1. Objectives:
1- Introduce the students to digest genomic DNA by restriction endonucleases.
2- Observe the results of digestion on agarose gel electrophoresis.

2. Introduction:
Restriction enzymes cut DNA up at specific sequences in the genome (blunt or sticky ends).
It is also known as restriction endonucleases , found in bacteria (and harvested from them for use).
Usually, restriction enzymes only cut the DNA at or near a very specific nucleotide sequence known as a recognition site.
For example, the commonly used restriction endonuclease EcoRI recognizes every point in DNA with the sequence GAATTC, and cuts at the point between the Guanine and Adenine.

5. This “restrictive” nature of these enzymes allows molecular biologists to point exactly where the DNA is to be cut.
In many cases, the recognition site of a restriction enzyme consists of a palindromic sequence where the order of the bases is read the same on each side of the helix.
The two sides of the helix are antiparallel and the recognition sequence reads from 5’ to 3’ on either side of the helix.

7. Restriction enzymes are part of a bacteria's ''immune'' system.
These are enzymes that cut DNA at specific sites (typically a four or a 6 base-pair sequence).
Bacterial DNA is modified to be protected by methylation while foreign DNA, such as incoming viruses, are not.

8. Usually, organisms that make restriction enzymes also make a companion modification enzyme ( DNA methyltransferase) that protects their own DNA from cleavage.
These enzymes recognize the same DNA sequence as the restriction enzyme they accompany, but instead of cleaving the sequence, they disguise it by methylating one of the bases in each DNA strand.

10. Thus, we can take a long piece of DNA and cut it with a restriction enzyme, generating numerous fragments.
Even a single-base change will destroy a restriction enzyme target site.
Likewise, even if a site is the same in two molecules, the length of DAN sequence between them may change.
Thus if two DNA molecules differ in sequence, they likely have different lengths for the fragments produced following treatment with restriction enzymes

11. Restriction Enzyme Digestion of human DNA:
Warm your TE/DNA mixture at 55C for minutes.
Pipet or light vortex to resuspend.
Prepare an enzyme digest of DNA by adding the required components to a clean microtube in the following order:
14 µl H2O
2 µl appropriate enzyme buffer (10X)
3 µl DNA
1 µl of enzyme (use BamHI, ClaI, EcoR, HaeIII, or HindIII)
Flick the tube to mix well and spin for 5 sec in the microfuge to bring all the components to the bottom.

12. Incubate at 37ºC in a water bath for two hours or overnight.
Run a gel (1% agarose gel as describe in Lab. 3 ) or freeze the samples until you have time to run the gel.
Record your observation.