We report an experimental demonstration of an ultracompact biochemical sensor based on a two-dimensional photonic crystal microcavity. The microcavity, fabricated on a silicon-on-insulator substrate, is designed to have a resonant wavelength (lambda) near 1.5 microm. The transmission spectrum of the sensor is measured with different ambient refractive indices ranging from n = 1.0 to n = 1.5. From observation of the shift in resonant wavelength, a change in ambient refractive index of delta(n) = 0.002 is readily apparent. The correspondence between absolute refractive index and resonant wavelength agrees with numerical calculation to within 4% accuracy. The evaporation of water in a 5% glycerol mixture is also used to demonstrate the capability for in situ time-resolved sensing.

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Cellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time and at physiological concentrations are not available. Here, we report a single-molecule approach based on zero-mode waveguides that simultaneously tracks transcription progress and the binding of ribosomal protein S15 to nascent RNA transcripts during early ribosome biogenesis. We observe stable binding of S15 to single RNAs immediately after transcription for the majority of the transcripts at 35 °C but for less than half at 20 °C. The remaining transcripts exhibit either rapid and transient binding or are unable to bind S15, likely due to RNA misfolding. Our work establishes the foundation for studying transcription and its coupled co-transcriptional processes, including RNA folding, ligand binding, and enzymatic activity such as in coupling of transcription to splicing, ribosome assembly or translation.

Step and flash imprint lithography (SFIL) is a technique that has the potential to replace photolithography for patterning resist with sub-100 nm features. SFIL is a low cost, high throughput alternative to conventional photolithography for high-resolution patterning. It is a molding process in which the topography of a template defines the patterns created on a substrate. The ultimate resolution of replication by imprint lithography is unknown but, to date, it has only been limited by the size of the structures that can be created on the template. It is entirely possible to faithfully replicate structures with minimum features of a few hundred angströms. SFIL utilizes a low-viscosity, photosensitive silylated solution that exhibits high etch contrast with respect to organic films in O2 reactive ion etching. In this article we describe the SFIL process, the development of a multilayer etch scheme that produces 6:1 aspect ratio features with 60 nm linewidths, a method for patterning high-aspect-ratio features over topography, and a metal lift-off process. A micropolarizer array consisting of orthogonal 100 nm titanium lines and spaces fabricated using this metal lift-off technique is reported.

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