I am currently working on diatoms and I was looking on this protocol by Filloramo et al., (2021). In the DNA extraction process they used EGTA in the lysis buffer. Is there a reason for using it specifically related to the diatoms. I have understood that they have different Affinity for Calcium ion and Magnesium ion during the chelation activity.
Article Re-examination of two diatom reference genomes using long-re...
Hello Beamlak Teshome
A phylum of algae comprising the diatoms are marine or freshwater unicellular organisms have cell walls (frustules) composed of pectin impregnated with silica. Ca2+ is a component of pectin which stabilizes their structure.
Ethylene diamine tetra acetic acid (EDTA) combines with all cations (such as Ca2+, Mg2+) in a 1:1 ratio regardless of the charge on the cation. Moreover, EDTA has a higher affinity for Mg2+ ions compared to Ethylene glycol tetra acetic acid (EGTA).
On the other hand, EGTA is also a chelating agent, but compared to EDTA, EGTA has a higher affinity for calcium ions and a lower affinity for magnesium ions. So, for cell lysis in the case of diatoms, EGTA is better suited for the purpose namely, used for cell wall loosening and SDS used for membrane solubilization.
Hope this helps.
Best Wishes.
EGTA can be preferred over EDTA for two reasons. Firstly, EGTA doesn't affect the natural activity of enzymes compared to EDTA, which in most cases does so. Secondly, EGTA can be used as the best buffer system for pH adjustment in living cells such as diatoms in a more easy way.
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