1. What is a restriction map, and how does it help identify a particular DNA?

2. What is a recognition sequence?

3. Go back to the NEBcutter site and once again custom digest PhiX174 DNA with DraI and MfeI, then view the gel. What happens to your predicted results when the % agarose is increased form 0.7% to 1.0%? Why did we use the 0.7%?

4. Can you use the NEBcutter program to come up with another set of restriction enzymes that would have also worked well to identify the PhiX174 DNA? What are your criteria for picking the enzymes?

5. (a) If your instructor provided you with DNA size markers to run alongside your digest samples, plot the known marker DNA fragment sizes in kb on the x-axis, and band migration measured from the well in cm on the y-axis on semi-log graph paper. Use the graph (called a standard curve, but should be more or less a straight line) to extrapolate each PhiX174 DNA fragment size from its corresponding band migration. Did all bands in a given lane add up to approximately 5.39 kb? Why or why not?

(b) If you did not run DNA size markers on your gel, did the banding pattern resemble the pattern predicted by NEBcutter? Why or why not?

6. Why was it a good idea to include a double digest instead of just two single ones?

7 . Why was it necessary to perform single DraI and MfeI digests in addition to the double DraI+MfeI digest?