Building from the “Ground” Up: Developing interfacial chemistry for solid-phase nucleic acid hybridization assays based on quantum dots and fluorescence resonance energy transfer

• QDs are excellent donors in fluorescence resonance energy transfer (FRET).
• QDs can be immobilized by multidentate surface ligands and biomolecular tethers.
• Oligonucleotides can show strong adsorption on QDs (pH and ligand dependent).
• Solid-phase QD–FRET nucleic acid hybridization assays with spectral multiplexing.
• Interfacial chemistry strongly influences analytical figures of merit and adsorption.

Improved diagnostic methods for the detection of specific nucleic acid biomarkers can potentially provide solutions to current challenges in healthcare, public safety, and environmental assessment. Here, we review the application of semiconductor quantum dots (QDs) in the development of nucleic acid hybridization assays that operate on the basis of fluorescence resonance energy transfer (FRET). Within the context of other important contributions to the field, we provide an account of our recent efforts and results toward multiplexed solid-phase hybridization assays. Emphasis is placed on interfacial chemistry, including the use of surface ligands and biomolecular tethers to immobilize QDs on a variety of solid substrates; factors affecting the non-specific adsorption of oligonucleotides on QDs; and different strategies for the biofunctionalization of immobilized QDs. The impact of interfacial chemistry on assay figures of merit such as sensitivity, selectivity, speed, or potential for regeneration is also considered. Further attention is paid to the design of FRET configurations that permit spectrally multiplexed detection of target nucleic acid sequences. Given that the intent of this review is to provide a consolidated framework upon which further advances can be made, we suggest some directions and challenges for future work.

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