Proof of concept for continuously-tunable terahertz bandpass filter based on a gradient metal-hole array.

A continuously-tunable terahertz (THz) bandpass filter based on the resonant electromagnetic-wave transmission through a metal-hole array featuring a gradually changing period was developed and fabricated on a silicon substrate using optical lithography. A gradient geometry of the metal-hole array yields a wide tunability of the filter transmission, when operating with a focussed THz beam. The filter was studied numerically, using the finite element method, and experimentally, using the THz pulsed spectroscopy. We find that the central wavelength of the filter transmission band can be tuned in the wide range of λc = 400-800 µm with the relative bandwidth of Δλ/λc ≃ ~0.4. Finally, Kapton-based anti-reflection coating was applied to the filter flat side, in order to suppress an interference pattern in the filter transmission spectrum. We believe that the developed filter holds strong potential for multispectral THz imaging and sensing due to its conceptual simplicity and case of operation. Moreover, the presented filter concept can be translated to other spectral ranges, where appropriate technologies are available for the fabrication of gradient sub-wavelength metal-hole arrays.

Portable system for microbial sample preparation and oligonucleotide microarray analysis.

We have developed a three-component system for microbial identification that consists of (i) a universal syringe-operated silica minicolumn for successive DNA and RNA isolation, fractionation, fragmentation, fluorescent labeling, and removal of excess free label and short oligonucleotides; (ii) microarrays of immobilized oligonucleotide probes for 16S rRNA identification; and (iii) a portable battery-powered device for imaging the hybridization of fluorescently labeled RNA fragments with the arrays. The minicolumn combines a guanidine thiocyanate method of nucleic acid isolation with a newly developed hydroxyl radical-based technique for DNA and RNA labeling and fragmentation. DNA and RNA can also be fractionated through differential binding of double- and single-stranded forms of nucleic acids to the silica. The procedure involves sequential washing of the column with different solutions. No vacuum filtration steps, phenol extraction, or centrifugation is required. After hybridization, the overall fluorescence pattern is captured as a digital image or as a Polaroid photo. This three-component system was used to discriminate Escherichia coli, Bacillus subtilis, Bacillus thuringiensis, and human HL60 cells. The procedure is rapid: beginning with whole cells, it takes approximately 25 min to obtain labeled DNA and RNA samples and an additional 25 min to hybridize and acquire the microarray image using a stationary image analysis system or the portable imager.

Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips.

A microchip method has been developed for massive and parallel thermodynamic analyses of DNA duplexes. Fluorescently labeled oligonucleotides were hybridized with oligonucleotides immobilized in the 100 x 100 x 20 mum gel pads of the microchips. The equilibrium melting curves for all microchip duplexes were measured in real time in parallel for all microchip duplexes. Thermodynamic data for perfect and mismatched duplexes that were obtained using the microchip method directly correlated with data obtained in solution. Fluorescent labels or longer linkers between the gel and the oligonucleotides appeared to have no significant effect on duplex stability. Extending the immobilized oligonucleotides with a four-base mixture from the 3'-end or one or two universal bases (5-nitroindole) from the 3'- and/or 5'-end increased the stabilities of their duplexes. These extensions were applied to increase the stabilities of the duplexes formed with short oligonucleotides in microchips, to significantly lessen the differences in melting curves of the AT- and GC-rich duplexes, and to improve discrimination of perfect duplexes from those containing poorly recognized terminal mismatches. This study explored a way to increase the efficiency of sequencing by hybridization on oligonucleotide microchips.