TABLE 1.
Sequences of primers used in this study
| PCR fragmenta | Forward primerb | Reverse primerb | bp (codons)c |
|---|---|---|---|
| A | 5′-gcgcgGCGTCGGTAGGCAAACTG-3′ | 5′-cgcccgccgcgccccgcgcccggcccgccg- cccccgcccgTGTGCCGGAGAAGTGGTC-3′ | −50-182 (−27 bp-53) |
| B | 5′-cgcccgccgccgcccgccgcgccccgcgcccgtcccgc- cgcccccgcccgGTCGTGGCAACCAAGGAC-3′ | 5′-gcgcgAGAACACCGCCTCGATTG-3′ | 131-284 (52-86) |
| C | 5′-CATTGCGTCAGCGGTACT-3′ | 5′-cgcccgccgccgcccgccgcgccccgcgccc- gtcccgccgcccccgcccgaaataataaaTG- GCAATACCGACCACAT-3′ | 212-403 (80-126) |
| D | 5′-cgcccgccgccgcccgccgcgccccgcgcccgtcccgccgcccc- cgcccgaaataataaaCACGCCACTGCTGAATTG-3′ | 5′-ACAGTTCATCCCGGTTCG-3′ | 340-588 (121-187) |
| E | 5′-cgtcccgcGCGGGCGTTGATCATCGTCG-3′ | 5′-cgcccgccgcgccccgcgcccggcccgccg- cccccgcccgCGGTGTGCCGGAGAAGTGGT-3′ | 3-186 (9-53) |
| SEQ | 5′-CGGCGTCATGGACCCTATATC-3′ | 5′-CCGCCAACAGTTCATCCC-3′ | −81-594 |
a
Primers sets amplify the PCR fragments for DGGE; SEQ, primers used to amplify pncA for sequencing.
b
Clamp sequences are in lowercase, and pncA-specific sequences are in uppercase.
c
The 5′ nucleotides of forward and reverse primers relative to the pncA open reading frame; −50, base pairs upstream of pncA initiation codon. The codons scanned by each PCR product represent the range of whole codons between the 3′ ends of primers and include a gap of 2 to 5 bp.