Saturday, February 25, 2012

How do you use restriction enzyme to cut DNA into different fragments?

I have the restriction enzyme and the DNA sample. What is the procedure in using the restriction enzyme to cut the DNA sample into different fragments? What materials/equipments do I need to use? Please be specific and not in too many technical terms. Thanks!How do you use restriction enzyme to cut DNA into different fragments?
To use restriction enzymes (RE):

1. You will have to know certain information about the RE that you are using--what are the optimal conditions under which the RE functions (particularly buffer pH, salt concentration, other ions necessary for enzyme activity, temperature).

2. To run the cleavage reaction, you will need sterile (DNase-free) buffer concentrate and distilled water; small test-tubes in which to run the reaction; a water bath to control the reaction temperature; pipettes for accurately measuring liquid volumes.

3. Not knowing whether you are cutting the DNA for separation of the fragments or cloning, I'll suggest from equipment for both:



Separation of fragments:

a. Separation medium (eg, agarose gel)

b. Marker dye(s) to follow migration of the sample

c. Power pack to supply electric current to effect separation of DNA fragments

d. Means of visualizing the DNA fragments in the gel--eg, dyes that react with the DNA



Cloning:

a. Plasmid in which you place the DNA fragment by ligation.

b. Enzymes that allow you to ligate (covalently join) a DNA fragment into the plasmid DNA; all the buffers, etc for the ligation reaction

c. A culture of a specific microbe (bacteria or yeast) into which you will transform (insert into cell) the recombinant (plasmid with ligated fragment) plamid.

d. Appropriate transformation solutions and growth media to allow the transformation to take place.

e. Selective solid growth media (agar plates with growth nutrients and an inhibitor that prevents NONtransformed cells from growing.How do you use restriction enzyme to cut DNA into different fragments?
They're not that complicated - a restriction enzyme is just a "DNA snipper". Most restriction enzymes will cut the DNA strand at a particular place at or near where there is a particular base sequence. The base sequence is generally palindromic (reads the same on the antisense strand as it does on the sense strand), and the enzyme will cut in the same place on each strand. There are a number of interesting details about how they work and what the results are, but that isn't what you're asking.

The recipe for a restriction digest is pretty simple. You need the DNA you're going to cut, the enzyme you're going to use, the particular buffer the enzyme prefers to work best in (a mixture of chemicals the particular enzyme needs, like Magnesium chloride and maybe ATP and perhaps other ingredients), a reaction tube for the components to be mixed in, and a source of heat to put some energy into the system.

Different enzymes prefer different temperatures to work best, but many of the most commonly used ones work best at a temperature of 37 degrees C. If you want to do a digest, you would mix the components in the tube, and then put the tube into a heating block or water bath at the desired temperature and let it sit for some time (a few hours to overnight, for instance). That's it! After that, everywhere there is a recognition site in the DNA, the enzyme should have snipped the DNA, like scissors cut a ribbon.

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