We have isolated rice plant DNA by the CTAB method, and we are aiming to amplify the particular region of rRNA. We have standardised the universal primers as well, which are working fine for other plant species except for rice, During gel visualisation we are able to find a very light and thin amplified DNA band that too only for one to two samples, we have checked the DNA integrity also. and since we have isolated DNA by CTAB method we didn't treat them with RNAse, so the ratio is showing 2.02, 2.03 somewhat. but the DNA quantity is good. what may be the possible reasons that we are getting less amplification of our desired region in DNA.?
One possible solution could be, if the universal primers don’t work for rice then design new primer sets specific for the particular rice gene and then validate them in silico then order them and check them on gel or you can try treat your sample with RNAse and see the effect.
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