By Andrei MIRZABEKOV, director of the V. A. Engelgardt Institute of Molecular Biology, Russian Academy of Sciences
The technology of biochips (forerunner of nanotechnologies in biology and medicine) has emerged at the junction of molecular biology, immunology, biochemistry, immunochemistry and other disciplines. Biochips make it possible to analyze a variety of organic samples simultaneously. This new trend in contemporary diagnostic methods has come into use in biology and medicine. It is being used by veterinary doctors and crime detection experts in agriculture, toxicology and ecoactivity as well as in other spheres. Our research institute has pioneered in its development.
Biochips and biological computers developed on their basis enable research scientists to obtain a vast array of unique data. The very idea appeared in 1989 as we, within the framework of the Human Genome Project, got down to deciphering, or, as biologists say, sequencing the DNA structure. Routine methods of decoding- with a genome read letter by letter-proved of little effect. Researchers of our institute suggested a method of genetic information sequencing in whole words. Now, in reading some phrase we find its component words in the dictionary. And a subsequent search for their overlapping (semantic compatibility) allows decoding the sense of the phrase and thus comparing the DNA structure. Such
Shorthand of biochip manufacture.
was the fundamental principle for the first biochips.
A typical biochip has the form of a small plate made of glass or organic matter. Using high-precision instruments, we mount dozens, hundreds and even thousands of microscopic fragments of DNA, RNA or other biological elements serving as probes; and we do it strictly at fixed distances. Such probes interact with a sample under study by the so-called "key-lock" principle, while an analyzer determines what probes in particular have reacted with the sample. In fact, we have a miniature biocomputer. Yet unlike an electronic microchip working in a binary system and having two basic distances: | 0 >- | 1 >- "Yes"-"No"- biochips perform much better. For instance, a protein microchip can retrieve data from as many as 10 6 options.
Biochips developed by us consist of semispherical gel cells mounted on the hydrophobic* surface of glass. Quite a number of cells can be put onto 1 mm 2 of the surface. Each of them is actually a specialized miniature "test tube" with a probe composed of DNA, RNA, protein, oligonucleotide, receptor, ligand**, etc., essential for carrying out chemical and enzymic reactions with the samples analyzed. These "minitubes", or probes, find themselves in conditions close to their state in solutions, whilst the three-dimensional structure of gel elements provides for the high sensitivity of a signal generated in a specific interaction with the sample. And thus a biochip actually evolves as a microlaboratory which is smaller than a pin-head in size and which makes hundreds or thousands of analyses simultaneously. Due to its high sensitivity, a biochip can detect and analyze as many as 10,000 molecules in a sample measuring a few nanometers. This is significantly above the sensitivity of the conventional diagnostic techniques.
Biochips make it possible to carry out thousands of chemical and enzymatic reactions simultaneously (DNA and RNA hybridization, antigen/antibody interaction, etc.) with the use of a minimum amount of analyzed substance. The result is determined by a pattern of glow in the microchip cells registered by a kit of instruments (videocamera cum computer and special software) designed by our institute in collaboration with the S. I. Vavilov State Optical Institute in St. Petersburg.
Owing to the small size of biochips, the high sensitivity of the videoanalyzer, the low manufacturing and servicing costs of the setup, this technology has a wide range of applications.
Thus, DNA microchips, based as they are on the principle of complementarity (base pairing) of two DNA strands (one is localized on the chip's surface, the other - stained with a luminescent label-is a sample analyzed), allow to identify both the DNA and proteins, study their structure and interaction, and spot changes caused by genetic diseases. One of the first applications of this technology is to control a poliovims used as a live vaccine for poliomyelitis. The thing is that this virus has a high rate of mutation and, therefore, it cannot be administered in some cases. That is why every new batch of polio vaccines has to be checked before use. Our biochips can detect mutants readily and with very high reliability.
Biochips can also diagnose leukosis caused by chromosomal inversions in the cell nuclei of hematopoietic tissue. This method is applied in one of Moscow's child clinics. It can identify the nature of disease and thus enables doctors to choose the most effective treatment strategy.
Tuberculosis has now staged a comeback throughout the world. Every year about thirty million contract this illness, and nearly two million die. What compounds the situation is that several years ago drug-resistant forms of microbacteria appeared. To curb the epidemic it is important to detect pathogens as fast as possible and find to what extent they are "indifferent" to particular drugs. Contemporary medicine, however, has no adequate techniques in its arsenal. The conventional (bacteriological) diagnostic method takes as long as five or six weeks.
We at our research institute have developed biochips for the identifi-
* Hydrophobic, or intolerant of water (water-repellent).- Ed.
** Ligands - in chemical complex compounds, molecules or ions linked directly to the central atom.- Ed.
The principle of biochip operation.
cation of tuberculosis and its drug-resistant forms. Our technique allows to detect a pathogenic agent in a matter of 6 to 8 hours. Its resistance to medication is assessed thereby, and the very diagnostics can be made in the laboratory of an ordinary hospital or a neighborhood clinic.
Besides, we have developed biochips for the identification of the agents of smallpox, hepatitis, cholera, and AIDS. Other biochips can be helpful in the effective studies of human polymorphism. From a genetic standpoint, individuals differ from one another in that out of 3 billion pairs of nucleotides only 2 to 3 million show distinctions. As to the functional significance, there might be but a few thousand different pairs. We are hoping that a further upgrading of our method will help produce a complete genomic portrait of each and everyone: spot hereditary damages, predisposition to particular diseases, sensitivity to medicines, narcotics, alcohol, and so forth.*
Our research center is also developing techniques for the more effective identification of the infectious agents of anthrax, plague and other diseases from what we might call a "gent's bag" of bioterrorists. There can be no doubt about the need of such studies, especially after the tragedy of 9/11, 2001, in New York City-all the more so that special tests carried out in our country have shown the inadequacy of traditional diagnostic methods. This problem can be resolved with much success only with the use of biochips.
Finally, we have amassed some experience in using cellular biochips for assessing the concentration of carcinogenic substances in food, for monitoring environmental conditions, for protection and prognostication in connection with man's economic activities.
That is why the booming industry of biochips worldwide is no chance phenomenon. Their further miniaturization is much the trend now (over the last decade the average dimensions of biochips fell off from 100 to 5 microns). All that is fully in keeping with Moor's Law** that holds both for electronic and for biological chips alike.
Our estimates show that these diagnostic biochips, if mass-produced, will be nonexpensive. Therefore, should the Russian Academy of Sciences, the Russian Academy of Medical Sciences and organizations that have a stake in the effort join hands in setting up a center for the production and use of biochips, it could supply them at low cost to research laboratories and medical institutions.
* See: V. Baranov, "Predisposition Genes, or the Diseases We Take", Science in Russia, No. l, 2003.- Ed.
** According to Moor's Law, the number of transistors in a crystal of one integrated circuit was doubling every year for the first fifteen years as of 1959, and thereafter such kind of doubling has been occurring every eighteen months or so. Simultaneously, in keeping with the exponential law, the characteristic dimensions of integrated circuit elements are down.- Ed.
Interviewed by Igor GORYUNOV.
Illustrations supplied by the author.
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