About DGGE and SSCP - (Dec/08/2003 )
I want to use DGGE or SSCP to analysis microbial diversity in pollutent soils, who can give me some notes, and which method (DGGE or SSCP) is better, and easier to apply.
If You are going to analyse SNP'S, as I proposed, it is better to use SSCP. SSCP is much easier and reliable in analysis of SNP's. On the other hand if yours PCR fragments are larger than 200 bp it will be better to use DGGE. DGGE will allow You to analyse DNA fragments as much as 600 bp. SSCP is better if you want to analyse microsatellytes, but in this case I recommend You to use AFLP. Both, SSCP and DGGE, require further sequencing of polymorphysms You will be find. At the end I would like to say that for my opinion it is better to use SSCP.
thank you Toni
I'm afraid my PCR fragments is larger than 200 bp, it's usually about 450 bp, wheather it can be use SSCP? according to your advice, DGGE may be the better choise, but it need design primer with GC-clamp, so the PCR conditions should optimized.
Although i did it ,but the result was unsatisfied. I don't konw wheather the PCR product shoud be purified, but I'm study the soil microbial diversity, it's no probolem with purified strains, but when analysis soil sample, some bands may be lost if the PCR products were purified,and I will lost some information.