BIO-CHIP A GIGANTIC INNOVATION

R.Sindhi Madhuri,A.Anurag Reddy Department of ECE. Institute of Aeronautical Engineering. Dundigal, Hyderabad. sindhimadhuri6280@gmail.com Abstract The development of biochips is a major drive of the rapidly growing biotechnology industry, which encompasses a very assorted range of research efforts including genomics, proteomics, 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 slighter spaces i.e. so called biochips. These chips are essentially miniaturized laboratories that can perform hundreds or thousands of simultaneous biochemical reactions. These paper insights on how biochips enable researchers to quickly screen large numbers of biological analytes for a variety of purposes, from disease diagnosis to detection of bioterrorism agents. Keywords: Biochips, genetic, DNA, Membrane, Micro arraying. I. INTRODUCTION BIOCHIP AND HISTORY OF chemical samples. A specially designed microscope can determine where the sample hybridized with DNA strands in the biochip. Biochips would help dramatically in accelerating the identification of the estimated 80,000 genes in human DNA, an ongoing world-wide research collaboration known as the Human Genome Project. The microchip is described as a sort of word search function that can quickly sequence DNA. In addition to genetic applications, the biochip is being used in toxicological, protein, and biochemical research. Biochips can also be used to rapidly detect chemical agents used in biological warfare so that defensive measures can be considered. The development of biochips has 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. 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. 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. 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. The enzyme functioned in the presence of glucose to decrease the amount of oxygen existing in 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[5]. In 1953, Watson and Crick announced their discovery of the now familiar double helix structure of DNA molecules and set the stage for

A biochip is a collection of miniaturized test sites (microarrays) arranged on a solid substrate that allows many tests to be performed at the same time in order to achieve higher throughput and pace. Typically, a biochip's surface area is no larger than a fingernail. Like a computer chip that can perform millions of mathematical operations in one second, a biochip can perform thousands of biological reactions, such as decoding genes in few seconds. A genetic biochip is designed to freeze into place the structures of many short strands of DNA (deoxyribonucleic acid), the basic chemical instruction that establishes the characteristics of an organism. Effectively, it is used as a test tube for real

genetics research that continues to the present day . The development of sequencing techniques in 1977 by Gilbert and Sanger 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, a method for amplifying DNA concentrations. This discovery made possible the detection of extremely small quantities of DNA in samples [6]. In 1986 Hood and co-workers devised a method to label DNA molecules with fluorescent tags instead of radiolabels, thus enabling hybridization experiments to be observed optically. The rapid technological advances of the biochemistry and semiconductor fields in the 1980s led to the huge scale development of biochips in the 1990s. At this time, it became obvious 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 the "chip") is just one piece of a complete analysis system. Transduction must be done to translate the actual sensing event (DNA binding, oxidation or reduction, etc.) into a format understandable by a computer, 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 micro arraying, to signal processing, requires a true multidisciplinary approach . One of the first commercial biochips was introduced by Affymetrix. This "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). The chips are produced using microlithography techniques traditionally used to fabricate integrated Circuits.

Figure 1: The Biochip Platform 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 variety of biochip technologies are either in development or being commercialized. Numerous advancements continue to be made in sensing research that enables new platforms to be developed for emerging applications. Cancer diagnosis through DNA is just one market opening. A variety of industries currently desire the capability 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, durability, and reusability. II. THE MAKING OF BIOCHIP 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 attain the placement, but typically robotic micro-

pipetting or micro- printing systems are used to place tiny spots of sensor material on the chip surface. As 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 are used to combinatorially synthesize hundreds of thousands of unique, singlestranded DNA sensors on a substrate one nucleotide at a time. One lithography step is needed per base type; thus, a total of four steps are 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 (1525 nucleotides). A reliability and cost factor restricts 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 mentioned above most microarrays consist of a cartesian grid of sensors. This approach is used mainly 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[10]. Each bead was uniquely encoded with a fluorescent signature. However, this encoding scheme is restricted in the number of unique dye combinations that can be used and successfully differentiated. III. BIOCHIP ARRAY TECHNOLOGIES Microarrays are not limited to DNA analysis, protein microarrays, antibody microarray and

chemical compound microarray but can also be produced using biochips. Randox Laboratories Ltd. has launched 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, and allows a significant drop in processing time and the amount of patient sample required. Biochip Array Technology is a fresh 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-labeled antibody is used, in competitive assays an enzyme labeled 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 sense and quantify very low levels of light. The test regions are located using a grid pattern then the chemiluminescence signals are analyzed by imaging software to rapidly and simultaneously quantify the individual analytes. IV. BIOCHIP TECHNOLOGY COMPONENTS AND ITS

