Linear Probe for Detection of mRNA in Cells

“…In the presence of Ds-ORN the sample containing 5E 2 -2 was four-fold brighter than 1E 2 because each perylene was separated by intervening base pairs ( Figure 2); this is similar to previously described enhancements. [15] The signal-to-background (S/B) ratio of 5E 2 -2 was 217 under these conditions. A probe containing perylene with a butylene linker that was optimized for DNA detection did not detect RNA under these conditions ( Figure S2).…”

Materials for FRET Analysis: Beyond Traditional Dye–Dye Combinations

“…Researchers have already demonstrated the potential of these DNA structures as fluorescent labels using some relatively simple DNA constructs. Accumulation of perylene-and pyrene-based fluorophores in DNA duplexes has been shown and produces fluorescent excimer structures very strongly, which possess large Stokes shifts, making them ideal donors in FRET applications [270,271]. Kumar and Duff engineered some unique DNA-protein complexes that demonstrated potential as light-harvesting complexes [272].…”