After treating cells with chitosan based particles and subsequentially isolating RNA (using for eg. regular RNA preps such as RNeasy, or mirVana) often the RNA recovery is very low and quality less good in comparison to non-treated cells. This is most of the times due to the chitosan polymer interacting quite strongly with the RNA after cell lysis. Are there any alternatives to improve the yields of such procedure?(chitosanase pre-treatment of cells is one, but quite expensive, thus it would be interesting to know of any possible alternative to this method).
I had a similar issue when treating soil with colloidal chitin. Trying to extract total DNA was indeed much more difficult than the untreated control, probably because of the polymer interaction during the extraction, and I would not be surprise if it does the same with RNA extraction. My guess would be to try to remove it with solvant, if possible. Check this reference: "Chitin and chitosan polymers: Chemistry, solubility and fiber formation" in Progress in Polymer Science, 34:641-78
http://www.sciencedirect.com/science/article/pii/S0079670009000318
They suggest diluted acids TCA–MC for solubilisation of chitosan.
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