TABLE 3.
Influence of primer design on species specificity
| Species chromosomal DNA and primer(s) | Species specificitya | Sequenceb | No. of oligonucleotides 5′ to 3′c |
|---|---|---|---|
| L. elongisporus | |||
| Chromosomal DNA | GGGCCAGCATCAGTTTGA-GCGGTAGGAGAATTGCGTAGGAATGTGGCT | ||
| LEL4 | + | GGAGAATTGCGTAGGAATGTGGCT | 122 |
| C. parapsilosis | |||
| Chromosomal DNA | GGGCCAGCATCAGTTTGA-GCGGTAGGATAAGTGCAAAGAAATGTGGCA | ||
| CPA3 | − | AGCATCAGTTTGA-GCGGTAGGATAAG | 141 |
| CPA4 | + | GCATCAGTTTGA-GCGGTAGGATAAGc | |
| Candida sp.d | |||
| Chromosomal DNA | GGGCCAGCATCAGTTTGG-GCGGTAGGACAATTGCAAAGAAATGTGGCA | ||
| CWO1 | − | AGCATCAGTTTGG-GCGGTAGGAC | 144 |
| CWO2 | + | GCATCAGTTTGG-GCGGTAGGACg | |
| C. sojae | |||
| Chromosomal DNA | GGGCCAGCATCAGTTTGG-GCGGTAGGAGAATTGCGATGGAATGTGGCA | ||
| CSO11 | + | AGCATCAGTTTGG-GCGGTAGGAGg | 143 |
| C. maltosa | |||
| Chromosomal DNA | GGGCCAGCATCAGTTTGG-ACGGTAGGACAATTGCGGTGGAATGTGGCA | ||
| CMA3 | + | TTTGG-ACGGTAGGACAATTGCGGc | 135 |
| C. tropicalis | |||
| Chromosomal DNA | GGGCCAGCATCAGTTTGG-GCGGTAGGAGAATTGCGTTGGAATGTGGCA | ||
| CTR2 | − | TTG-GCGGTAGGAGAATTGCGTT | 132 |
| CTR21 | +e | TGG-GCGGTAGGAGAATTGCGTTt | |
| CTR22 | + | TGG-GCGGTAGGAGAATTGCGTTa | |
| C. viswanathii | |||
| Chromosomal DNA | GGGCCAGCATCAGTTTGG-GCGGCAGGACAATCGCGTGGGAATGTGGCA | ||
| CVI2 | + | TTGG-GCGGCAGGACAATCGCGTG | 132 |
| C. albicans | |||
| Chromosomal DNA | GGGCCAGCATCGGTTTGGAGCGGCAGGATAATGGCGGAGGAATGTGGCA | ||
| CAL4 | − | GGCCAGCATCGGTTTGGAGCGGC | 146 |
| C. dubliniensis | |||
| Chromosomal DNA | GGGCCAGCATCGGTTTGGAGCGGTAGGATAATGGCGGGGGAATGTGGCA | ||
| CDU1 | − | GGCCAGCATCGGTTTGGAGCGGT | 146 |
| C. albicans | |||
| Chromosomal DNA | TTGGTATTTTGCATGTTGCTCTCTCGGGGGCGGCCGCTGCGGTTTACCG | ||
| CAL5 | + | TGTTGCTCTCTCGGGGGCGGCCG | 182 |
| C. dubliniensis | |||
| Chromosomal DNA | TTGGTATTTTGCAAGTTACTCTTTCGGGGGTGGCCTCTGCGGTTTACCG | ||
| CDU2 | + | AGTTACTCTTTCGGGGGTGGCCT | 182 |
+, species-specific primer; −, primer that is not species-specific and that yielded PCR DNA fragments with chromosomal DNAs from two or more species.
Terminal nucleotides in lowercase represent deliberately introduced mismatches. C. albicans and C. dubliniensis have a base insertion (A at position 129 of C. albicans), and a gap has been inserted in the sequences of the first seven species in order to align the sequences (see reference 16 for aligned sequences of all species in this study).
Number of oligonucleotides from the 5′ end of the primer to the 3′ end of the D1/D2 sequence. Apparent discrepancies among starting positions and distances to the 3′ end as indicated in Table 2 (PCR fragment lengths) are due to insertions and deletions downstream from the starting position among the different species.
A new Candida species that will be described elsewhere.
CTR21 was able to distinguish C. tropicalis but consistently did not produce a DNA fragment as intense as that produced by CTR22.