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. 2013 Sep 23;2013:162645. doi: 10.5402/2013/162645

Table 3.

Optimized conditions for DGGE analysis.

Amplicon Primers set Optimal parameters (DGGE analysis)
Amount of DNA template in PCR reaction Voltage, V Time, hrs Denaturant range, (%) Amount of amplicon (per lane), μg Gel staining methods
V3–V5; 16S rRNA 338F-GC*/518R 300 ng 75 16 35–75 4.5 EtBr
V6–V8, 16S rRNA 948F-GC*/L1401 300 ng 75 18 40–65 1.5
3
Silver stain
EtBr
rpoB 1698F-GC*/2043R 600 ng 75 16 30–60 0.3 EtBr, silver stain

*GC clamp added to the 5′ end of the primers 338F, 948F, and 1698F, 5′CGCCCGCCGCGCGCGGCG GGCGGGGCGGGGGCACGGGGGG-3′.