Team:Cambridge/Protocols/Restriction Enzyme Digestion

From 2011.igem.org

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==Restriction Enzyme Digestion==
==Restriction Enzyme Digestion==
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protocol description
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A method that allows to create a restriction map of a given DNA fragment. Widely used to test for the correct integration of a cloned sequence into a vector.
===Theory===
===Theory===
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How it works
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Restriction enzymes, also called restriction endonucleases, are enzymes naturally found in bacteria which serve as a protection against foreign DNA found in a cell which usually implies a phage infection. The enzymes introduce a double-strand cuts in the DNA leaving either blunt or sticky single-strand ends, recognizing specific, usually 4bp or 6bp palindromic sequences.
===Practice===
===Practice===
* '''Master mix preparation'''
* '''Master mix preparation'''
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: 2.0μl of DNA
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For 2.0μl of DNA solution add:
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: 0.5μl of each restriction enzyme (or the respective amount of water for the control with uncut plasmids)  
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:* 0.5μl of each restriction enzyme (or the respective amount of water for the control with uncut plasmids)  
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: 0.1μl of BSA - ''acetylated Bovine Serum Albumin enhances the performance of restriction enzymes''
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:* 0.1μl of BSA - ''acetylated Bovine Serum Albumin enhances the performance of restriction enzymes''
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: 5.9μl of water
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:* 5.9μl of water
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: 1.0μl of 2×NEBuffer
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:* 1.0μl of 2×NEBuffer
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* '''Check for the compatibility of restriction enzymes chosen'''
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* '''Procedure'''
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To check if the two selected restriction enzymes can perform effective catalysis in the same solution, go to the website of [http://www.neb.com New England Biolabs] → select [http://www.neb.com/nebecomm/DoubleDigestCalculator.asp? Double Digest Finder] → choose which restriction enzymes you want to use → follow the digest recommendations.
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:# Mix DNA solution with the suitable amount of the master mix. As a control, repeat the same procedure with uncut DNA (prepare a master mix that does not contain restriction enzymes).
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:# Incubate at 37°C for 2 hours.
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:# Perform [[Team:Cambridge/Protocols/Gel_Electrophoresis | gel electrophoresis]] (10μl of DNA-restriction enzyme mixture in each well). Remember about molecular weight markers that help to assess the size of separated DNA fragments.
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:# Compare with predicted fragment sizes. You can create a restriction map using [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE - A plasmid Editor].
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*'''Tips on Restriction Enzyme Usage'''
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:* Store restriction enzymes in the freezer, at around -20°C.
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:* Never make up restriction digests with the restriction enzyme composing more than 1/10 of the final volume. The reason is that restriction enzymes are stored in glycerol, and at concentrations above 10%, glycerol not only inhibits the digestion but also changes enzyme specificity (star activity). 
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:* Check for the compatibility of the restriction enzymes chosen.
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: To check if the two selected restriction enzymes can perform effective catalysis in the same solution, go to the website of [http://www.neb.com New England Biolabs] → select [http://www.neb.com/nebecomm/DoubleDigestCalculator.asp? Double Digest Finder] → choose which restriction enzymes you want to use → follow the digest recommendations.
===Safety===
===Safety===
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The safety implication of the procedure.
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The main safety considerations are related to gel electrophoresis, namely:
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* The use of SYBR Safe dye, in staining the DNA on the agarose gel. As it is a relatively toxic substance, make sure that all gloves, tubes and pipette tips that were in any contact with the dye are treated as [https://2011.igem.org/Team:Cambridge/Safety#Waste_Disposal hazardous chemical waste].
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* Heating the solution of agarose in TAE buffer in a microwave. Care must be taken to avoid superheating.  
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Latest revision as of 20:21, 21 September 2011

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OVERVIEW
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Contents

Restriction Enzyme Digestion

A method that allows to create a restriction map of a given DNA fragment. Widely used to test for the correct integration of a cloned sequence into a vector.

Theory

Restriction enzymes, also called restriction endonucleases, are enzymes naturally found in bacteria which serve as a protection against foreign DNA found in a cell which usually implies a phage infection. The enzymes introduce a double-strand cuts in the DNA leaving either blunt or sticky single-strand ends, recognizing specific, usually 4bp or 6bp palindromic sequences.

Practice

  • Master mix preparation

For 2.0μl of DNA solution add:

  • 0.5μl of each restriction enzyme (or the respective amount of water for the control with uncut plasmids)
  • 0.1μl of BSA - acetylated Bovine Serum Albumin enhances the performance of restriction enzymes
  • 5.9μl of water
  • 1.0μl of 2×NEBuffer
  • Procedure
  1. Mix DNA solution with the suitable amount of the master mix. As a control, repeat the same procedure with uncut DNA (prepare a master mix that does not contain restriction enzymes).
  2. Incubate at 37°C for 2 hours.
  3. Perform gel electrophoresis (10μl of DNA-restriction enzyme mixture in each well). Remember about molecular weight markers that help to assess the size of separated DNA fragments.
  4. Compare with predicted fragment sizes. You can create a restriction map using [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE - A plasmid Editor].
  • Tips on Restriction Enzyme Usage
  • Store restriction enzymes in the freezer, at around -20°C.
  • Never make up restriction digests with the restriction enzyme composing more than 1/10 of the final volume. The reason is that restriction enzymes are stored in glycerol, and at concentrations above 10%, glycerol not only inhibits the digestion but also changes enzyme specificity (star activity).
  • Check for the compatibility of the restriction enzymes chosen.
To check if the two selected restriction enzymes can perform effective catalysis in the same solution, go to the website of [http://www.neb.com New England Biolabs] → select [http://www.neb.com/nebecomm/DoubleDigestCalculator.asp? Double Digest Finder] → choose which restriction enzymes you want to use → follow the digest recommendations.

Safety

The main safety considerations are related to gel electrophoresis, namely:

  • The use of SYBR Safe dye, in staining the DNA on the agarose gel. As it is a relatively toxic substance, make sure that all gloves, tubes and pipette tips that were in any contact with the dye are treated as hazardous chemical waste.
  • Heating the solution of agarose in TAE buffer in a microwave. Care must be taken to avoid superheating.