An on-chip thin film photodetector for the quantification of DNA probes and targets in microarrays

Integrated Optoelectronic Device for Detection of Fluorescent Molecules

This paper presents the development of a compact optoelectronic device suitable for on-chip detection of fluorescent molecules. In order to obtain a highly integrated device, a long-pass multi-dielectric filter has been integrated with thin-film amorphous silicon photosensors on a single glass substrate. Filter rejects the excitation light, allowing the reduction of the distance between the source and the fluorescent site and avoiding the use of external optical component. The compatibility of the technological processes determined the materials and the temporal sequence of the device fabrication. The developed device has been designed for the fluorescence detection of ruthenium complex based molecules and tested, as a proof of concept, for the detection of double-stranded DNA down to 0.5 ng. Results demonstrate the correct operation of the integrated system in both rejecting the excitation light and in detecting the fluorescent signal, demonstrating the suitability of this optoelectronic platform in practical biomedical applications.

The Enhanced Light Absorptance and Device Application of Nanostructured Black Silicon Fabricated by Metal-assisted Chemical Etching

We use metal-assisted chemical etching (MCE) method to fabricate nanostructured black silicon on the surface of C-Si. The Si-PIN photoelectronic detector based on this type of black silicon shows excellent device performance with a responsivity of 0.57 A/W at 1060 nm. Silicon nanocone arrays can be created using MCE treatment. These modified surfaces show higher light absorptance in the near-infrared range (800 to 2500 nm) compared to that of C-Si with polished surfaces, and the variations in the absorption spectra of the nanostructured black silicon with different etching processes are obtained. The maximum light absorptance increases significantly up to 95 % in the wavelength range of 400 to 2500 nm. Our recent novel results clearly indicate that nanostructured black silicon made by MCE has potential application in near-infrared photoelectronic detectors.

Nucleic acid-based diagnostics for infectious diseases in public health affairs

Infectious diseases, mostly caused by bacteria and viruses but also a result of fungal and parasitic infection, have been one of the most important public health concerns throughout human history. The first step in combating these pathogens is to get a timely and accurate diagnosis at an affordable cost. Many kinds of diagnostics have been developed, such as pathogen culture, biochemical tests and serological tests, to help detect and fight against the causative agents of diseases. However, these diagnostic tests are generally unsatisfactory because they are not particularly sensitive and specific and are unable to deliver speedy results. Nucleic acid-based diagnostics, detecting pathogens through the identification of their genomic sequences, have shown promise to overcome the above limitations and become more widely adopted in clinical tests. Here we review some of the most popular nucleic acid-based diagnostics and focus on their adaptability and applicability to routine clinical usage. We also compare and contrast the characteristics of different types of nucleic acid-based diagnostics.

Integrated detection of intrinsic fluorophores in live microbial cells using an array of thin film amorphous silicon photodetectors

Two-dimensional fluorescence spectroscopy (2D FS) provides a non-invasive means to assess cell condition without the introduction of changes to the cell environment. The method relies on the measurement of the excitation-emission fluorescence intensity matrix of key intrinsic fluorophores, like aromatic amino acids, enzyme cofactors, and vitamins. Commonly used detection systems are complex, with multiple bandpass filters, and are hard to miniaturize. Here, an amorphous silicon photodetector array system integrated with amorphous silicon-carbon alloy filters designed to detect three key fluorophores - tryptophan (Trp), reduced nicotine adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) - is demonstrated. These intrinsic fluorophores were detected in pure solutions and also in suspended yeast cells. The array system was used to monitor changes in intrinsic fluorophore concentration when a yeast cell solution was subject to a thermal shock stress.

Heterogeneous immunoassays in microfluidic format using fluorescence detection with integrated amorphous silicon photodiodes

Miniaturization of immunoassays through microfluidic technology has the potential to decrease the time and the quantity of reactants required for analysis, together with the potential of achieving multiplexing and portability. A lab-on-chip system incorporating a thin-film amorphous silicon (a-Si:H) photodiode microfabricated on a glass substrate with a thin-film amorphous silicon-carbon alloy directly deposited above the photodiode and acting as a fluorescence filter is integrated with a polydimethylsiloxane-based microfluidic network for the direct detection of antibody-antigen molecular recognition reactions using fluorescence. The model immunoassay used consists of primary antibody adsorption to the microchannel walls followed by its recognition by a secondary antibody labeled with a fluorescent quantum-dot tag. The conditions for the flow-through analysis in the microfluidic format were defined and the total assay time was 30 min. Specific molecular recognition was quantitatively detected. The measurements made with the a-Si:H photodiode are consistent with that obtained with a fluorescence microscope and both show a linear dependence on the antibody concentration in the nanomolar-micromolar range.

