Self-Assembled Quantum Dot-Sensitized Multivalent DNA Photonic Wires

Abstract

Combining the inherent scaffolding provided by DNA structure with spatial control over fluorophore positioning allows the creation of DNA-based photonic wires with the capacity to transfer excitation energy over distances greater than 150 Å. We demonstrate hybrid multifluorophore DNA-photonic wires that both self-assemble around semiconductor quantum dots (QDs) and exploit their unique photophysical properties. In this architecture, the QDs function as both central nanoscaffolds and ultraviolet energy harvesting donors that drive Förster resonance energy transfer (FRET) cascades through the DNA wires with emissions that approach the near-infrared. To assemble the wires, DNA fragments labeled with a series of increasingly red-shifted acceptor-dyes were hybridized in a predetermined linear arrangement to a complementary DNA template that was chemoselectively modified with a hexahistidine-appended peptide. The peptide portion facilitated metal-affinity coordination of multiple hybridized DNA-dye structures to a central QD completing the final nanocrystal-DNA photonic wire structure. We assembled several such hybrid structures where labeled-acceptor dyes were excited by the QDs and arranged to interact with each other via consecutive FRET processes. The inherently facile reconfiguration properties of this design allowed testing of alternate formats including the addition of an intercalating dye located in the template DNA or placement of multiple identical dye acceptors that engaged in homoFRET. Lastly, a photonic structure linking the central QD with multiple copies of DNA hybridized with 4-sequentially arranged acceptor dyes and demonstrating 4-consecutive energy transfer steps was examined. Step-by-step monitoring of energy transfer with both steady-state and time-resolved spectroscopy allowed efficiencies to be tracked through the structures and suggested that acceptor dye quantum yields are the predominant limiting factor. Integrating such DNA-based photonic structures with QDs can help create a new generation of biophotonic wire assemblies with widespread potential in nanotechnology.

Materials for FRET Analysis: Beyond Traditional Dye–Dye Combinations

“…Such systems have potential use in solar cells, nanoscale photonic devices, and other optoelectronic applications [269,567,568]. More commonly, these multi-FRET configurations are developed as a means to extend the optical ruler and are used to elucidate biological configurations, study protein and DNA interactions, and for biosensing applications [135,210,365,366,412,413,569].…”

“…Altering donor/acceptor spacing is facile in this configuration and allows fine-tuning of FRET efficiency [569]. Such fine-tuning and control of multi-FRET using DNA constructs has been used for light harvesting and charge separation using DNA nanostructures [269,567], development of combinatorial FRET-tags for SNP detection, [571] and DNA-based photonic wires [568].…”

“…Medintz et al developed a multi-FRET maltose biosensor using QDs (initial donor) functionalized with Cy3-labeled MBP that further bound Cy3.5-labeled b-cyclodextrin, a sugar analogue that was displaced from the QD-MBP complex in the presence of maltose [71]. Boeneman et al developed DNA photonic wires using a QD modified with an ssDNA backbone template that bound four separate short complementary sequences (labeled with different dyes) ( Figure 6.29) [568]. The system was used to study the sequential FRET from the initial QD donor to Cy3/Cy5/Cy5.5/Cy7, and it was found that while the initial QD-quenching efficiency was high (80-90%), the amount of energy subsequently emitted by Cy5 and Cy5.5 was relatively low at $2.2 and 1%, respectively, with the Cy7 acting as an IR quencher.…”

Intra/Inter-Particle Energy Transfer of Luminescence Nanocrystals for Biomedical Applications

“…They used FRETsensitized emission from QD to mCherry to confirm the intracellular protein assembly. Recently, the same group demonstrated the hybrid multifluorophore DNA-photonic wires that both self-assemble around QDs and QDs function as UV energy harvesting to drive FRET cascades through the DNA wires with emission which approach near-infrared (see Figure 2(c)) [26]. The peptide portion facilitated metalaffinity coordination of multiple hybridized DNA-dye structures to a central QD completing the final nanocrystal-DNA photonic wire structure.…”

One-pot Synthesis of Quencher Labeled Hairpin DNA–CdTe QDs Conjugate for Target DNA and Deoxyribonuclease I Detection

“…8,9 Other strategies use thiolated or polyhistidine modified DNA to conjugate with the QDs. 10,11 However, most of these coupling strategies are complex, technically demanding, time consuming, and expensive.…”