Table 1 Criteria for oligonucleotide probe selection
Oligo selection criterion | probes satisfying the rule [%] | Rule symbol |
|---|---|---|
Oligonucleotide properties | ||
Melting temperature = 70°C (+/- 8°C) | 97.18% | T |
Nucleotide composition: oligonucleotide cannot have a contiguous single nucleotide base repeat longer than 8 bases AND probe GC content fits the 20-to-60% range AND each base cannot constitute more than 40% of the oligonucleotide sequence | 85.33% | C |
Secondary structure | ||
Stem of potential hairpin structure cannot be longer than 8 bases | 99.20% | H |
Probe specificity | ||
Minimum Hamming distance to non-target parts of genome > 25 | 99.45% | D |
Substring: not more than 20 contiguous bases common to other (non-target) parts of genome | 99.02% | S |