Restriction Digestion of Plasmid, Cosmid, and Phage DNAs

Principle
The following is a generalized example of a restriction digest. Estimate the amount of DNA needed in your digest and scale up accordingly. To visualize a digest on an ethidium bromide-stained agarose gel, you will need to take the size of the fragments and the total size of the clone DNA into account (e.g., 10–50 ng of intact lambda-sized genomes (~50 kb) are easily seen on gels but if cut into small (~1 kb fragments), the relative proportion of the clone DNA in each fragment is ~1/50 and more DNA (500–1000 ng) should be loaded in order to see them.

If preparing a large number of digests at a time and the DNAs are at the same concentration, prepare a cocktail of the reaction mix then divide it among the tubes of DNA.

Time Required
1.5 hours

Procedure
A general rule of thumb is to use 1 mg clone DNA/ 10 mL in the final digest
reaction mix (recommendation 1 µg/20 µL).
Reaction Mix:

1. Put the water and buffer into the tube first, then add the enzyme (avoid putting enzyme into water first, as it may start to break down). Put the DNA in last and mix by tapping the tube with your finger.
2. Quickspin to remove bubbles (DNA will adhere to bubble surface and becomes inaccessible to the enzyme). Incubate at the recommended temperature for 1 hour.
3. Stop the reaction by adding 2.5 µL 5 X Ficoll dye mix if the sample is to be loaded directly onto a gel; otherwise stop the reaction by placing it at –20°;C or add 0.5 µL of 0.5 M EDTA.