Knight:Restriction Digest

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(Procedure)
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#Add 1 &mu;L of each enzyme. <br>Vortex enzyme before pipetting to ensure that it is well-mixed.  <br>Also, the enzyme is in some percentage of glycerol which tends to stick to the sides of your tip.  To ensure you add only 1 &mu;L, just touch your tip to the surface of the liquid when pipetting.
#Add 1 &mu;L of each enzyme. <br>Vortex enzyme before pipetting to ensure that it is well-mixed.  <br>Also, the enzyme is in some percentage of glycerol which tends to stick to the sides of your tip.  To ensure you add only 1 &mu;L, just touch your tip to the surface of the liquid when pipetting.
#Place in thermal cycler ([http://www.mjr.com/ MJ Research], PT-200) and run digest protocol.
#Place in thermal cycler ([http://www.mjr.com/ MJ Research], PT-200) and run digest protocol.
-
##4-6 hour incubation at 37&deg;C <br> Use a longer incubation time if you have time or are worried about the efficiency of cutting.
+
##4-6 hour incubation at 37&deg;C <br> Use a longer incubation time if you have time or are worried about the efficiency of cutting.  I think this time can be shortened to 2 hrs while still cutting to completion.
##20 mins at 80&deg;C to heat inactivate enzyme.<br> This step is sufficient to inactivate even Pst I.
##20 mins at 80&deg;C to heat inactivate enzyme.<br> This step is sufficient to inactivate even Pst I.
##4&deg;C forever (or until you pull the reaction out of the thermal cycler).
##4&deg;C forever (or until you pull the reaction out of the thermal cycler).
#Generally, use some method of [[Purification of DNA | DNA purification]] to eliminate enzymes and salt from the reaction.
#Generally, use some method of [[Purification of DNA | DNA purification]] to eliminate enzymes and salt from the reaction.

Revision as of 15:19, 9 October 2006

Materials

Digest Mix

Example - 50 μL reaction. 100 μL reactions are also common especially if your DNA to be cut is dilute.

  • 5 μL EcoR I buffer (for all digests with BioBricks enzymes, we use EcoR I buffer. It keeps things simple and seems to work).
  • X μL DNA (usually ~1 μg depending on downstream uses).
  • 0.5 μL 100X BSA (added to all digests because BSA never hurts a restriction digest)
  • 1 μL BioBricks enzyme 1 (regardless of the volume of the reaction, 1 μL enzyme is used because generally this represents a 10-25 fold excess of enzyme and is therefore sufficient for most digests. Also, it can be difficult to accurately pipet less than 1 μL of enzyme since it is sticky due to the glycerol content.)
  • 1 μL BioBricks enzyme 2
  • (42.5 - X) μL deionized, sterile H2O

Procedure

  1. Add appropriate amount of deionized H2O to sterile 0.6 mL tube
  2. Add restriction enzyme buffer to the tube.
    Vortex buffer before pipetting to ensure that it is well-mixed.
  3. Add BSA to the tube.
    Vortex BSA before pipetting to ensure that it is well-mixed.
  4. Add appropriate amount of DNA to be cut to the tube.
    Vortex DNA before pipetting to ensure that it is well-mixed.
  5. Add 1 μL of each enzyme.
    Vortex enzyme before pipetting to ensure that it is well-mixed.
    Also, the enzyme is in some percentage of glycerol which tends to stick to the sides of your tip. To ensure you add only 1 μL, just touch your tip to the surface of the liquid when pipetting.
  6. Place in thermal cycler (MJ Research, PT-200) and run digest protocol.
    1. 4-6 hour incubation at 37°C
      Use a longer incubation time if you have time or are worried about the efficiency of cutting. I think this time can be shortened to 2 hrs while still cutting to completion.
    2. 20 mins at 80°C to heat inactivate enzyme.
      This step is sufficient to inactivate even Pst I.
    3. 4°C forever (or until you pull the reaction out of the thermal cycler).
  7. Generally, use some method of DNA purification to eliminate enzymes and salt from the reaction.
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