Microarray Technology

DNA Microarray is one such technology which enables to analyze the expression of many genes in a single reaction quickly and in an efficient manner. DNA Microarray technology has empowered the fundamental aspects underlining the growth and development of life as well as to explore the genetic causes of anomalies occurring in the functioning of the human body.


Theoretical overview of a Microarray steps involves:
1. Extraction of mRNA
2. Make labelled cDNA  through reverse transcription
3. Mixing of samples & hybridize to cDNA microarray
4. Wash to remove non specific binding
5. Spin & scan
6. Analyze

"A typical microarray experiment involves the hybridization of an mRNA molecule to the the DNA template from which it is originated. Many DNA samples are used to construct an array. The amount of mRNA bound to each site on the array indicates the expression level of the various genes". This number may run in thousands. All the data is collected and a profile is generated for gene expression in the cell.

A DNA “chip” or microarray is prepared on a small solid base such as a piece of glass  divided into a grid of tiny squares. To each square is attached a different and specific piece of DNA, typically a short DNA sequence that can act as a probe for a particular gene. DNA corresponding to thousands of different genes can be accommodated on a single array no bigger than a microscope slide. A single stranded DNA sample of interest is cut up and then washed over the chip. Any sequence in the sample that matches a sequence on the chip will hybridise to it and, if the sample is suitably labeled (usually with a fluorescent tag) the pattern of matches can be visualised and analysed by computer, giving a read-out of the presence or expression level of hundreds of different sequences simultaneously. Microarray Technique An array is an orderly arrangement of samples where matching of known and unknown DNA samples is done based on base pairing rules. An array experiment makes use of common assay systems such as microplates or standard blotting membranes. The sample spot sizes are typically less than 200 microns in diameter usually contain thousands of spots. Thousands of spotted samples known as probes (with known identity) are immobilized on a solid support (a microscope glass slides or silicon chips or nylon membrane). The spots can be DNA, cDNA, or oligonucleotides. These are used to determine complementary binding of the unknown sequences thus allowing parallel analysis for gene expression and gene discovery. An experiment with a single DNA chip can provide information on thousands of genes simultaneously. An orderly arrangement of the probes on the support is important as the location of each spot on the array is used for the identification of a gene.

Types of Microarrays

Depending upon the kind of immobilized sample used construct arrays and the information fetched, the Microarray experiments can be categorized in three ways:

1. Microarray expression analysis: In this experimental setup, the cDNA derived from the mRNA of known genes is immobilized. The sample has genes from both the normal as well as the diseased tissues. Spots with more intensity are obtained for diseased tissue gene if the gene is over expressed in the diseased condition. This expression pattern is then compared to the expression pattern of a gene responsible for a disease.
2. Microarray for mutation analysis: For this analysis, the researchers use gDNA. The genes might differ from each other by as less as a single nucleotide base.
A single base difference between two sequences is known as Single Nucleotide Polymorphism (SNP) and detecting them is known as SNP detection.
3. Comparative Genomic Hybridization: It is used for the identification in the increase or decrease of the important chromosomal fragments harboring genes involved in a disease.

Microarrays are useful when one wants to survey a large number of genes quickly or when the sample to be studied is small. Microarrays may be used to assay gene expression within a single sample or to compare gene expression in two different cell types or tissue samples, such as in healthy and diseased tissue. Because a microarray can be used to examine the expression of hundreds or thousands of genes at once, it promises to revolutionize the way scientists examine gene expression. This technology is still considered to be in its infancy; therefore, many initial studies using microarrays have represented simple surveys of gene expression profiles in a variety of cell types. Nevertheless, these studies represent an important and necessary first step in our understanding and cataloging of the human genome.

With new advances, researchers will be able to infer probable functions of new genes based on similarities in expression patterns with those of known genes. Ultimately, these studies promise to expand the size of existing gene families, reveal new patterns of coordinated gene expression across gene families, and uncover entirely new categories of genes. Furthermore, because the product of any one gene usually interacts with those of many others, our understanding of how these genes coordinate will become clearer through such analyses, and precise knowledge of these inter-relationships will emerge. The use of microarrays may also speed the identification of genes involved in the development of various diseases by enabling scientists to examine a much larger number of genes. This technology will also aid the examination of the integration of gene expression and function at the cellular level, revealing how multiple gene products work together to produce physical and chemical responses to both static and changing cellular needs