DNA extraction

Today I completed the final round of DNA extractions from my Belize Porites samples collected in November using the Qiagen DNeasy Blood and Tissue kit. Based on my experience in previous extraction efforts (see previous post), I was generous with tissue quantity. And again, in many cases the tissue was so loosely attached to the skeleton that it was easy to either scoop or scrape off with little skeletal material. As before, I used a single elution volume of 50 ul, which was passed though the column twice. I only evaluated yield this time on the Nanodrop. All samples were in the range of 100 – 400 ng/ul. Based on comparative Qubit results from last time, these Nanodrop values may overestimate yield by approximately double. Also note that most samples had significant absorbance around 230 nm, suggesting the presence of salts, carbohydrates, or phenolic compounds.

Note here that some of the samples in this batch were Porites porites (ppor) as opposed to Porites astreoides (past). Also included in this batch were three samples collected from the top, middle, and bottom of a single P. astreoides colony (w, for within).

Here is the Nanodrop report:




I also ran these samples on a gel. I followed this gel protocol with one modification: I used 1 ul of all samples mixed with 4 ul AE buffer and 1 ul loading dye. There appears to be high molecular weight DNA in all visible samples.


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