Biochip

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The development of biochips is a major thrust of the rapidly growing biotechnology industry, which encompasses a very diverse range of research efforts including genomics, proteomics, computational biology, and pharmaceuticals, among other activities. Advances in these areas are giving scientists new methods for unraveling the complex biochemical processes occurring inside cells, with the larger goal of understanding and treating human diseases. At the same time, the semiconductor industry has been steadily perfecting the science of microminiaturization. The merging of these two fields in recent years has enabled biotechnologists to begin packing their traditionally bulky sensing tools into smaller and smaller spaces, onto so-called biochips. These chips are essentially miniaturized laboratories that can perform hundreds or thousands of simultaneous biochemical reactions. Biochips enable researchers to quickly screen large numbers of biological analytes for a variety of purposes, from disease diagnosis to detection of bioterrorism agents.

1 History
2 Microarray fabrication
3 Protein Biochip Array and Other Microarray Technologies
4 Bioethics
5 See also
6 References

[edit] History

The development of biochips was a long history, starting with early work on the underlying sensor technology. One of the first portable, chemistry-based sensors was the glass pH electrode, invented in 1922 by Hughes (Hughes, 1922). Measurement of pH was accomplished by detecting the potential difference developed across a thin glass membrane selective to the permeation of hydrogen ions; this selectivity was achieved by exchanges between H⁺ and SiO sites in the glass. The basic concept of using exchange sites to create permselective membranes was used to develop other ion sensors in subsequent years. For example, a K⁺ sensor was produced by incorporating valinomycin into a thin membrane (Schultz, 1996). Over thirty years elapsed before the first true biosensor (i.e. a sensor utilizing biological molecules) emerged. In 1956, Leland Clark published a paper on an oxygen sensing electrode (Clark, 1956_41). This device became the basis for a glucose sensor developed in 1962 by Clark and colleague Lyons which utilized glucose oxidase molecules embedded in a dialysis membrane (Clark, 1962). The enzyme functioned in the presence of glucose to decrease the amount of oxygen available to the oxygen electrode, thereby relating oxygen levels to glucose concentration. This and similar biosensors became known as enzyme electrodes, and are still in use today.

In 1953, Watson and Crick announced their discovery of the now familiar double helix structure of DNA molecules and set the stage for genetics research that continues to the present day (Nelson, 2000). The development of sequencing techniques in 1977 by Gilbert (Maxam, 1977) and Sanger (Sanger, 1977) (working separately) enabled researchers to directly read the genetic codes that provide instructions for protein synthesis. This research showed how hybridization of complementary single oligonucleotide strands could be used as a basis for DNA sensing. Two additional developments enabled the technology used in modern DNA-based biosensors. First, in 1983 Kary Mullis invented the polymerase chain reaction (PCR) technique (Nelson, 2000), a method for amplifying DNA concentrations. This discovery made possible the detection of extremely small quantities of DNA in samples. Second, in 1986 Hood and coworkers devised a method to label DNA molecules with fluorescent tags instead of radiolabels (Smith, 1986), thus enabling hybridization experiments to be observed optically.

The rapid technological advances of the biochemistry and semiconductor fields in the 1980's led to the large scale development of biochips in the 1990's. At this time, it became clear that biochips were largely a "platform" technology which consisted of several separate, yet integrated components. Figure 1 shows the makeup of a typical biochip platform. The actual sensing component (or "chip") is just one piece of a complete analysis system. Transduction must be done to translate the actual sensing event (DNA binding, oxidation/reduction, etc.) into a format understandable by a computer (voltage, light intensity, mass, etc.), which then enables additional analysis and processing to produce a final, human-readable output. The multiple technologies needed to make a successful biochip -- from sensing chemistry, to microarraying, to signal processing -- require a true multidisciplinary approach, making the barrier to entry steep. One of the first commercial biochips was introduced by Affymetrix. Their "GeneChip" products contain thousands of individual DNA sensors for use in sensing defects, or single nucleotide polymorphisms (SNPs), in genes such as p53 (a tumor suppressor) and BRCA1 and BRCA2 (related to breast cancer) (Cheng, 2001). The chips are produced using microlithography techniques traditionally used to fabricate integrated circuits (see below).

