I suggest to use 8 to 10% gel (polyacrylamide concentration) having a gradient of 30-40/60-80. By the way, which primers you are using??

I also suggest you to use a 8% gel polyacrylamide concentration. I have being using 8% polyacrylamide concentration for ca. 200 bp PCR amplicons and it is working well. Concerning denaturant concentrations it will depend on nucleotide compositions that you will have in your environmental samples that are unknown, and that will also depend on the chosen primers. For instance, for aquatic bacteria, using the primer pair 338GC/518, I got good resolution by using a gradient of 35-80%. On the other hand, for the same samples and using the primer pair 984GC/1378, a good resolution was obtained by using a polyacrylamide concentration of 6% (since amplicons have ca. 433 bp, and thus a bit longer than those got with 338GC/518) and with a gradient of 52.5 -75%.

By the way, which microbial group are you targeting, bacteria? Or fungi?

Hi Istianti Nurisa!!!

To separate 200pb in DGGE you should use a gel with 8-10% (polyacrylamide concentration). The denaturing gradient will depend on the environmental sample, GC content of microbial and primers that were used. Therefore, advise perform a gradient of 0-100 and selecting the lowest gradient in which the fragments were concentrated.

I would use acrylamide concentration 6% and the denaturing gradient between 20 and 30% if the taergated amplicons are around 200bp size.