Magic Chip

Introduction

     Imagine a device no bigger than a credit card that could extract your DNA from a drop of blood and map your entire genetic code while you wait. Within a short period of time the proneness to any illness or disease could be mapped and studied. This is not a snippet from a fiction movie. Biologists and engineers will have ONE working in just a few years, because the tool that makes it possible, a genetic microarray known as the " DNA chip ", already exists. Able to scrutinize tens of thousands of genes at once, the DNA chip's astonishing abilities are astounding biologists.

     "Using these chips, people can in one afternoon confirm work that takes several years using conventional gene-sequencing processes", says

     Ed Hurwitz of Affymetrix, the Silicon Valley company that pioneered the technology. The chips aren't just about increased speed. Using them, researchers can do things that were previously almost impossible, such as, uncovering the genetic machinations behind the complex biochemistry of organisms. With a yeast cell, for example, virtually all of its 6200 genes can be represented on just four chips. It is then possible to take "snapshots" that reveal which genes are active, which are dormant and how these patterns change during the organism's life cycle.

      As of now all the 6200 genes of the yeast cell have been represented and it won't be too long before all the 100 000 human genes are mapped by the chips. The chips would radically change our ability to discover drugs, infectious processes and even disease processes that we didn't know about before. What silicon chips did for computers, DNA chips may do for biological research. Systems Biology will be the challenge of the 21st century and the best and most efficient way to understand the biology of systems will be to use tools such as these chips.

     The similarities between silicon chips and their gene-oriented counterparts begin with the way they are made. Like computer chips, most DNA chips are produced by computer-controlled micro printing. In computer chips, the process lays down microscopic circuits and switches; in DNA chips, it puts down the stuff of genes.

 Making of the chips

     The chips are made by first coating a surface like glass or silica with a sticky chemical. Then at precise locations, nucleotides are attached. These include the four "bases" adenine (A), cytosine (C), guanine (G) and thymine (T). The nucleotides are then linked to form short chains with different sequences. Some chipmakers build the chip first and then stick them on to the surface, while others build them onsite by adding molecules one by one. When finished, the microarray is dotted with nucleotides, ranging from just a few dozens to tens of thousands of short strands of nucleotides.

     This repertoire of sequences lets the DNA chip do its work - searching out specific sequences from an organism's genome. The method works because DNA consists of two strands along which "A" on one strand always binds with "T" on the other and "C" on one strand always binds with "G" on the other. This gives the double helix a "complementary nature". 

     To pick out a gene, the strings on the DNA chip don't have to be too long. A typical gene may contain 10 000 pairs of nucleotides, or more. But within a gene's chain there's usually a short sequence, no more than 25 bases long, unique to that gene. By encoding that short, unique chain on a chip geneticists can represent the whole gene. This shorthand makes the entire process manageable.    

 Usage of chips

     To use the chip, a physician or lab technician extracts a sample of an organism's DNA from a bit of blood or tissue. The DNA is purified, replicated, split into single strands and finally cut up by enzymes into small pieces. Each piece in this DNA hash is then tagged with a fluorescent molecule. At the moment, lab technicians do this work, but all these processes could soon be carried out in computer-controlled reaction chambers squeezed onto the same chip as the microarrays.

      This mixture is then washed over the chip. If a DNA strand in the hash meets a complementary counterpart on the chip, the matching sections zip together to form a double strand. The better the match, more the bonds between the strands, and stronger the join. The array is then flushed with a chemical solution that breaks apart all but the best-matched double strands. In theory, the pair that remain are perfect fits. In practice, however, there is a 5% error rate. So a typical chip has built-in redundancies - additional test sites with the same unique DNA fragment, each offering a second opinion on the results of the others.

     When the flushing is complete, a computer reads the location of any fluorescent tags shining from the chip's surface and matches those locations to its record of the nucleotide chains deposited at those points. The result - a full catalogue display of all the genetic ingredients.

Disease Specificity

     The chips can also specialize in specific maladies, replicating the handful of specific genes implicated in a particular illness from arthritis to HIV. For example, Larry Brody and Joseph Hacia at the National Institutes of Health, near Washington DC are studying the human BRCA1 and BRCA2 genes, which are implicated in hereditary breast cancer. When breast cancer runs in a family, as many as 80% of the women affected show mutations in either or both of these genes. The mutations make a women's chance of developing the disease as high as 85%.

     The two scientists are testing chips that lay out the complete sequence of "healthy" BRCA1 and BRCA2 genes - 5000 and 10 000 base pairs, respectively. The researchers flood a chip with a sample of BRCA genes from a woman whose family has a history of the disease. If her genetic sample matches point by point, i.e. if complementary sequences bind to all the strings on the microarray, she has normal BRCA genes and a clean bill of life. If there are mismatches, that is, one or more strings don't find complementary partners, she's at a risk of developing the disease.

