Hey there everyone,
I have some coral specimens which were preserved in absolute ethanol and stored at room temperature for 18 months in a covered box. (Unfortunately, very oldddd specimens). I have recently ran CTAB extraction with the coral specimens and all of the extracted DNA show heavily smeared bands on a 1.2% agarose gel. (gel image attached).
I wish to ask how would you deal with old, probably degraded coral specimens? And could I still get successful amplification with this kind of nucleic acids quality? Finally, could you give some comments on the gel image about the integrity of my dna samples please?
Thank you!!
Following my experience, you have degraded DNA, most likely becuase it was a room temperature. Usually you should keep them at -20 degrees. It happened to me and finally what I did for my genetic analysis was to aplify COI gen. This mitocondrial DNA is enought small to get amplify even if the sample is dedegraded. You will get less varibility but it works for population genetic analysis. I hope it helps!! Also, I was working with fish, so not sure if it works with coral.
Thanks, Amalia Jurado-Mc Allister. It's nice to know that degraded DNA doesn't mean a dead end. We went on quite a trip for coral sampling and wouldn't have the resources to repeat it. In my case I would amplify using ITS2 and psbAncr primers for the zooxanthellae in the coral, both of these primers required relatively short-length amplification (200-400bp). Hope it will turn out OK! I appreciate your words ; )
Hi again Hai, I don't see what it shouldn't work. I got pretty nice amplification and they were around 500 bp. Best of the luck in the lab!!! :)
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