Molecular probe design. (a) The deep blue color represents the 40-base sequence similarity domain (the Homer), which is divided into two 20-base segments. The aquamarine color represents the 20-base oligonucleotide barcode from the Tag4 array. The yellow color represents the 36-base domain for the two 20 base PCR primers. The two 20 base primers overlap by 4 bases at the 5' ends. The total length is 96 bases. The 5' end is phosphorylated. (b) The molecular probe mixture is incubated with the denatured target DNA under annealing conditions. Where sufficient sequence similarity exists between the molecular probe and the target single-stranded DNA (indicated by the deep blue color), 40 bp of duplex DNA are formed. The 5'-phosphorylated end of the molecular probe is adjacent to the 3'-hydroxyl end of the probe with no bases missing.