The current biochip implant system is actually a fairly simple device. Todays, biochip implant is basically a small (micro) computer chip, inserted under the skin, for identification purposes. The biochip implant system consists of two components; a transponder and a reader or scanner. The transponder is the actual biochip implant. The biochip system is a radio frequency identification (RFID) system, using low-frequency radio signals to communicate between the biochip and reader. The reading range or activation range, between reader and biochip is small, normally between 2 and 12 inches. The transponder: The transponder is the actual biochip implant. It is a passive transponder it contains no battery or energy of it's own. In comparison, an active transponder would provide its own energy

source, normally a small battery. Because the passive biochip contains no battery, or nothing to wear out, it has a very long life, up to 99 years, and no maintenance overheads. Being passive, it's inactive until the reader activates it by sending it a low-power electrical charge. The reader "reads" or "scans" the implanted biochip and receives back data (in this case an identification number) from the biochip. The communication between biochip and reader is via low-frequency radio waves. A. Components of Biochip The biochip-transponder consists of four parts; computer microchip, antenna coil, capacitor and the glass capsule. B. Computer Microchip The microchip stores a unique identification number from 10 to 15 digits long. The storage capacity of the current microchips is limited, capable of storing only a single ID number. AVID (American Veterinary Identification Devices), claims their chips, using a nnn-nnn-nnn format, has the capability of over 70 trillion unique numbers. The unique ID number is etched or encoded via a laser onto the surface of the microchip before assembly. Once the number is encoded it is impossible to alter. The microchip also contains the electronic circuitry necessary to transmit the ID number to the reader. International Journal of Emerging Technology and Advanced Engineering Website: www.ijetae.com (ISSN 2250-2459, Volume 2, Issue 3, March 2012) C. Antenna Coil This is normally a simple, coil of copper wire around a ferrite or iron core. This tiny, primitive, radio antenna receives and sends signals from the reader or scanner. D. Tuning Capacitor The capacitor stores the small electrical charge (less than 1/1000 of a watt) sent by the reader or scanner, which triggers the transponder. This activation allows the transponder to send back the ID number encoded in the computer chip. As radio waves are utilized to communicate between the transponder and reader, the capacitor is tuned to the same frequency as the reader. E. Glass Capsule The glass capsule holds the microchip, antenna coil and capacitor. It is a small capsule, the smallest measuring 11 mm in length and 2 mm in diameter, about the size of an uncooked grain of rice as shown in figure 2 and 3. The capsule is made of biocompatible material such as soda lime glass. After assembly, the capsule is hermetically

(air-tight) sealed, so no bodily fluids can touch the electronics inside. Because the glass is very smooth and susceptible to movement, a material such as a polypropylene polymer sheath is attached to one end of the capsule. This sheath provides a compatible surface which the bodily tissue fibers bond or interconnect, resulting in a permanent placement of the biochip.

Figure 2: Actual Biochip Capsule

Figure 3. Components of a Biochip The biochip is inserted into the subject with a hypodermic syringe as shown in figure 4. Injection is safe and simple, comparable to common vaccines. Anesthesia is not required nor recommended. In dogs and cats, the biochip is usually injected behind the neck between the shoulder blades. Trovan, Ltd., markets an implant, featuring a patented "zip quill", which you simply press in, no syringe is needed. According to AVID "Once implanted, the identity tag is virtually impossible to retrieve. The number can never be altered."