     "Without the chips, it's relatively easy to screen for a mutation when you know what to look for. But the problem is that BRCA1 has more than 500 known mutations and more are being found out all the time. Most researchers feel that using conventional methods, one tends to study only those locations, where a variation is expected. But, by using DNA chips, you can get the entire data report of a DNA sample and easily determine the place of variation and also the factors, which could have influenced the variation.

     This capability should help to tailor medicines to the specific genetic character of any one individual. In a few years, the human genome project will be complete and biologists will have a rough idea of the average genetic make-up of a human being. But specific variations from the normal are often crucial in determining a person's susceptibility to disease or their response to drugs. Chips will enable doctors to take a quick snapshot of a person's genes to see which treatment is the best and which drugs to avoid.

     The DNA chip will be a powerful tool for understanding patterns of gene expression in cells. A gene expresses itself when it acts as a template to make its own distinctive protein. The strength of a gene's expression depends on how much of that protein it causes to be made. Having an easy way to measure the strength of a gene's expression would be extremely useful to biologists.

     But a gene doesn't make its own proteins directly. Instead, the cell extracts the information needed to make a protein and dispatches it to protein making areas in the form of RNA. The amount of protein manufactured is directly proportional to the translation of RNA's. So, by measuring the amount of RNA in a sample, researchers can easily figure out the amounts of protein being produced.

Gene expression

     To measure gene expression on a chip, designers arrange snippets of DNA on the wafer that matches various genes. This time, however, each gene is represented by thousands of identical strands. Researchers then isolate the RNA from a patient's sample, chop it up, tag it with a fluorescent flag, and wash it over the chip. Each RNA fragment binds to the strand of the gene from which it was created. So, if a gene is strongly expressed, RNA fragments might bind to most of the strands representing that gene on the array, whereas those of a weakly expressed gene will gather only a few bits of RNA. In this way, biologists can calculate the proportions of each version of RNA represented and learn how strongly each gene is expressed.

     We can, for example, use gene expression to study what the body is doing to fight a bacterial infection - or what the bacteria are doing to survive in the host. The chip gives elaborate data of genetic patterns in the normal and infected states 100 to 1000 times faster than conventional methods. It tells us which of the genes are in play during the infection process and also the genes one should attack in the bacteria to inhibit its growth. It also shows the strongest response exhibited by the body of the host. In this way it will help in studying the mechanism of action of both the host and the pathogen during the course of an infection.

      Being able to read expression patterns also enables scientists to distinguish between people with apparently identical diseases. Studying the expression patterns of tens of thousands of genes, illnesses such as Lymphoma, can be distinguished by revealing sub-groups of patients with different patterns of gene expression. Tiny differences can be a matter of life and death, for each sub-group may respond differently to the same treatment regime. By understanding the genetic behavior of a specific form of a disease and its reaction to different treatments, therapies can be more carefully designed for each patient. People are now using these expression patterns to determine if patients are at high risk and need quick and radical treatment or to less dramatic therapy over a long period of time.

Drug Design

      Chips could be used to fine tune drug design as well as for medical diagnosis. Drug companies test a huge number of potential drugs against a spectrum of biochemicals to determine their interactions. They also try thousands of variations of any promising compound to see which ones maximize benefits and minimize side effects. Chips can speed these screening processes by years.    

Role of DNA chips in plants

     This approach isn't limited to just humans. Agricultural biologists are using the devices to read plants' designs as well. Shauna Somerville, a plant biologist at Stanford University, is part of a team using chips to explore the detailed architecture of thale cress (Arabidopsis thaliana), a weed related to broccoli that has had more of its gene sequenced than any other plant.

     Botanists hope to use the chips to understand how plants cope with the stress caused by heat, drought, excess rain or the lack of certain nutrients. By charting genetic responses to specific stresses, they may be able to engineer more versatile plants that thrive in more varied environments. Researches also hope to read the genetic signatures of the changes in plants bred for specific advantages like, drought tolerance or cold hardiness, and then engineer the same changes in other strains.

      DNA chips may even help to turn plants into chemical factories. There has been some work on producing biodegradable plastics from plants. Ultimately, DNA chips will give botanists a much better understanding of the processes going on inside plant cells. That would help them to make better choices in the modifications to be made to the plants, while developing hardier and more productive strains.   

     As the demand for DNA chips and the computers that read the results grow, the cost of both should plummet in the near future. Chips now cost as much as $ 2000 each to make and some of the equipment needed to make and read them is TEN times more expensive than the chip.    

      The DNA chips are set to revolutionize every aspect of biology and within three to five years, virtually every scientist will have access to these chips at an affordable price low enough to rival that of disposable needles for syringes.

**This article was graciously submitted to www.cheresources.com for publication by Shankara Narayanan K.R. from Bangalore, India.  The author can be reached for questions/comments at thinkbig@rediffmail.com