So we’ve isolated our RNA and now we’re going nuts to ensure its quality is acceptable for microarray analysis.
Well, maybe we’re being harsh when we say we’re going nuts – it is really important to ensure that our RNA is not degraded.
We’re doing this using electrophoresis technique. This ensues forcing our product through a network of cross linked polymers (referred to as the “gel”).
RNA is negatively charged so we can pull it through the gel using its electromagnetic attraction to positive charge (and that’s exactly what we do!).
Smaller, negatively charged fragments move farther down the gel while larger fragments end up higher on the gel. In the end, we can see the different components of our product by observing all the fragments at different positions on the gel.
This technique will allow us to make sure our RNA isn’t degraded. Good RNA will show us a certain set of bands (2 bands with a smear above) while degraded RNA will show us the same pattern but with an additional band at the bottom.
Can you guess what that small fragment at the bottom is?
It’s degraded RNA – we’re crossing our fingers that we don’t see it (wish us luck!).