DNA microarrays are solid supports, usually of glass or silicon, upon which DNA is attached in an organized, pre-determined grid fashion.
Each spot of DNA, called a probe, represents a single gene.
DNA microarrays can analyze the expression of tens of thousands of genes simultaneously.
There are several synonyms for DNA microarrays, such as DNA chips, gene chips, DNA arrays, gene arrays, and biochips.
Principle of DNA Microarray Technique
- The principle of DNA microarrays lies on the hybridization between the nucleic acid strands.
- The property of complementary nucleic acid sequences is to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs.
- For this, samples are labeled using fluorescent dyes.
- At least two samples are hybridized to chip.
- Complementary nucleic acid sequences between the sample and the probe attached on the chip get paired via hydrogen bonds.
- The non-specific bonding sequences while remain unattached and washed out during the washing step of the process.
- Fluorescently labeled target sequences that bind to a probe sequence generate a signal.
- The signal depends on the hybridization conditions (ex: temperature), washing after hybridization etc while the total strength of the signal, depends upon the amount of target sample present.
- Using this technology the presence of one genomic or cDNA sequence in 1,00,000 or more sequences can be screened in a single hybridization.
Types of DNA Microarrays
There are 2 types of DNA Chips/Microarrays:
- cDNA based microarray
- Oligonucleotide based microarray
Spotted DNA arrays (“cDNA arrays”)
- Chips are prepared by using cDNA.
- Called cDNA chips or cDNA microarray or probe DNA.
- The cDNAs are amplified by using PCR.
- Then these immobilized on a solid support made up of nylon filtre of glass slide (1 x 3 inches). The probe DNA are loaded into a a spotting spin by capillary action.
- Small volume of this DNA preparation is spotted on solid surface making physical contact between these two.
- DNA is delivered mechanically or in a robotic manner.
Oligonucleotide arrays (Gene Chips)
- In oligonucleotide microarrays, short DNA oligonucleotides are spotted onto the array.
- Small number of 20-25mers/gene.
- The main feature of oligonucleotide microarray is that each gene is normally represented by more than one probe.
- Enabled by photolithography from the computer industry
- Off the shelf
Requirements of DNA Microarray Technique
There are certain requirements for designing a DNA microarray system, viz:
- DNA Chip
- Target sample (Fluorescently labelled)
- Fluorescent dyes
Steps Involved in cDNA based Microarray