I have extracted sunflower DNA a dozen times now. I get one consistent problem a gelatinous film coprecipitating with my DNA (carbohydrates/polysaccharaides). I also get sharp smelling phenolic compounds. These occur regardless of DTT/2-BME addition.
I found a paper detailing the use of 2-butoxyethanol (2-BE) to remove strawberry polysaccharides and phenolics. The researcher’s idea is to perform a two-step precipitation:
1. 2.5-4.0 volumes of 2-BE and 80 mM Na+ (from sodium acetate) – this step is reported to remove polysaccharides. Incubate on ice and spin.
2. The supernatant is harvested and treated with 1.0 volume of 2-BE, cooled and centrifuged.
3. The pellet is washed sequentially with 2-BE and ethanol.
The quantified reduction of polysaccharides is between 50-97%. Their DNA wash digestible and able to undergo self ligation post-digestion.
The nice thing about this technique is that it can be applied to all DNA extractions used in the lab and should cleanup existing, dirty DNA. More over the chemical is ~$40 for 1000 mL
I’ll report back.