DNA microarray:

DNA microarray:
  • A DNA microarray also known as gene chips, DNA chip, or biochip is a collection of microscopic DNA spots attached to a solid surface.
  • DNA microarrays are used to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles (10−12 moles) of a specific DNA sequence, known as probes or reporters.
  • A probe can be a short section of a gene or other short DNA sequence that are used to hybridize a complementary DNA (cDNA) or cRNA sample that are called target under high-stringency conditions.
  • The Probe-Target Hybridization event is usually detected by a quantifiable signal generation from the fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative nucleic acid sequences in the target. 
  • Principle of working
    • cDNA probes (> 200 nt), usually produced by PCR, attached to either nylon or glass supports
    • Oligonucleotides (25-80 nt) attached to glass support
    • Oligonucleotides (25-30 nt) synthesized in situ on silica wafers (Affymetrix)
    • Probes attached to tagged beads.

The main principle behind microarray technology
  • It is the hybridization between two DNA strands. The property of complementary nucleic acid sequences to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs is the main force of recognizing complementary partner.
  • A high number of complementary base pairs in a nucleotide sequence allow tighter non-covalent bonding between the two strands. After washing off of non-specific bonding sequences, only strongly paired strands will remain hybridized.
  • So fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the strength of the hybridization determined by the number of paired bases, the hybridization conditions such as temperature, and washing after hybridization.

Limitations of microarrays

Hybridisation-based approaches are high throughput and relatively inexpensive, but have several limitations which include:
  • reliance upon existing knowledge about the genome sequence;
  • high background levels owing to cross-hybridisation;
  • limited dynamic range of detection owing to both background and saturation signals;
  • comparing expression levels across different experiments is often difficult and can require complicated normalisation methods
Advantages of Microarray in DNA Detection
  • DNA microarrays can be used to measure changes in expression levels, to detect single nucleotide polymorphisms (SNPs), or to genotype or resequence mutant genomes.
  • Revolution in the analysis of genetic information
  • Hybridization is a highly parallel search by each molecule for matching partner on an affinity matrix.
  • Specificity and affinity of complementary base pairing.
  • Use of glass as a substrate, fluorescence for detection and the development of new technologies for synthesizing or depositing DNA have allowed the miniaturization of DNA arrays with increases in information content.
  • "DNA chip”/ "DNA microarray" allows to collect more information about DNA sequences in an afternoon than an army of scientists could collect in years using earlier several techniques.
  • DNA chips promise to carry the science of understanding genomes to a whole new level, and to bring tools for getting DNA-sequence information out of research labs into doctors' offices, the better to tailor-fit medical treatments to an individual's particular genetic makeup.


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