Richard Lab:Restriction Digest

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This protocol is typically used to do bio-brick digests with the restriction sites consisting of the following configuration:



  • Prepared DNA from miniprep, PCR, or Gel Extraction
  • Restriction Endonucleases
    • With corresponding 10X buffer. NEBuffer 2 can be used for most applications but check this chart to be sure.
  • BSA (optional)
  • Phosphatase
  • Distilled water


  1. Quickly vortex all ingredients (Buffer, BSA, DNA, Enzymes) before beginning
  2. Add the following in a micro-centrifuge tube
    1. 5μl of Buffer
    2. 1μl of BSA
    3. 40μl of DNA solution (Dilute PCR products 1:4)
  3. Vortex Enzymes and add 20 units (1μl) of each to the tube
  4. Incubate reaction in a 37°C water bath for at least one hour (I like 1:45).
  5. Heat kill the digest for 15 minutes at 75°C.
  6. If digesting a vector add 10 units (1µl) phosphatase) and 5µl Phosphatase Buffer and incubate an additional 45 minutes at then heat kill againat 75°C for 15 min.
  7. Store digested DNA in the freezer (-20°C).


Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!

  • If you're not getting good digestion it might be because your enzyme is bad. Double the digestion time and see.
  • Longer digest gives more complete digestion, especially if you have >1µg of DNA, but can sometimes give nonspecific digestion
  • Beware the the NEB double digest chart. For EcoRI and PstI double digest it recommends using the EcoRI NEBuffer. However based on my digests both NEBuffer 2 and 3 work better; with NEBuffer 2 giving the most complete double digestion. It is funny that thye recommend the Eco buffer because they also say that Pst only exhibits 50% activity with that buffer.


For more information you can check out the other restriction digest protocols.


or instead, discuss this protocol.

BioStream version

Following is the Richard Lab:Restriction Digest protocol in BioStream, a high-level programming language for expressing biology protocols. What you see here is the auto-generated text ouput of the protocol that was coded up in BioStream (see Source code). More information about BioStream can be found on my home page. Feel free to mail me your comments/ suggestions.Vaishnavi

Text Output

Richard Lab:Restriction Digest protocol

Source Code

Richard Lab:Restriction Digest protocol - source code

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