Lab 02 - Restriction Enzyme Digestions (REDs) and analysis of lambda DNA

A micrograph of multiple bacteriopages

Restriction enzymes are one of the most basic and important tools in molecular biology. They evolved in bacteria to attack and cut (cleave) foreign DNA, mostly from bacteriophages (viruses that "eat" bacteria). But hey have been isolated to be used in the lab, and are useful to cut any kind of DNA, not just viral.

Cleaving DNA is the first step in any technique that involves recombinant DNA technology. There are techniques that use special enzymes to paste (ligate) different fragments of DNA. For instance a gene can be ligated into a plasmid that can be inserted into bacteria to make many copies of it via bacterial reproduction (cloning), something we will do in a few weeks.

Today we used lambda DNA (DNA from the common lambda bacteriophage) as the substrate to be cleaved with three different restriction enzymes: EcoRI, HindIII, and PstI.

We then ran our first agarose gel electrophoreses of the quarter (there shall be many more), and here are the results. Click on each pic to get a full size image of each gel:

For the lab report:

• The lab report is due Thursday Dec 11th.
• If you can answer the questions on page 44 of "exercise 3" in the lab manual you'll have a solid discussion of results section. Use them as a guide to get ideas to discuss.
• In one of the four posted pictures the samples are significantly smeared. In your discussion include your thoughts (or findings) on what may have caused this.
  
• Include a picture of your gel. If you turn in the one printed in the lab (on thermal paper) you can label the lanes with an ultrafine point permanent marker (sharpies and the like).
• A pdf file of a semi-log paper page will be e-mailed to you for your convinience.
  

Research questions

• The gels we used were pre-poured for us. They were 1% agarose gels. What does this mean?
• If you want to improve the resolution of the gel (making bands sharper, improving separation of bands of similar size) what can you do different when preparing the gel?

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