So chatting with a undergrad that was shadowing me last week before my surgery we got on the topic of DNA damage and that a primary endogenous source of DNA damage comes in the form of hydrolytic damage causing loss of bases, as well as base modification (18,000 events per cell per day). Similarly another major cause of damage created in the cell is reactive oxygen species that arise as a result of mitochondrial leakage (3-4,000 events per cell per day).
What usually occurs is that as a result of mitochondrial metabolism molecular oxygen is converted to superoxide (·O2-). This ROS species is not particularly dangerous to DNA because it is short-lived and gets rapidly converted to peroxide by superoxide dismutase (H2O2). Peroxide is what poses a huge threat to DNA because when peroxide is in close proximity with our DNA it gets converted to hydroxyl radical (·OH) through what is called the Fenton Reaction.
Fe2+ + H2O2 --> Fe3+ + ·OH + -OH
British chemist Hank Fenton discovered this reaction way way back in 1894 but I’m going to assume he had no appreciation for how potent a genotoxic insult this simple reaction would play in our bodies. The key part of this reaction lies in ferrous iron (Fe2+) found in the DNA that plays a key role in the conversion of peroxide to hydroxyl radical.
A common form of oxidative DNA damage is the conversion of guanine to 8-oxo-guanine, which while in the syn conformation, can mispair with adenine. The end game is that the damage has resulted in a mutation, but fear not there are specialized enzymes called DNA glycosylases that can remove this damage base and incorporate the proper nucleotide triphosphate. If you are interested this pathway is called base excision repair and the particular DNA glycosylase that is predominantly responsible for the removal of 8-oxo-guanines from our genome is called OGG1.
So lets end this post on why you toss in some EDTA in addition to Tris when resuspending DNA. Its because we use it to chelate these metal ions like iron so that it cannot participate in the Fenton reaction and cause damage to our precious DNA samples in addition to binding other metal ions required for enzymatic activity by nucleases, which can further degrade your sample.
Postscript: One last note on DNA storage, which we debate back and forth endlessly with each other. Most of us store DNA at 4 °C for short-term use, but keep most of our precious samples at -80 °C for long-term storage. You can store DNA at -20 °C but you run the risk of it falling out of solution but vortexing will easily bring it back into solution. Note this is fine for plasmids, but vortexing will rip the shit out of genomic DNA so be kind to it and store it at -80 °C. And one last bit, don’t store DNA in a freezer model that automatically defrosts, this freeze thaw cycle will end up degrading your DNA.
Values of DNA damage come from: PMID 12760027