The diagram shows a schematic representation of a DNA re-sequencing microarray experiment. The array is based on a reference sequence on length n bases (up to 30Kb), represented in a series of n overlapping ("tiled") oligonucleotide probes each of length 25. For each probe, three variant probes are included that vary the middle (13th) base, one for each of the three alternative code letters. In the example, given a reference DNA sequence AGCC at positions 1, 2, 3, & 4, the four probes tiling position 1 are (top to bottom) TGCC, GGCC, CGCC, and AGCC. The same arrangement occurs for probes tiling positions 122-124: note that the order of the variant bases in each set of probes is constant (T, G, C, A = 1st , 2nd, 3rd, 4th).
Consider
an experimental DNA sequence
that
has a single nucleotide polymorphism
(SNP) at position 4: AGCT.
The complementary strand ~~~TCGA~~~ will
match
the middle position of only one of the four variant
probe
sequences at each tiling
position: that probe will anneal preferentially to the
experimental DNA,
because the mismtach
will interfere with annealling to the other oligos. The
pattern of
annealing on the
chip is read by a computer (blue array). In this case,
template
annealing to the 4th, 2nd,
3rd, and 1st probes at positions 1,2,3,
and
4 "re-sequences" this region, indicates that the
original (complementary) sequence is AGCT.