Combinatorial decoding: an approach for universal DNA array fabrication

A fiber optic microsphere-based oligonucleotide array is described that employs the sequence of the oligonucleotide probe attached to each microsphere as positional identifiers. Each microsphere serves as an immobilized array feature, functionalized with a unique single-stranded oligonucleotide sequence and randomly distributed into an array of microwells. To determine the sequences attached to individual microspheres, a series of fluorescently labeled combinatorial-pooled oligonucleotide target solutions was designed. Each combinatorial decoding solution is intended to identify the nucleotide at a particular position on every microsphere in the array. The combinatorial target solutions were synthesized by linking the four possible nucleotides at each position to four different fluorescent reporter dyes. As such, when the solutions were hybridized to the array, one of four possible fluorescent responses was generated for each position on a microsphere probe sequence. Adjusting the stringency of hybridization enabled single-base mismatch discrimination, and the signal with the highest intensity corresponded to the perfect nucleotide match. By consecutively exposing the array to a series of combinatorial decoding pool solutions, it was possible to simultaneously determine the sequence of every randomly positioned oligonucleotide-functionalized microsphere in the array. Once mapped, the microsphere array can be used for any typical genomic microarray experiment.

Fluorescence-based fibre optic arrays: a universal platform for sensing

Optical fibres provide a universal sensing platform as they are easily integrated with a multitude of different sensing schemes. Such schemes enable the preparation of a multitude of sensors from relatively straightforward pH sensors, to more complex ones, including artificial olfaction sensors, high-density oligonucleotide arrays, and high-throughput cell-based arrays. Imaging fibre bundles comprised of thousands of fused optical fibres are the basis for an optically connected, individually addressable parallel sensing platform. Fibre optic imaging bundles possess miniature feature sizes (3-10 micron diameter fibres), allowing high-density sensor packing (approximately 2 x 10(7) sensors per cm2). Imaging fibre bundles transmit coherent images enabling combined imaging and sensing, relating the responses monitored by the sensor to observable physical changes. The individual fibre cores can also be selectively etched to form a high-density microwell array capable of housing complementary sized microsensors. The miniature feature sizes facilitate a faster response and more sensitive measurement capabilities. The platform is extremely versatile in its sensing design, allowing the sensing scheme to be tailored to fit the experimental design, whether for monitoring single analytes or more complex multiplexed assays. A number of sensing schemes and applications are described in this review.

High-density, microsphere-based fiber optic DNA microarrays

A high-density fiber optic DNA microarray has been developed consisting of oligonucleotide-functionalized, 3.1-microm-diameter microspheres randomly distributed on the etched face of an imaging fiber bundle. The fiber bundles are comprised of 6000-50000 fused optical fibers and each fiber terminates with an etched well. The microwell array is capable of housing complementary-sized microspheres, each containing thousands of copies of a unique oligonucleotide probe sequence. The array fabrication process results in random microsphere placement. Determining the position of microspheres in the random array requires an optical encoding scheme. This array platform provides many advantages over other array formats. The microsphere-stock suspension concentration added to the etched fiber can be controlled to provide inherent sensor redundancy. Examining identical microspheres has a beneficial effect on the signal-to-noise ratio. As other sequences of interest are discovered, new microsphere sensing elements can be added to existing microsphere pools and new arrays can be fabricated incorporating the new sequences without altering the existing detection capabilities. These microarrays contain the smallest feature sizes (3 microm) of any DNA array, allowing interrogation of extremely small sample volumes. Reducing the feature size results in higher local target molecule concentrations, creating rapid and highly sensitive assays. The microsphere array platform is also flexible in its applications; research has included DNA-protein interaction profiles, microbial strain differentiation, and non-labeled target interrogation with molecular beacons. Fiber optic microsphere-based DNA microarrays have a simple fabrication protocol enabling their expansion into other applications, such as single cell-based assays.

High-density fiber-optic genosensor microsphere array capable of zeptomole detection limits

The detection limit of a fiber-optic microsensor array was investigated for simultaneous detection of multiple DNA sequences. A random array composed of oligonucleotide-functionalized 3.1-microm-diameter microspheres on the distal face of a 500-microm etched imaging fiber was monitored for binding to fluorescently labeled complementary DNA sequences. Inherent sensor redundancy in the microarray allows the use of multiple microspheres to increase the signal-to-noise ratio, further enhancing the detection capabilities. Specific hybridization was observed for each of three sequences in an array yielding a detection limit of 10(-21) mol (approximately 600 DNA molecules).