Gene Chips

By 2005 all human gene sequences should be determined, what can we do with this information? One answer is the introduction of oligonucleotide microarray chips, or gene chips.

‘Gene chip’ is a general term used to describe a new technology that can identify various allele polymorphisms or mutations. A polymorphism is a difference in DNA sequence between one person and another. Analysing each polymorphism can be very time consuming, gene chips allow lots and lots of polymorphisms to be tested at one time very quickly.

Affymetrix Inc. holds the registered trademark of GeneChip®, however this is not the only brand available. This new developing technology allows gene specific diagnosis and therapies by either identifying or predicting a genetic component of a disease. The principle by which these ‘chips work is not new, the theory of protein arrays was done in the 1980’s by Rodger Ekins et al. Oligonucleotide arrays however have only been possible since the development of manufacturing techniques made possible by the collaboration of biologists and engineers using techniques perfected in the semi-conductor industry, allowing the necessary macromolecular detail in chip design.

Gene chips are glass or nylon substrates with thousands of spots of oligonucleotides bound to their surface designed to hybridise to a labelled unknown nucleic acid. Hybridisation or base pairing describes the process of binding between 2 stretches of complementary nucleic acid. This is between the ‘probe’ and the ‘target’, the definition of which varies in publications. According to B. Phimister(Nature Genetics) a probe is a tethered nucleic acid with known sequence, whereas a target is the free nucleic acid whose identity/abundance is being detected.

A Simplified explanation

A known reference DNA sample is created, based on a known sequence of a particular version of a gene(allele), this is then bound to a chip. When the unknown DNA sample to be analysed is taken, it is converted from RNA to DNA by RT-PCR and a flourescent (light emmiting)label is attached. Several different nucleic acid sections can be amplified up each with a different label.

These are then exposed to the chip, if the gene is the same as the probe i.e. identical allele, then it will stick to that DNA on the chip. The chip is then exposed to a specific wavelength of light, falling on the RNA 'label' which then emmits light and is detected - hence you can see if a particular DNA sequence with a given property is present.

Uses of these Chips

These ‘chips’ can be used in mutation analysis and geneotyping, this can be used to identify various alleles and unknown mutations of a specific gene i.e. expression profiling. This technology can also reflect relative concentrations of target nucleic acid i.e. mRNA. This allows gene expression of several genes to be measured at any one time giving an insight in to the interaction of complex expression patterns. Genome analysis and comparison between different species can now be done in a fraction of the time as each experiment does not have to be done singularly as in the past due to the miniturisation of the whole process. This also allows the more rapid identification of known genes in other species, for instance an oncogene known in a model species can be found in humans much more rapidly.


DNA chips offer a vast improvement in many areas of molecular biology; it’s contribution being its ability to greatly speed up investigative experiments. This potentially opens the gates of possibilities in the field as wide as imagination can carry it. Could for instance an entire human genome be represented on one chip, and what would that mean for society. Who holds this information and how it is used could have a profound effect, not only on molecular biology but society in general.

Ref. - Phimister, B.(1999) Going global. Nature Genetics volume 21 supplement p 1
D. D. Shoemaker, E. E. Schadt, C. D. Armour, Y. D., He, P. Garrett-Engele, P. D. McDonagh, P. M. Loer ..., Experimental annotation of the human genome using microarray technology, Nature Volume 409 Number 6822 Page 922 - 927 (2001) .

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