Editing Biochip (section)

==Microarray fabrication==
[[File:Sarfus.DNABiochip.jpg|thumb|300px|3D [[Sarfus]] image of a DNA biochip]]
The microarray&mdash;the dense, two-dimensional grid of biosensors&mdash;is the critical component of a biochip platform. Typically, the sensors are deposited on a flat substrate, which may either be passive (''e.g.'' silicon or glass) or active, the latter
consisting of integrated electronics or [[microtechnology|micromechanical]] devices that perform or assist signal transduction. [[Surface chemistry]] is used to [[covalent bond|covalently bind]] the sensor molecules to the substrate medium. The fabrication of microarrays is non-trivial and is a major economic and technological hurdle that may ultimately decide the success of future biochip platforms. The primary manufacturing challenge is the process of placing each sensor at a specific position (typically on a [[Cartesian coordinate system|Cartesian]] grid) on the substrate. Various means exist to achieve the placement, but typically robotic micro-pipetting<ref>M. Schena, D. Shalon, R. W. Davis, and P. O. Brown, "Quantitative monitoring of gene expression patterns with a complementary DNA microarray," ''Science'' 270, pp.&nbsp;467–470, 1995</ref> or micro-printing<ref>G. MacBeath, A. N. Koehler, and S. L. Schreiber, "Printing small molecules as microarrays and detecting protein-ligand interactions en masse," ''J. Am. Chem. Soc.'' 121, pp.&nbsp;7967–7968, 1999</ref> systems are used to place tiny spots of sensor material on the chip surface. Because each sensor is unique, only a few spots can be placed at a time. The low-throughput nature of this
process results in high manufacturing costs.

Fodor and colleagues developed a unique fabrication process (later used by [[Affymetrix]]) in which a series of microlithography steps is used to [[Combinatorial chemistry|combinatorially synthesize]] hundreds of thousands of unique, single-stranded DNA sensors on a substrate one [[nucleotide]] at a time.<ref>S. P. Fodor, J. L. Read, M. C. Pirrung, L. Stryer, A. T. Lu, and D. Solas, "Light-directed, spatially addressable parallel chemical analysis," ''Science'' 251, pp.&nbsp;767–773, 1991</ref><ref>A. C. Pease, D. Solas, E. J. Sullivan, M. T. Cronin, C. P. Holmes, and S. P. Fodor, "Light-generated oligonucleotide arrays for rapid DNA sequence analysis," ''Proc. Natl. Acad. Sci.'' 91, pp.&nbsp;5022–5026, 1994</ref>  One lithography step is needed per base type; thus, a total of four steps is required per nucleotide level. Although this technique is very powerful in that many sensors can be created simultaneously, it is currently only feasible for creating short DNA strands (15&ndash;25 nucleotides). Reliability and cost factors limit the number of photolithography steps that can be done. Furthermore, light-directed combinatorial synthesis techniques are not currently possible for proteins or other sensing molecules.

As noted above, most microarrays consist of a Cartesian grid of sensors. This approach is used chiefly to map or "encode" the coordinate of each sensor to its function. Sensors in these arrays typically use a universal signalling technique (''e.g.'' fluorescence), thus making coordinates their only identifying feature. These arrays must be made using a serial process (''i.e.'' requiring multiple, sequential steps) to ensure that each sensor is placed at the correct position.

"Random" fabrication, in which the sensors are placed at arbitrary positions on the chip, is an alternative to the serial method. The tedious and expensive positioning process is
not required, enabling the use of parallelized self-assembly techniques. In this approach, large batches of identical sensors can be produced; sensors from each batch are then combined and assembled into an array. A non-coordinate based encoding scheme must be used to identify each sensor. As the figure shows, such a design was first demonstrated (and later commercialized by Illumina) using functionalized beads placed randomly in the wells of an etched [[fiber optic]] cable.<ref>F. J. Steemers, J. A. Ferguson, and D. R. Walt, "Screening unlabeled DNA targets with randomly-ordered fiber-optic gene arrays," ''Nature Biotechnology'' 18, pp.&nbsp;91–94, 2000</ref><ref>K. L. Michael, L. C. Taylor, S. L. Schultz, and D. R. Walt, "Randomly ordered addressable high-density optical sensor arrays," ''Analytical Chemistry'' 70, pp.&nbsp;1242–1248, 1998</ref> Each bead was uniquely encoded with a fluorescent signature. However, this encoding scheme is limited in the number of unique dye combinations that can be used and successfully differentiated.