The Dnachips

THE DNACHIPS

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". 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. For example, with a yeast cell, 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. 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.

What are DNAchips?

DNAchips are the DNA microarrays, which are the orderly arrangements of DNA samples fabricated by high-speed robotics on glass nylon or gold substrate. DNA chips will enable cliniciansÐ'--and in some cases even patients themselvesÐ'--to quickly and inexpensively detect the presence of a whole array of genetically based diseases and conditions, including AIDS, Alzheimer's disease, cystic fibrosis, and some forms of cancer. Moreover, the technology could make it possible to conduct widespread disease screening cost-effectively, and to monitor the effectiveness of patient therapies more effectively.

Theoretical Principles

A variety of recent technological breakthroughs have made possible the development of DNA chips. Fundamentally, however, genetic chips are the result of achievements in two fields: molecular biology and microfabrication technology.

1. Molecular biology: Research in molecular biology has laid the groundwork for the development of clinical laboratory tests and therapies involving genetic probes. Fundamental advances include the use of polymerase chain reaction (PCR) or other amplification techniques to make copies of a nucleic acid sample, which can then be tested using a genetic probe that, is, a known gene and its molecular structure. Also essential to the development of DNA chips has been the creation of gene sequencers, machines that have automated the biochemical tests necessary to identify genetic sequences using gene probes.

But the roots of gene probe technologies go back, to the base-pairing rules discovered in the 1950s by James Watson and Francis Crick. Watson and Crick determined that the DNA molecules found in living organisms are composed of a structure of two twisted strands (the famous double helix) latticed together with pairs of nitrogenous bases: adenine, cytosine, guanine, and thymine. They also discovered that these bases always recur in the same two pairs: adenine with thymine, and cytosine with guanine. Thus, by knowing part of the molecular structure of a specific genetic segment, one can determine the other part.

Moreover, these uniquely complementary strands of DNA can be sought out by using one of the strands to test for its biochemical mate; this is the basis of a gene probe. The process of one strand of DNA matching up with its counterpart strand is called hybridization. It is this technique that is used to determine a base-pair sequence in a DNA sample, also called genetic sequencing. Hybridization can be performed either in solution or on a solid support. At present, however, most DNA-chip companies use a solid-phase technique.

Once hybridization has been completed, phosphorescent chemicals that bind to the hybridized sequences are scanned with a light source, making it easy to detect their presence with automated colorimetric or fluorimetric equipment.

2. Microfabrication Technologies: The second technological trend that is making DNA-chip products possible encompasses the steady improvements in nano- and microscale fabrication techniques. Developed initially for use in computer chip manufacturing, these techniques are now being exploited in a variety of other disciplines, including DNA-chip manufacturing. These achievements have made possible the application of organic structures (e.g., segments of DNA and reagents) onto a substrate of inorganic materials. Unlike computer chips, which use silicon-based wafers, DNA microarrays are fabricated onto glass or plastic wafers or are placed in tiny glass tubes and reservoirs.

How Genetic Sequencing Works

Sequencing, the process of finding the molecular structure of a DNA fragment, employs the Watson-Crick rules of hybridization, whereby each strand of DNA can bond only to a chemical mirror image via two sets of four bases: adenine (A), cytosine (C), guanine (G), and thymine (T).

Step 1: Determine chemical structure of fragment.

Representing all or part of a DNA strand of interest, short fragments of DNA (typically involving 5Ð'-25 base pairs) are identified.

Step 2: Separate strands.

DNA is denatured (separated) and placed in solution or on a solid substrate, forming a reference segment for the DNA fragment of interest.

Step 3: Introduce sample.

Unknown DNA sample is introduced to the reference segment. If present, the complement of the reference segment will hybridize (bond) to it.

Step 4: Identify result.

Chemicals that bond to successful hybridization help researchers identify results. Such