Design and synthesis of complete n-mer arrays. (A)N-mer arrays containing duplex probes suitable for ligation to target DNA molecules were created as follows: The array-based probes contained a 20-base constant anchor sequence and an n-base combinatorial sequence. A 20-mer complementary oligonucleotide was hybridized to the constant anchor sequence of the probes generating duplex probes with 5′ n-mer overhangs. The duplex probe acts as a template to direct the ligation of 5′-phosphoryl DNA molecules. (B) One quadrant of an 8-mer array showing the probe intensity pattern generated by chemical ligation of a 1.2-kb HIV DNA target. An expanded view is also shown to better illustrate the individual probe features.
