Question

Restriction enzymes, also known as restriction endonucleases, are enzymes that cut a DNA molecule at a particular place. They are essential tools for recombinant DNA technology. The enzyme "scans" a DNA molecule, looking for a particular sequence, usually of four to six nucleotides. Once it finds this recognition sequence, it stops and cuts the strands. This is known as enzyme digestion. On double stranded DNA the recognition sequence is on both strands, but runs in opposite directions. This allows the enzyme to cut both strands. Sometimes the cut is blunt, sometimes the cut is uneven with dangling nucleotides on one of the two strands. This uneven cut is known as sticky ends. In your experiment, you used Type II restriction enzymes that are known for leaving sticky ends on your plasmid.

a. Why do we choose to use Type II restriction enzymes instead of Type I restriction enzymes that leave a blunt end?

b. Bacteria, such as E.Coli, produce those restriction enzymes to cleave genes. This does not make any biological sense, why would a specie produce proteins that will cut their own genome. Can you please explain why do bacteria produce restriction enzymes in the first place, and why don’t they worried about the safety of their own genome? After all, they do not have nuclear membrane for protections.

Answer 1

Type I restriction enzyme recognize the sequence and make a cut at some distant end of the DNA whereas and Type II restriction enzyme recognize the palindrome sequence and cut at the same site. Characterization and fragment size determination is easy with type II restriction enzymes therefore it better to use type II restriction enzyme in blunt end digestion.

Bacteria produce different type of restriction enzymes that provide the resistance for phage DNA or foreign DNA. But bacterial restriction enzymes also contain methylase activity these enzyme methylate their own genome and protect it from the self chopping and it degrade the foreign DNA that is non methylated at those sites.