Figure 1. Biochips are a platform that require, in addition to microarray technology, transduction and signal processing technologies to output the results of sensing experiments.

Today, a large variety of biochip technologies are either in development or being commercialized. Numerous advancements continue to be made in sensing research that enable new platforms to be developed for new applications. Cancer diagnosis through DNA typing is just one market opportunity. A variety of industries currently desire the ability to simultaneously screen for a wide range of chemical and biological agents, with purposes ranging from testing public water systems for disease agents to screening airline cargo for explosives. Pharmaceutical companies wish to combinatorially screen drug candidates against target enzymes. To achieve these ends, DNA, RNA, proteins, and even living cells are being employed as sensing mediators on biochips. Numerous transduction methods can be employed including surface plasmon resonance, fluorescence, and chemiluminescence. The particular sensing and transduction techniques chosen depend on factors such as price, sensitivity, and reusability.

[edit] Microarray fabrication

The microarray -- the dense, two-dimensional grid of biosensors -- 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 micromechanical devices that perform or assist signal transduction. Surface chemistry is used to 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 grid) on the substrate. Various means exist to achieve the placement, but typically robotic micro-pipetting (Schena, 1995) or micro-printing (MacBeath, 1999) 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 combinatorially synthesize hundreds of thousands of unique, single-stranded DNA sensors on a substrate one nucleotide at a time (Fodor, 1991; Pease, 1994). 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 (15-25 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 signaling 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 (Steemers, 2000; Michael, 1998) Each bead was uniquely encoded with a fluorescent signature. However, this encoding scheme is limited in the number of unique dye combinations that be can be used and successfully differentiated.

[edit] Protein Biochip Array and Other Microarray Technologies

Microarrays are not limited to DNA analysis; protein microarrays, antibody microarray, Chemical Compound Microarray can also be produced using biochips. Randox Laboratories Ltd. launched Evidence®, the first protein Biochip Array Technology analyzer in 2003. In protein Biochip Array Technology, the biochip replaces the ELISA plate or cuvette as the reaction platform. The biochip is used to simultaneously analyze a panel of related tests in a single sample, producing a patient profile. The patient profile can be used in disease screening, diagnosis, monitoring disease progression or monitoring treatment. Performing multiple analyses simultaneously, described as multiplexing, allows a significant reduction in processing time and the amount of patient sample required. Biochip Array Technology is a novel application of a familiar methodology, using sandwich, competitive and antibody-capture immunoassays. The difference from conventional immunoassays is that the capture ligands are covalently attached to the surface of the biochip in an ordered array rather than in solution.

In sandwich assays an enzyme-labelled antibody is used; in competitive assays an enzyme-labelled antigen is used. On antibody-antigen binding a chemiluminescence reaction produces light. Detection is by a charge-coupled device (CCD) camera. The CCD camera is a sensitive and high-resolution sensor able to accurately detect and quantify very low levels of light. The test regions are located using a grid pattern then the chemiluminescence signals are analysed by imaging software to rapidly and simultaneously quantify the individual analytes.

Details about other array technologies can be found in the following pages: Antibody microarray and Chemical Compound Microarray.

[edit] Bioethics

When the question of ethics come up there is never a clear cut answer, nor should there be. Since no one has actually implemented many types of future biotechnology, interpreting moral issue at this point is very difficult. However, this debate is relevant today and it is critical to begin debate now. Arthur Caplan of University of Pennsylvania School of Medicine explains that “Crossing into this area will be so startling, so momentous, and so socially unnerving that the prospect of doing so demands proactive ethical, theological, and scientific discussion.”

Bioethics is the collaborative investigation of biology, scientific technology, and ethical issues. Van Potter’s definition in 1971 states that bioethics is “biology combined with diverse humanistic knowledge forging a science that sets a system on medical and environmental priorities for acceptable survival.”

Genetic research has many life altering benefits. Genetic research can be used to prevent genetic defects, eliminate disease and replace vital organs. This will save many lives. However, we must realize the potential impact on life itself. Scientists are advised to come up with plans and submit these plans to associated groups with both scientific and ethical expertise for review, before entering into development of new biotechnology. Reviews should be conducted nationally and or internationally. As well, the development should be contained in strict biological confinement until the implications are understood.

