Rights: The University of Waikato Published 20 November 2007 Download

A chemical called ethidium bromide had been added to the gel. It binds to the DNA fragments in the gel. It also fluoresces, or lights up, under UV light. This means that the DNA fragments can be seen in UV light. The DNA fragments shine up as 'bands'. Each band contains DNA fragments of the same size (because they have travelled the same distance through the gel).
A 'reference ladder' can also be run in the gel. This contains a mixture of DNA fragments of known size. Comparing the bands in your DNA sample with the bands in the reference ladder allows you to work out how big the DNA fragments are in a particular band. DNA size is measured in base pairs (bp), or kilo-base pairs. (Remember that DNA is a chain of nucleotides, each nucleotide consisting of a phosphate group, a sugar, and a base. DNA is also double stranded. One base pair therefore represents one pair of nucleotides in the double stranded DNA molecule. A molecule that is 200bp long would consist of 200 pairs of nucleotides).



There is a very small amount of DNA in the gel, and it has been separated into fragments, which makes it hard to see. Remember, though, that the gel contains ethidium bromide, a chemical which binds to the low levels of DNA and makes it possible to see them under UV light. The different bands you see on the screen therefore show where the DNA fragment is on the gel.

Clare Eagleton (Genesis R&D Here you can see is a positive at 1.5 kb, like we expected.

Narrator: The size of the DNA fragments can be determined by looking at the reference ladder, which was also loaded into the gel.

Sam (Student): How do you know that it’s a 1.5 kb band?

Clare Eagleton Genesis R&D Well, on the side here you’ve got the 1.5+ kb reference marker, and they all have different sizes, like 100 base pairs right up to 12,000 base pairs. And this one here represents 1.5 kb, and you can see your comb is in line with that.

Sam (Student): Awesome.