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I have extracted DNA oligonucleotide of size 77 bp from a crushed 10% PAGE gel using 3 rounds of $\ce{LiClO4}$ in water. The extracted elute was dried down in a vacuum centrifuge to a certain volume and then precipitated with 5 volumes of Ethanol before taking a spec on a NanoDrop. I do have a significant peak, characteristic of a DNA oligonucleotide, at 260 nm with a $A260/A280 ≃ 1.75$.

However, I also get a peak at 380 nm. I used to get this since a long time but I could not understand what it meant (did not find any literature reference). I do not want to worry about it too much, as long as I have my oligo, but I would like to know what it is. A colleague of mine also got the same peak, though not very prominent, who did not do a PAGE purification but direct UV Spec after Phenol/Chloroform extraction and $\ce{LiClO4}$ in acetone precipitation.

What would you suggest?

[Note: For your information, I have already asked this question here on ResearchGate. Out of all the answers, Paul's seem to be quite rational. However, I wanted to see if anyone has any other opinions]

Thanks a lot for your answers.

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  • $\begingroup$ I did not understand what was the edit that you made @kmm? $\endgroup$ – Somdeb Mar 30 '18 at 21:29
  • $\begingroup$ I was fixing some of the mathjax formatting. $\endgroup$ – kmm Mar 30 '18 at 22:40
  • $\begingroup$ I guess I would like to close this question. I have already got answers on the ResearchGate forum. Thank you! $\endgroup$ – Somdeb Apr 1 '18 at 15:51

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