Ethics is concerned with what is morally good and bad or right and wrong. Obviously, with regards to bioethics there is a thin line between what is ethical and what is not. Scientists have an ethical obligation as do individuals to do what is right. There is no question whether or not biotechnology is a powerful new tool for modifying living organisms to benefit humankind. However, because biotechnology is so new to us we have yet to understand the risks involved with altering organisms. Until all the safety issues are resolves and ethical standards are put into stone government oversight is crucial.

[edit] See also

[edit] References

W. S. Hughes, “The potential difference between glass and electrolytes in contact with water,” J. Am. Chem. Soc. 44, pp. 2860–2866, 1922.
J. S. Schultz and R. F. Taylor in Handbook of Chemical and Biological Sensors, J. S. Schultz and R. F. Taylor, eds., ch. Introduction to Chemical and Biological Sensors, pp. 1–10, Institute of Physics Publishing, Philadelphia, 1996.
L. C. Clark, Jr., “Monitor and control of blood tissue O2 tensions,” Transactions of the American Society for Artificial Internal Organs 2, pp. 41–84, 1956.
L. C. Clark, Jr. and C. Lyons, “Electrode system for continuous monitoring in cardiovascular surgery,” Annals of the New York Academy of Sciences 148, pp. 133–153, 1962.
D. L. Nelson and M. M. Cox, Lehninger Principles of Biochemistry, Worth Publishers, New York, 2000.
A. M. Maxam and W. Gilbert, “A new method for sequencing DNA,” Proc. Nat. Acad. Sci. 74, pp. 560–664, 1977.
F. Sanger, S. Nicklen, and A. R. Coulson, “DNA sequencing with chainterminating inhibitors,” Proc. Nat. Acad. Sci. 74, pp. 5463–5467, 1977.
L. M. Smith, J. Z. Sanders, R. J. Kaiser, P. Hughes, C. Dodd, C. R. Connell, C. Heiner, S. B. H. Kent, and L. E. Hood, “Fluorescence detection in automated DNA sequence analysis,” Nature 321, pp. 61–67, 1986.
P. Fortina, D. Graves, C. Stoeckert, Jr., S. McKenzie, and S. Surrey in Biochip Technology, J. Cheng and L. J. Kricka, eds., ch. Technology Options and Applications of DNA Microarrays, pp. 185–216, Harwood Academic Publishers, Philadelphia, 2001.
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. 467–470, 1995.
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. 7967–7968, 1999.
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. 767–773, 1991.
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. 5022–5026, 1994.
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. 91–94, 2000.
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. 1242–1248, 1998.
K. L. Gunderson, S. Kruglyak, M. S. Graige, F. Garcia, B. G. Kermani, C. Zhao, D. Che, T. Dickinson, E. Wickham, J. Bierle, D. Doucet, M. Milewski, R. Yang, C. Siegmund, J. Haas, L. Zhou, A. Oliphant, J.-B. Fan, S. Barnard, and M. S. Chee, “Decoding randomly ordered DNA arrays,” Genome Research 14(5), pp. 870–877, 2004.
C. Roberts, C. S. Chen, M. Mrksich, V. Martichonok, D. E. Ingber, and G. M. Whitesides, “Using mixed self-assembled monolayers presenting RGD and (EG)3OH groups to characterize long-term attachment of bovine capillary endothelial cells to surfaces,” J. Am. Chem. Soc. 120, pp. 6548–6555, 1998.
H. Schmeck, "Blazing the Genetic Trail." Bethesda, MD: Howard Hughes Medical Institute, 1991.

http://www.accessexcellence.org/RC/AB/IE/Future_Of_Genetic_Research.html

Interview of A. Caplan, "Should We or Shouldn't We?" http://web.reed.edu/reed_magazine/spring06/features/life_in_venice/should_we.html
Vahid Bemanian, Frøydis D. Blystad, Live Bruseth, Gunn A. Hildrestrand, Lise Holden, Endre Kjærland, Pål Puntervoll, Hanne Ravneberg and Morten Ruud, "What is Bioethics?" Dec 1998.

http://www.uib.no/People/mblpp/bioethics/Bioethics.html