Gene expression analysis with an integrated CMOS microarray by time-resolved fluorescence detection

DNA microarrays have proven extraordinarily powerful for differential expression studies across thousands of genes in a single experiment. Microarrays also have the potential for clinical applications, including the detection of infectious and immunological diseases and cancer, if they can be rendered both reliable and cost-effective. Here we report the first practical application of an active microarray based on integrated circuit technology, completely obviating the need for external measurement instrumentation while employing protocols compatible with traditional fluorescence-based surface bioassays. In a gene expression biodosimetry study, we determine the differential activity of genes from leucocytes in irradiated human blood. Quantum dots are used as fluorescence labels to realize filterless, time-gated fluorescence detection on an active complementary metal-oxide-semiconductor (CMOS) microarray with 100-pM sensitivity. Improvements in surface chemistry should allow sensitivities that approach the microarray hardware limit of less than 10 pM. Techniques for covalent attachment of DNA capture strands to the CMOS active microarrays allow integrated sensors to be placed in immediate proximity to hybridized analyte strands, maximizing photon collection efficiencies.

Progress in chip-scale photonic sensing

Chip-scale integrated planar photonic sensing systems for portable diagnostics and monitoring are emerging, as photonic components are integrated into systems with silicon (Si), Si complementary metal-oxide semiconductor, and fluidics. This paper reviews progress in these areas. Medical and environmental applications, candidate photonic sensors, integration methodologies, integrated subsystem demonstrations, and challenges facing this emerging field are discussed in this paper.

Single base mismatch detection by microsecond voltage pulses

A single square voltage pulse applied to metal electrodes underneath a silicon dioxide film upon which DNA probes are immobilized allows the discrimination of DNA targets with a single base mismatch during hybridization. Pulse duration, magnitude and slew rate of the voltage pulse are all key factors controlling the rates of electric field assisted hybridization. Although pulses with 1 V, lasting less than 1 ms and with a rise/fall times of 4.5 ns led to maximum hybridization of fully complementary strands, lack of stringency did not allow the discrimination of single base mismatches. However, by choosing pulse conditions that are slightly off the optimum, the selectivity for discriminating single base mismatches could be improved up to a factor approximately 5 when the mismatch was in the middle of the strand and up to approximately 1.5 when the mismatch was on the 5'-end and. These results demonstrate that hybridization with the appropriate electric field pulse provides a new, site-specific, approach to the discrimination of single nucleotide polymorphisms in the sub-millisecond time scale, for addressable DNA microarrays.

Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips

Single, square voltage pulses in the microsecond timescale result in selective 5'-end covalent bonding (immobilization) of thiolated single-stranded (ss) DNA probes to a modified silicon dioxide flat surface and in specific hybridization of ssDNA targets to the immobilized probe. Immobilization and hybridization rates using microsecond voltage pulses at or below 1 V are at least 10(8) times faster than in the passive control reactions performed without electric field (E), and can be achieved with at least three differently functionalized thin-film surfaces on plastic or glass substrates. The systematic study of the effect of DNA probe and target concentrations, of DNA probe and target length, and the application of asymmetric pulses on E-assisted DNA immobilization and hybridization showed that: (1) the rapidly rising edge of the pulse is most critical to the E-assisted processes, but the duration of the pulse is also important; (2) E-assisted immobilization and hybridization can be performed with micrometre-sized pixels, proving the potential for use on microelectronic length scales, and the applied voltage can be scaled down together with the electrode spacing to as low as 25 mV; and (3) longer DNA chains reduce the yield in the E-assisted immobilization and hybridization because the density of physisorbed single-stranded DNA is reduced. The results show that the E-induced reactions can be used as a general method in DNA microarrays to produce high-density DNA chips (E-immobilization) and speed the microarray-based analysis (E-hybridization).