Thursday, December 18, 2014

How to analyze oligonucleotides on a Q Exactive

Sorry if I've posted this before, but it keeps coming up.  Can I verify my oligonucleotides on a Q Exactive?  Sure you can!

And the nice people listed above made an awesome step-by-step tutorial on how to do it. You can download the PDF of this method here.  I've messed around with this some here and there, and you really need to get the right column and buffer configuration to pull it off.  Really small nucleotides will adhere to C-18 enough to be okay, but they won't be great.  Using this buffer configuration and column I was able to get masses on darned big oligos on an Orbitrap Fusion on a friend's facility.

Cautions I would throw out there:  1) The oligos I have seen so far have been DIRTY.  Most oligo synthesizing companies will HPLC purify them for a reasonable additional charge.  I'd probably do that if I could.  I'd also consider clean up columns or maybe a quick diversion to waste.

If you just want to verify sequence identity you can use the University of Albany's

nice mass calculator.  You can find this friendly tool here.

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