Diffraction-limited ultrasensitive molecular nano-arrays with singular nano-cone scattering

Abstract

Large-library fluorescent molecular arrays remain limited in sensitivity (1 Â 10 6 molecules) and dynamic range due to background auto-fluorescence and scattering noise within a large (20-100 lm) fluorescent spot. We report an easily fabricated silica nano-cone array platform, with a detection limit of 100 molecules and a dynamic range that spans 6 decades, due to point (10 nm to 1 lm) illumination of preferentially absorbed tagged targets by singular scattering off wedged cones. Its fluorescent spot reaches diffraction-limited submicron dimensions, which are 10 4 times smaller in area than conventional microarrays, with comparable reduction in detection limit and amplification of dynamic range. Commercially available fluorescent micro-arrays based on target labeling, northern blot, or enzyme-linked immunosorbent assay (ELISA) are limited to a detection threshold of 1 to 10 Â 10 6 molecules per fluorescent spot, 1-23 thus requiring cell culturing or Polymerase Chain Reaction (PCR) amplification for many applications. The low sensitivity is often due to broad illumination, which creates auto-fluorescence noise. Even if point illumination and pin-hole filtering of non-focal plane noise are implemented in a confocal setup, the large and non-uniform fluorescent spots create scattering noise over each 20-100 lm element, which degrades the detection limit. 4 Smaller spots can, in theory, be introduced by nano-sprays and nano-imprinting. However, directing the targets to such small areas then becomes problematic. Real-time PCR is, in principle, capable of detecting a single molecule but is limited in its target number 5 and is hence slow/ expensive for large-library assays. A large-library platform with much better detection limit than the current fluorescent microarrays would transform many screening assays. Ideally, this platform would not use the confocal configuration. Instead, it would direct the target molecules to a submicron spot and illuminate them with a nearby point source that does not require scanning.A promising platform is the optical fiber bundle array, 6 with more than 10 4 fibers and targets, in principle. With its endoscopic configuration, these fiber bundles are most convenient for in situ and real-time biosensing modalities in microfluidic biochips and microfluidic 3-D cell cultures. Consequently, the optical sensing is typically carried out in the transmission mode, with the optical signals transmitted through the optical fibers to a detector. Microwell arrays at the distal end of imaging fiber, with molecular targets captured and transported to the microwells by microbeads, are the most popular among these optical fiber arrays. Although detection limit better than 1 Â 10 6 molecules per bead has been reported, the bar-coded beads limit the target number of this platform. 7,8 Our previous work 9,10 has shown that plasmonics at nanotips can enhance local electric field by three orders of magnitude. However, conduction loss and quenching of fluorescence 11,12 by the metal substrates limit the use o...

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