I am looking for suggestions for improving amplification of soil DNA using ITS primers. The soil samples range in concentration from 9-40 ng DNA/ul). Attached are photos of gel confirmation using 5 ul DNA in the PCR (wells 1-24: samples diluted to 10 ng/ul, wells 25-48: samples undiluted). 1:100 dilutions of a subset of samples yielded even weaker bands on the gel.

I am using ITS4-Fun and 5.8S-Fun primers as described in Taylor et al 2016 (https://aem.asm.org/content/aem/early/2016/10/03/AEM.02576-16.full.pdf) to target fungal genes for amplicon sequencing. Thermocycler conditions are 96C for 2 min, 27 cycles of denaturation at 94C for 30sec, 58C for 40sec, 72C for 2 min, with final extension at 72C for 10 min. I am using the following PCR reagents per sample: 21.5 ul Platinum SuperMix High Fidelity (Invitrogen 12532016), 0.5 ul bovine serum albumin (BSA 20 mg/ml; Fisher BP675-1), 1.25 ul of each ITS primer, 5 ul template DNA. I prepare the PCR cocktails in a stripwell plate inside a cold plate.

The only thing I can think of to try is to increase the number of cycles in the thermocycler. Any suggestions would be greatly appreciated.

More Kendall Beals's questions See All
Similar questions and discussions