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   Protocol by PKU 2010


         Notebook > Protocols > DNA Double Digestion Protocol

Contents 1 DNA Double Digestion Protocol 1.1 Materials: 1.2 Procedure: 1.3 Tips: 1.4 References:

DNA Double Digestion Protocol

Materials:

• DNA sample(s) in water or TE buffer

• 10x digestion buffer

• Restriction enzymes (EcoRI or SpeI or XbaI or PstI)

• DNA loading buffer (if electrophoresis is subsequent)

• Agarose gel 1.5% (or different depending on expected band sizes)

Procedure:

1. Test the concentration of the DNA sample(s).

2. Pipet the following into a microfuge tube:

20uL reaction system     50uL reaction system

DNA around 1ug     around 2.5ug

10x Digestion buffer 2uL     5uL

1st Enzyme 1-1.5uL     2.5-4uL

2ndEnzyme 1-1.5uL     2.5-4uL

ddWater Rest of volume Rest of volume

3. Incubate at recommended temperature (37.0 degrees) for 2 or 4 hours (0.5~2hfor enzymes of NEB, 4h for enzymes of Takara).

4. Take 2 to 5 uLof the digested sample, add loading buffer, and run it on the agarose gel to check the result, or take the entire sample to run to extract a wanted fragment).

Tips:

1. DNA:

• For identification of DNA, use 0.4 ug/uL DNA; (or 2uL from a nice DNA mini prep)

• For cloning, 1ug/uL DNA is enough.

2. Buffer: we’d better use the buffer that comes with the enzyme, which means buffers from other company may cause some abnormal results.

3. Enzyme: the maximum volume that an enzyme can be used is 1/10 of the total reaction volume (example: 2 uL for 20 uL reaction system). If you want to do overnight digestion, add less enzyme (example: 1 uL for 20 uL reaction system). It is necessary to point that too many enzymes will reduce the efficiency of enzyme digestion with glycerol in it.

4. Gel: make sure to run the uncut DNA as a control along with the digested DNA sample(s). And, always run a DNA marker!

References:

• Current protocols in molecular biology (3.1.1-3.1.2)