A DNA chip
is a small piece of silicon glass (~1 cm2) to which a
number of synthetic, single-stranded DNA oligonucleotides
bonded [left]. Oligos function as DNA
probes: they "stick"
(anneal) selectively only to those DNA
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
in a heterogeneous mixture of genes, for example the presence of
particular allele against the background of a complete genome.
effect, oligos act like molecular "velcro."
"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
the DNA sequences of
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
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
that the individual is homozygous
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 accommodate hundreds of thousands of oligos.