IGEM:Brown/2007/Lab Protocols/Ligation Setup-from Brodsky

Setting Up the Ligation: Determine how much DNA is needed. Usually start with about 2 ul of of backbone, which usually translates into about .2ug of DNA. A good rule for estimating DNA concentrations is that the limit of detection of a medium sized piece of DNA (about 5kb) on an agarose gel with 20 wells is about 50-100 ng, therefore 0.2 ug will be a thin but very clear band on a gel. Also remember that the larger the piece of DNA, the more ethidium bromide it will bind and therefore the brighter it will appear, so if a 10 kb piece and a 1 kb piece appear to have the same brightness the 1 kb piece actually has a 10x higher concentration of ethidium bromide as the 10 kb piece.

Calculations:

1. # of base pairs in your backbone DNA * 660 ug DNA/umole base pair= # of ug/umole for your backbone.

2. divide .2 ug of backbone DNA by the # of ug/umole for your backbone = micromoles of backbone you have

3. Calculate the number of ug of insert needed. Maniatis suggest using a 10 nM concentration of termini. In a 30 ul ligation this will be 3 * 10^-6 uMoles of insert.

4. # of base pairs in your insert * 660 ug/umole base pair=# of ug/umole for your insert.

5. # of ug/umole * 3* 10^-6 uMoles of insert = # of ug insert needed in your ligation. This should be about the same number as a 10 fold molar excess of insert over backbone.

If you do these calculations for a 10 kb backbone and a 1 kb insert, you will need .2 ug of backbone and 2 ug of insert in a 30 ul ligation reaction.

Set up the ligations as follows:

BB-Ligase: .2ug BB, 0ug Insert, 3ul 10X buffer, 0ul ligase, up to 30 ul sterile miliQ. BB+Ligase: .2ug BB, 0ug Insert, 3ul 10X buffer, 1ul ligase. BB + Insert: .2ug BB, your calculation of ug for insert, 3ul 10X buffer, 1ul ligase. Insert Only: 0ug BB, your calculation of ug for insert, 3ul 10X buffer, 1ul ligase.

-Let Ligations go for 2 hours to overnight.

-Transform 20 ul into competent E. Coli (see transformation protocol.)