Figure 5: The Biochip Reader V. MAJOR ROLE OF BIOCHIP IN MEDICAL FIELD In their fight against cancer, doctors have just gained an impressive new weapon to add to their armory. Researchers at the U.S. Department of Energy's Argonne National Laboratory have developed a chip that can save lives by diagnosing certain cancers even before patients become symptomatic. The new technology, known as a biochip, consists of a one-centimeter by one centimeter array that comprises anywhere between several dozen and several hundred dots or small drops. Each of these drops contains a unique protein, antibody or nucleic acid that will attach to a particular DNA sequence or antigen. A tumor, even in its earliest asymptomatic phases, can slough off proteins that find their way into a patient's circulatory system. These proteins trigger the immune system to kick into gear, producing antibodies that regulate which proteins belong and which do not. Antibodies are the guardians of what goes on in the body," as mentioned by Tim Barder, president of Eprogen, Inc., which has licensed Argonne's biochip technology to search for new biomarkers that indicate cancer. If a cancer cell produces aberrant proteins, then it is very likely that the patient will have an antibody profile that differs from that of a healthy person. You can look for similarities and differences in autoantibody profiles to look for clues and markers that provide early indicators of disease. In their hunt for cancer indicators, Eprogen uses a process called 2dimesional protein fractionation, which sorts thousands of different proteins from cancer cells by both their electrical charge and their hydrophobicity or stickiness. The 2-D fractionation process creates 960 separate protein fractions, which are then arranged in a single biochip containing 96-well grids. Eprogen scientists then probe the microarrays with known serum or plasma auto- antibodies produced by the immune systems of cancer patients. By using cancer patients own auto-antibodies as a diagnostic tool, doctors could potentially tailor treatments based on their personal autoantibody profile [6]. This technology is really designed to take advantage of the information contained within the patient's own biology and what that makes this technique unique is that scientists can use the actual expression of the patient's disease as a means of obtaining new and better diagnostic information that

Figure 4: Hypodermic Syringe F. The reader The reader consists of an "exciter" coil which creates an electromagnetic field that, via radio signals, provides the necessary energy (less than 1/1000 of a watt) to "excite" or "activate" the implanted biochip. The reader also carries a receiving coil that receives the transmitted code or ID number sent back from the "activated" implanted biochip. This all takes place very fast, in milliseconds. The reader also contains the software and components to decode the received code and display the result in an LCD display. The reader can include a RS-232 port to attach a computer. G. How it works The reader generates a lowpower, electromagnetic field, in this case via radio signals, which activates the implanted biochip as depicted in figure 5. This activation enables the biochip to send the ID code back to the reader via radio signals. The reader amplifies the received code, converts it to digital format, decodes and displays the ID number on the reader's LCD display. The reader must normally be between 2 and 12 inches near the biochip to communicate. The reader and biochip can communicate through most materials. International Journal of Emerging Technology and Advanced Engineering Website: www.ijetae.com (ISSN 2250-2459, Volume 2, Issue 3, March 2012) 133

doctors could use to understand and fight cancer better. Biochips have already shown promise in diagnostic medicine, according to Argonne biologist Daniel Schabacker, who developed the technology. In addition to Eprogen, three other companies have licensed biochips. One of these companies, Akonni Biosystems of Frederick, Md., has already produced dozens of assays, which it markets under the TruArray brand name. Similarly Safeguard Biosystems, licensed biochips for veterinary diagnostic applications. When a biochip is tailored to detect upper respiratory diseases which is exposed to a swab when taken from a patient's mouth, for instance, the binding patterns of the proteins or nucleic acids in the array cause the dots to "light up" when scanned and analyzed with a computer. Computer algorithms decode the dot pattern produced by the biochip. The computation of statistical likelihood of each possible infection and provide this information to the doctor. Suppose someone shows up to the hospital with an upper respiratory infection ailment. The first thing a doctor is going to want to know is whether the infection is viral or bacterial, this is especially true in pediatrics. And ideally, they'd really like to have a single test that they can run very rapidly that will identify exactly which disease you have from a dozen top targets. The development of products like TruArray will soon revolutionize doctors' ability to quickly diagnose a number of diseases. For example, while existing rapid strep tests performed by many pediatricians take only a few minutes to process, they yield so many false negatives those doctors routinely send out the samples for subsequent rounds of more thorough, time consuming and expensive analysis [3]. Platform lies in the fact that we can screen a single sample for multiple viral and bacterial infections at the same time. Soon, doctors will no longer need to order as many expensive and timeconsuming tests, and can instead obtain accurate diagnoses that will enable them to quickly provide their patients with targeted treatment strategies. Though the analysis of a sample on a biochip can take 30 minutes, scientists can have much more confidence in the accuracy of the diagnosis. Biochips give us the ability to run a test that allows your doctor to figure out exactly what you're suffering from during the time that you're in his or her office. While biochips will allow doctors to more quickly and authoritatively explain you, they might also be used for patients who exhibit symptoms of much

