Question: Why does my gDNA sample have two bands on an agarose gel?
Answer: One technique that can be used to determine the size of the fragments in a gnomic DNA (gDNA) sample is agarose gel electrophoresis. At 10x Genomics we do not use agarose gels to evaluate DNA size, although many users do utilize this technique.
The gel image below (Figure 1) shows a gDNA sample that was run on a 0.5% agarose gel. The detection of two bands for the gDNA can be explained by:
- DNA above a certain size cannot enter the gel matrix at all (let's assume 100 kb; the actual size depends on a variety of factors including pore size of the agarose matrix, the voltage settings, buffer composition, etc.). Everything above 100 kb stays in the well and everything below migrates into the gel.
- For the DNA that migrates into the gel, the fragments are running as a compressed band. In this gel, the gDNA runs as a single band and is above 10 kb but below the size limit at which it wouldn't enter the gel at all (e.g. 100 kb). This is very common with gDNA preps and is the expected result.
Figure 1. Two gDNA samples run on an agarose gel.
Products: Genome, Exome