Between CTAB and QIAGEN DNeasy Mini Kit extraction methods which will produce the cleanest and largest amount of DNA for Araliaceae? I am specifically working with leaf material from Polyscias (Tetraplasandra).
Some more factors are important to answer this question:
is it fresh material, silica dried fresh material or herbarium material?
And what do you want to do with the DNA and in what part are you interested (Chloroplast, Core or Mito ? ).
Cleanest and largest amount is impossible. Usually while "cleaning" DNA you lose a lot, so you have to decide what is more important for you. I like CTAB, you get A LOT more DNA, it is by far cheaper and quality is also quite good. If you are not satisfied with the quality you can perform some purification steps (Precipitation, using kits or whatever)
Some more factors are important to answer this question:
is it fresh material, silica dried fresh material or herbarium material?
And what do you want to do with the DNA and in what part are you interested (Chloroplast, Core or Mito ? ).
Cleanest and largest amount is impossible. Usually while "cleaning" DNA you lose a lot, so you have to decide what is more important for you. I like CTAB, you get A LOT more DNA, it is by far cheaper and quality is also quite good. If you are not satisfied with the quality you can perform some purification steps (Precipitation, using kits or whatever)
Aloha Sebastian. Answers to your questions: fresh material/silca dried fresh material, Nuclear/Chloroplast DNA. I had a feeling those two would not be synonymous. There seems to be a mix of kits and CTAB in the literature but CTAB looks like it can be tweaked for different groups and you can Cesium band to clean it.
I would suggest CTAB. I am working with a problematic plants and I am using CTAB. Actually I am not using any kit (to see the protocol, follow the link for the paper) but still I got easily amplifiable DNA. As sebastien said, you can perform some purification steps to improve the quality.
The adavantages of CTAB are high yield, long intact DNA and cost efficiency. But, CTAB may not work in all systems. Recently, we were extracting DNA from Falopia japonica (Polygonaceae) leaf. The final product looked OK by nanodrop. However, on gels there was no DNA! All the product seemed to be form by polyphenolic compounds instead of DNA!. We had to use Qiagen column which provided DNA. But as with most kits the yield is relativley low (one microgram) and DNA is fragmented to less than 10kb.
Recommedation - in an unknown system run the first extractions with both kit and CTAB and then choose the most convenient method.
In general CTAB is much more cheaper and provides big amount larger fragments. Quagen kit provide less but quite more pure DNA. I used both in my studies and both were worked pretty well for my reasons. But sometimes some chemicals which may present in samples can affected on DNA isolation - polyphenoles, terpenoids and some other chemicals compounds, mostly secondary metabolites. Also it need to note that some such compounds may affect on PCR as inhibitors.
But all depends on what you plan to do wit obtanied DNA:
what study you want to provide - genome sequencig, short fragment sequensing, restriction analysis, AFLP or something else
what concentration you need
what fragments lenth you need
what genome you interested to study - cp, mt of nuclear
If you want to determine what technique will be the most suitable for your object, you may try different and compare results. Another good way - to search for techniques in papers on Araliaceae genetics.
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