Comparison of microarray hybridization versus solution-phase melting temperatures. DNA microarrays containing 2-base (diamonds) or 3-base (squares) mismatches across the entire length of the 30-mer oligonucleotide probe for multiple transcripts were hybridized to complex target prepared from total RNA isolated from kidney. The intensity for each mismatch, represented as a percent of the perfect match signal, for three probes, (A) M62388, (B) M86443, and (C) NM013226, is shown. The change in melting temperature of a 3-base mismatch of a DNA oligonucleotide with a complementary RNA oligonucleotide (triangles) is plotted for measurements made in stringency wash buffer in (A) and (B). Bases are numbered starting from the 5' end. The surface (5') and solution (3') ends of the oligonucleotide probe are indicated by the arrows.