From 2007.igem.org

Quantitation

1. Take the extracted DNA and run a gel to find out the concentration (per μL) of your DNA.
   • 1 μL plasmid + 4 μL ddH₂O + 1 μL Loading Dye
   • 1 μL insert + 4 μL ddH₂O + 1 μL Loading Dye

Gel Lane	Fragment
1	HindIII Ladder (5 μL)
2	HindIII Ladder (2 μL)
3	HindIII Ladder (1 μL)
4	Blank
5	Plasmid (All of it)
6	Blank
7	Insert (All of it)
8	Blank
9	1 Kbp Ladder (3 μL)

2. Ensure that the plasmid and inserts are at the correct lengths using the 1 Kbp ladder.
3. Note that 2 μL of HindIII will twice as bright as 1 μL of HindIII, and 5 μL of HindIII will be five times as bright. So to determine concentration, estimate the intensity of the bands compared with the 3 HindIII ladders and assign it a relative intensity factor. Read off the concentration value on the Ladder card, and multiply by the relative intensity factor to determine your sample concentration in ng/μL.

Jump to [http://igem.skule.ca/lab/protocols/quantitation.htm BlueGenes]