need a method for oligonucleotide visualization - (Nov/27/2013 )
If I have an oligonucleotide of 22 bases, and the best readout for an assay I want to perform would be whether or not this oligonucleotide remains intact.
I can't run it on an agarose gel because it's too small, right? Is there a simple method I can use, or maybe a bioanalyzer? I know that I can run a PCR with this oligo as a primer and see if it works, but I need something faster and quantitative.
A 20% PAGE gel will resolve fragments of this size. Some HPLC systems will also be able to separate these. You could also do mass spec on the fragment.
I am sure you can see a clear band on an agarose gel if it is intact. Just do it to see what you have. BTW, Is it RNA or DNA, single or double-stranded?
It's ssDNA. I'll probably try agarose, if it doesn't work I'll try PAGE. If that doesn't work then this readout is not suitable, since I need to run the assay on a daily basis so it doesn't make sense to use HPLC or mass spec. Thanks!
Why would you ever need to check an oligo every day? Freezers work, mostly, and it will be stable in TE at room temperature for months.
It's part of the experiment. We are developing a method for detection of point mutations, and whether or not the oligo is intact can tell me whether or not there is a mutation.