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Hi All,

I always surprise to see the mucilagenous like substances that are formed, once the DNA pellet is dissolved in TE buffer.Becos of this, i get negative PCR results. What could be the possible solution to overcome this problem ??

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What lineage are you working on? In the algal world we have significant challenges owing to polysaccharides co-extracting with the DNA. In our lab we have found that the best solution is to add potassium acetate to red algal extraction buffers and CaCl2 to extraction buffers for brown algae (both known to precipitate the respective polysaccharides). We have also found that the former is effective for some inverts that are prone to mucilage , but we have not tested this extensively. See Saunders (1993, J. Phycol. 29: 251-254). We also outline our updated methods in the upcoming 'Methods in Molecular Biology, DNA barcodes: methods and protocols' edited by Kress & Erickson. 
Dear Gary Thanks a lot for ur information.. My lineage is "Medicinal Plants". Also, i work in dried fruit powders of medicinal plants...when i extract DNA from those dried samples, they are obtained as almost degraded ones and the DNA turns into jelly form after a week..and instead of white pellet, the DNA is coloured from light brown to dark brown.. i suspect them to be polyphenols and polysaccharides...Could you suggest me with some ideas to rectify my problem?
You should chat with the folks at Guelph (especially Natalia Ivanova). We use salts as indicated previously to deal with the polysaccharides, but she got us using acetone to clean up the polyphenolics, which saved us a lot of time and money on our extractions. We combined her method with our own to develop a rapid solution to both problems, at least for the brown algae (see McDevit & Saunders 2009, Phycological Research 2009; 57: 131–141).
Dear Gary, i would chat with natalia as per your suggestion. But i couldn't access the article that you suggested me to refer (McDevit & Saunders 2009, Phycological Research 2009; 57: 131–141)..Could you please send me the article to my email address dhivyas87@gmail.com.
Here you are. I hope that it helps.
Attachments:
Dear Gary, Thanks a lot for sending me the article...i would go through it...pls help me in future for further clarificatios..

Yes you can use statistics to analysis to analysis your DNA sequence data. You can use the following analysis

1.

Multple array & clustring analysis

2. Hierarchical clustering
3. K-means clustering
4. Self Organising Maps
5. PCA
6. Distance measures

7. Parsimany analysis

 

Manimekalan

Thank You Sir! for the valuable information :)
The formation of mucilagenous substances may be due to high content of polysaccharides and polyphenolic compounds (this problem is mainly found in medicinal plants). So, the best way to avoid is to use 2% PVP (polyvinyl pyrrilidone).

Dear Dhivya,

I am also having similar issues with my DNA, I am working on the gelatinous freshwater algae.

My question is, is there any possible ways by which I can remove the gelatinous material directly from my DNA (finished product).

Thanking you in anticipation.

Regards

deepak

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