Principle of a DNA microarray chip:
use as Variant Detector Arrays (VDAs)
(after SM Carr et al. 2008. Comp. Biochem. Physiol. D, 3:11)
A DNA chip
is a small piece of silicon glass (~1 cm2) to which a large
number of synthetic, single-stranded DNA oligonucleotides ("oligos") have been chemically
bonded [left]. Oligos function as DNA
probes: they "stick"
(anneal) selectively only to those DNA
molecules
whose nucleotide sequences are exactly complementary: T pairs with A, and G with C. They can therefore be used to identify the presence of specific DNA
sequences
in a heterogeneous mixture of genes, for example the presence of a
particular allele against the background of a complete genome. In
effect, oligos act like molecular "velcro."
A
computer
"reads" the pattern
of annealing and "reports"
which alleles are present.
DNA chips can be used s Variant Detector
Arrays (VDAs) to look for
DNA sequences that differ by single nucleotide polymorphisms ("SNPs"). In
this
example,
the DNA sequences of the four
oligos
highlighted in the first bloc differ only at the last
position. To determine which alleles are present,
genomic DNA from
an individual is isolated, fragmented, tagged with a fluorescent dye,
and applied
to the chip. The genomic DNA
fragments anneal only to those oligos to
which they are perfectly
complementary: in this case, the allele with the ~T~ SNP allele
binds to the ~~A oligo, and
the allele with the ~C~ SNP allele binds to the ~~G oligo.
A computer reads the position of the two fluorescent tags and
identifies the individual as a
C / T heterozygote. [The single spots in the other three
columns indicate
that the individual is homozygous at
the
three
corresponding SNP positions].
The 4 x 4 arrays fits in one corner of a 256-oligo chip (lower right). The current generation of microarrays can accomodate hundreds of thousands of oligos.