I am extracting RNA from poplar roots using the sigma Spectrum Plant Total RNA kit and finding that the extracts are colored brown at the end of the protocol. Using an additional Zymo RNA cleanup column does not help with this. I also tried adding PVP to the lysis buffer because I heard this can help remove polyphenols but this did not help either. Despite the brown color, Nanodrop purity readings are not terrible. The A260/A280 is around 1.6 and the A260/A230 is around 1.1. I know these good be better but I have had success using extracts with similar ratios. Will the brown color be a problem? Is there anything I can do to remove it? The Qiagen RNEasy Powerclean Pro kit seems to advertise that it can effectively remove pigments. Maybe this would be a better cleanup than the Zymo kit?
I usually extract RNA from the root using the Nzytech kit and I do not get colored RNA. Maybe, you could try another kit, or put less amount of sample in the columns.
After passing through gDNA removing column, mixed the elute with equal amount of absolute ethanol (or your kit recommended solution), then you will see some precipitate. Centrifuge it for some seconds, and use clear supernatant for RNA column. You will get Clean and Clear RNA. I used to meet this problem while extracting RNA from Chinese Tallow young leaves and roots
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