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

摘要

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