The DNA pellet that just won't resuspend - DNA extraction Large Scale (Aug/08/2005 )
Yes the polyphenols do bind to the DNA if you don't have things like PVP present. If you want to know more about this then look at the literature on plant nucleic acid extraction.
Daniel
Improved automated DNA sequencing
Thank you for clearing that up 
I guess I'll throw away that old DNA sample and start over then. Is SDS better than CTAB? I'll ask around and see if I can get some Sodium D-isoascorbate for tomorrow.
Thank you
Phil
Hi Phil,
Check your PM - I've sent you a copy of the article. 
They compare CTAB method and SIA method for RNA extraction from various plants, and (not surprisingly) find SIA method works better for their samples. I'm not sure if you can say that SDS works "better" than CTAB, but in this instance, with the SIA addition for these samples, it does.
One thing that you want to note is that sodium isoascorbate will turn the extraction buffer orange if you store it for some time. I used mine immediately, but even the next day my extraction buffer was orange and starting to crystallize. I haven't tried to do another extraction (yet), but will be making fresh buffer and probably storing it in the dark. The first bottle is still sitting on my lab bench and I'm curious as to how dark an orange it will become (or maybe I'm just to lazy to throw it out) 
If you can't find sodium D isoascorbate lying around in someones lab it's available from Sigma (Sodium D-isoascorbate monohydrate) Cat # 496332 (250g) for $42.
Good luck!
Nicole
Hello all,
I've read the article that you sent me Nicole (Thank you ) but I wasn't able to get any Sodium isoascorbate, however we do have some Sodium borohydride (NaBH4). The article mentions it as a strong reductant but how strong? I wasn't able to get the reference so I don't know what concentration I should use in my extraction buffer. What make a reductant strong or weak? Is it the amount of electrons that they can give? how do you tell that from looking at their structure? my chemistry isn't any good 
Phil
This isn't exactly the same issue, but I dealt with complex soil DNA (microbial) and had problems with soil organics binding to the extracted DNA. One thing you might try is to electrophorese the pellet in a relatively low percentage agarose gel. The high MW DNA would migrate slowly, while the charged organics would migrate out of the DNA. I would then cut out the agarose plug that held the DNA and purify it from that. It worked nicely for PCR, etc. Before this step, it wouldn't
Attached is one photo of a gel purification run - you can see the genomic DNA at the top, and in the far right lanes, the soil organics (humics/fulvics) that were removed from the DNA via electrophoresis.
Dave Knaebel
I've read the article that you sent me Nicole (Thank you
) but I wasn't able to get any Sodium isoascorbate, however we do have some Sodium borohydride (NaBH4). The article mentions it as a strong reductant but how strong? I wasn't able to get the reference so I don't know what concentration I should use in my extraction buffer. What make a reductant strong or weak? Is it the amount of electrons that they can give? how do you tell that from looking at their structure? my chemistry isn't any good Phil
What every you do, don't use the Sodium borohydride!
That kind of reduction power would chemically hydrate double bonds, reduce aldehyde and ketone groups into alcohols... Guanidine, thymidine and cytocine have ketone groups. And if you add this to an acidified medium, you are going to get a small flame of hydrogen burning.
In layman's terms the reducing power of a compound is determine by how weakly it holds onto electrons. If the compounds hold onto electron is weak, then it is a strong reducing agent. Electron structure and electro negativity of the elements that compose the compound give some hint on the reducing power.
I think when they mean strong reducing agent, they ment strong from the point of a biologist. (not from the point of a chemist)