Types and Characteristics of DNA Chips
A DNA chip consists of a few hundred to ten thousand types of DNA fragments which are densely placed on a glass or resin substrate. Nucleic acid targets such as DNA and RNA extracted from a sample are hybridized onto the DNA chip. A variety of analyses on DNA and RNA can be performed including determination of base sequences of the targets, analysis of gene mutations, measurements of gene expression levels and copy numbers, and analysis of methylation states.
DNA chips are largely divided into the following types.
Types of DNA chips
- cDNA chips
A cDNA chip consists of a collection of cDNA fragments which are reverse transcripts of gene transcription products (mRNA). These cDNA fragments are immobilized on a substrate. The probes are the cDNA fragments previously adjusted according to the PCR method. A cDNA chip is produced by spotting the fragments on the substrate using a spotter. The lengths of cDNA are generally not uniform. Nucleic acid probes for detection can be spotted ranging from a few hundred nts (nucleotides) to over a thousand nts.
- Oligo DNA chips
An oligo DNA chip is a DNA chip whose probe is the chemically synthesized oligo DNA after genes corresponding to exons in the region of 20-100 nts are selected. Since the probe is shorter than a cDNA chip, its specificity is high and cross hybridization can be inhibited.
- BAC clone chips
A BAC clone chip is a DNA chip whose probe is a template amplified by PCR. The template is a genome region incorporated into a comprehensive BAC (bacterial artificial chromosome) clone which various research institutions used in decoding the genome sequence of various organisms. BAC is a vector that can clone a gene of 100-300 kb long. A BAC clone chip is used to analyze the number of genomic DNA copies in such methods as the CGH array.
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