Energy Transfer of an excited state donor to an accepter has long been used measure distances on the nanoscale. Förster Resonance Energy Transfer (FRET) has led the field in use but is typically limited to 80 Å, by utilizing a fluorescent dye donor and an accepting dipole whether that be another dye or a black hole quencher. Nanometal Surface Energy Transfer (NSET) has extended the reach of the molecular ruler to distances exceeding
400 Å, by replacing the accepting molecule with a metal nanoparticle. The extension can be attributed to an enhanced coupling of the electromagnetic field of the dipole to that of the metal nanoparticle. NSET accurately predicts the extent of this coupling by incorporating the size dependent optical and electronic properties of the accepting nanoparticles. Our group has shown the usefulness of NSET as a molecular ruler by observing conformational changes in Hammerhead RNA and is currently investigating uses in small molecule detection utilizing aptamers.
Aptamers are nucleic acid sequences with strong, selective affinities for binding target molecules. They have become popular tools in nanotechnology as they offer better selectivity than anti-bodies while maintaining high levels of target-bound stability. More importantly, nucleic acid aptamer strands are easily modifiable, making them applicable to a variety of chemical instrumentations and techniques. Here in the Strouse lab, we are interested in employing these aptamers in designing optical sensors for target detection. We construct molecular beacon-style optical probes for small-molecule detection using the aptamers appended to gold nanoaprticles. These concentration-based optical assays combine the distance-based theory for energy transfer, NSET, with conformationally-active aptamers. In our work with the ATP DNA aptamer, we show that this molecular-beacon based approach is useful for spanning several magnitudes of target concentration detection (pM-mM) by relocating the specific aptamer sequence in the stem-loop configuration. In addition, by studying these systems optically, site-specific binding information is available that is inaccessible by NMR, EPR, electrochemical detection, etc. The future of this work entails multiple flourescent-dye labels on the aptamers to triangulate distal changes in the nucleic acid's conformation.Back to Research