QUANTITATING DNA USING AGAROSE GEL
Get H3 marker (in freezer box). This marker is 50ng/l.
1. Label two tubes:
A
B
1l Dye
1l Dye
1l DNA
2l DNA
2. Load gel as follows:
2l H3---------1l A--------2l B----------4l H3
3. Run gel at 100V for about 40 minutes. Take picture and then calculate
the DNA concentration as follows:
4. You are going to be comparing your DNA to the marker's ladder bands.
There are three kinds of DNA that will run on the gel: nicked,
relaxed/linear, and supercoiled. You shouldn't have any nicked DNA if
your DNA prep was clean, so there should be two markings on each lane
- the top one is linear DNA, and the bottom is supercoiled (if there is
nicked DNA, that will be above the linear DNA line).
5. The marker will have bands as follows (from top of gel to bottom):
23.13Kb, 9.4, 6.7, 4.3, 2.2, and 2.0. Its total Kb is 48.5.
6. Pick the marker band that is the closest to your DNA sample's band, for
both linear and supercoiled. For example, if your DNA sample's linear
band matched the marker's 9.4 band and it's supercoiled band matched
the marker's 6.7 band, the calculation would be as follows:
Linear DNA = 9.4 frag of  x 50ng/l x #l marker (2) x
48.5Kb total 
intensity of band (if half as bright, use 1/2 ) / #l DNA sample loaded (e.g.
1l)
Add this to:
Supercoiled DNA = 6.7 frag of 
x 50ng/l x 2l marker
48.5Kb total 
loaded x intensity (twice as bright = 2) / 1l DNA sample loaded
Your result will be the concentration of DNA in ng/l.