My project concerns analysis of the microbial community of sediments from aquaculture systems in concrete tanks supplied with fresh sea water. We followed a molecular approach through PCR cloning and DGGE based on 16SrRNA sequences.
A short fragment (586bp) of 16S bacterial rDNA was amplified. Five sediment samples were analysed. The PCR products (approximately 2ug) were resolved on DGGE gel of 30-60% urea/formamide superimposed on a 6% polyacrylamide gel. Conditions were 60oC, 200V, 5hrs. The gel was run in 1xTAE buffer and stained with SYBR-Gold (freshly made) for 45min.
My issue is that the gel picture shows a few bands. More specifically in the lower part of the gel I can see some very faint bands.
Is there any way that I can intensify these faint bands?
You can try nested PCR with primer containing GC Clamp, if you haven't used it earlier.
silver staining is capable of staining a few pg dna but the sybr dyes need about 25pg for a good signal
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