DNA Microarray: Introduction, Definition, Principle, Detection method

DNA Microarray: Introduction, Definition, Principle, Detection Method and Its Application

Introduction of DNA Microarray

Genes and their expression profiles were previously researched on a case-by-case basis. We can now look at numerous genes at once thanks to DNA microarray technology. It enables quantitative and qualitative comparisons of two cells’ gene expression patterns.

Definition of DNA microarrays

DNA chips are also referred to as arrays since they are arranged in a specific pattern. These chips are also known as gene chips and biochips. Each DNA fragment encoding a gene is assigned a specific place on the array. To identify individual gene sequences, use the location of each mark. Up to 30000 spots can be stored on a single slide.

Principle of DNA microarrays

Principle-based hybridization probing uses fluorescently labeled nucleic acid molecules- “mobile probes” Spots are single-stranded DNA fragments, strongly attached to the slide. RNA or cDNA is tagged with a fluorescent dye.
Probe – a standardized set of DNA sequences. Target or sample – labeled experimental DNA or RNA. Autoradiography laser scanning fluorescence detection devises an enzyme detection system.

Detection methods Hybridization method in DNA Microarray

A microarray is used to incubate target DNA that has been tagged. Probes with high GC content hybridized more strongly than those with high AT content, matching the target hybridized more strongly than probes with mismatches, insertions, and deletions. Methods that are both radioactive and non-radioactive -Biotin or digoxigenin labeling necessitates autoradiography gas-phase ionization, phase ionization phosphoimagers for direct detection.

Fluorescence detection method in DNA Microarray

Multiplexing- one target DNA may be labeled with more than one fluorochromes. Hybridization can be screened using automatic scanners.
Characteristic features of DNA chips:
Parallelism– allows parallel acquisition and analysis of massive data and meaningful comparison between genes or gene products represented in the microarray.
Miniaturization–involves miniaturization of DNA probes and reaction volumes thus reducing time and reagent consumption. Multiplexing –it involves multicolor fluorescence allow the comparison of multiple samples in a single DNA chip. Automation–manufacturing technologies permits the mass production of DNA chip and automation leads to proliferation of microarray assays by ensuring their quality, availability and affordability Types of DNA chips Two types-

Oligonucleotide based
chips cDNA based chips

Technical application in DNA Microarray

Green represents control DNA, where either DNA or cDNA derived from normal tissue is hybridized to the target DNA. Red represents Sample DNA, where either DNA or cDNA is derived from diseased tissue hybridized to the target DNA. Yellow represents a combination of control and sample DNA, where both hybridized equally to the target DNA. Black represents areas where neither the control nor the sample DNA hybridized to the target DNA.
Spotted microarrays
Probes are oligonucleotides,cDNA, or small fragments of PCR products that
correspond to mRNAs and are spotted onto the microarray surface.
Oligonucleotide microarrays
There are commercially available designs that cover complete genomes from companies such as GE Healthcare, Affymetrix, Ocimum Biosolutions, or Agilent.

Applications of DNA microarray

Detection of single nucleotide polymorphisms (SNPs) Characterization of mutant
Genetic mapping
Proteomics
In cancer

Tumor formation involves simultaneous changes in hundreds of cells and variations in genes.
Gene microarrays have been used for comparative genomic hybridization. In this technique, genomic DNA is fluorescently labeled and used to determine the presence of gene loss or amplification

The conversion of a non-invasive tumor to an invasive tumor also warrants research.

Antibiotic treatment
Early detection of oral precancerous lesions

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