Question: Do you use an RNA sequence?

Claire Shooter answered on 16 Jun 2014:

Hi, great question!

I’m interested in studying DNA but I sometimes use RNA as a tool to help me do this:

At the moment I’m interested in looking at a couple of genes in a particular part of the genome. That means that about 98% of the DNA I extract from cells is not interesting to me, and if I sequence all of that I’m just wasting time and money that could be better used by focusing on the few megabases of DNA I’m interested in (one megabase is one million base pairs of DNA).

This is where RNA is useful: the DNA I want to sequence is floating about in a test tube in small fragments. Some fragments are from bits of the genome I’m interested in, some are not. To separate them out, I designed a lot of pieces of RNA that are the reverse compliment of the sequence that I want (this means the RNA contains all the opposite bases to the DNA, so they fit together). These little bits of RNA will bind to any of the pieces of DNA that has sequence from the region I’m interested in. The clever bit is that the bits of RNA are bound to a small magnetic particle called a biotin label. After I have mixed up all the DNA and RNA, I put my test tube on a magnet. The RNA with the magnetic particle binds to the magnet, taking all the pieces of DNA that its stuck to along with it! All I have to do then is remove all the stuff that isn’t magnetic and I’m only left with DNA from genomic regions that I actually care about.

This is the only time I personally use RNA, but lots of people do really fascinating things with it