VDA chipo Carr et al. 2007

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 accommodate hundreds of thousands of oligos.


Text material 2013 by Steven M. Carr