more serious infections. By adding just a few more drops to the chip's array, Schabacker claimed, lab technicians could test for a whole slate of biotoxins and especially virulent diseases from the plague to smallpox to anthrax [4]. Other infections, such as those caused by Multidrug Resistant Tuberculosis (MDR-TB) and the often deadly Methicillin-resistant Staphylococcus aureus (MRSA), can be quickly diagnosed with biochips like Akonni's TruArray assay, according to Daitch. The most important thing with these types of infections is that you have to be right and get the answer quickly. Some of the tests out there, though marginally quicker than ours, are so inaccurate that they're almost useless. Especially when you're talking about anthrax or plague, you have to be confident in your diagnosis or else risk causing a panic. VI. BIOCHIP IS UP TO THE MARK OF THE MONSTER The biochip technology was originally developed for monitoring fisheries as mentioned, its use now includes, over 300 zoos, over 80 government agencies in at least 20 countries, pets also , electronic branding of horses, monitoring lab animals, fisheries, endangered wildlife, automobiles, garment tracking, hazardous waste and according to the experts.. To date, over 7 million animals have been chipped. The major biochip companies are A.V.I.D. (American Veterinary Identification Devices), Trovan Identification Systems, and Destron-Fearing Corporation. And according to most modern-day sayings the implanted biochip is the soon-coming in humans also. VII.COMMON MYTHS ABOUT BIOCHIPS IMPLANTS A. With a biochip can be used to track you or your pets location, anywhere in the world- The current biochip and reader has a maximum range of 12 inches. Pets are located by shelters, vets and find a lost pet and reading its biochip. The technology does not exist to globally locate something as small as a biochip. B. A biochip can store and update your financial, medical, demographic data, basically everything about you- The common scenario is, an implanted biochip can be scanned to pay for groceries, obtain medical procedures, conduct financial transactions. C. One major concern with a implanted biochip is theftAccording to the authorities a chip implant

would contain your financial world, medical history, health care it would contain your "electronic life". If cash no longer existed and if the worlds economy was totally chip oriented; there would be a huge "black-market" for chips! Since there is no cash and no other bartering system, criminals would cut off hands and heads, stealing "rich-folks" chips.

VII. CONCLUSION Biochips promises to bring genomics, the study of all the genes in existing organisms, out of the research laboratory and into the everyday practice of medicine. If genomics delivers on its promise, health care will shift from a focus on detection and treatment to a process of prediction and prevention. The biochip space lies at the intersection between high technology chip manufacturing, signal processing, software skills and more traditional molecular biology and genomics. The market for biosensors and biochips is interdisciplinary and growing and has applications in a number of core research areas. This paper presents a valuable context addition for those in both academia and industry. As this fast maturing field already boasts sales of products, biochips are likely to have a significant business future. We can expect that advances in microfluidic biochip technology will enable the miniaturization of devices that will allow highly sensitive analysis of complex biological interactions in real time that to with a low cost perception. References [1] Cady, NC (2009). "Microchip-based PCR Amplification Systems". Lab-on-a-Chip Technology: Biomolecular Separation and Analysis. Caister Academic Press. [2] Fan et al. (2009). "TwoDimensional Electrophoresis in a Chip". Lab-on-aChip Technology: Biomolecular Separation and Analysis. Caister Academic Press. [3] 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. 767773, 1991. [4] 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. 185216, Harwood Academic Publishers, Philadelphia, 2001. [5] 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. [6] Herold, KE; Rasooly, A (editor) (2009). Lab-on-a-Chip Technology: Fabrication and Microfluidics. Caister Academic Press. [7] W. S. Hughes, The potential difference between glass and electrolytes in contact with water, J. Am. Chem. Soc. 44, pp. 2860 2866, 1922. [8] A. M. Maxam and W. Gilbert, A new method for sequencing