restriction enzymes

Meaning: Restriction enzymes (restriction endonucleases) are bacterial enzymes that defend against viruses by cutting phosphodiester bonds in foreign DNA at specific recognition sequences, usually 4 to 8 base pairs long. Sites used in cloning are typically palindromic: read 5′→3′, both strands have the same sequence (EcoRI cuts GAATTC). Staggered cuts leave single-stranded sticky ends that base-pair with complementary ends; straight cuts leave blunt ends.

On the MCAT: In cloning passages, a plasmid and an insert are cut with the same enzyme, mixed, and sealed by DNA ligase. On a gel, DNA is negatively charged and runs toward the positive electrode; shorter fragments travel farther. A linear molecule cut at n sites gives n + 1 fragments; a circular plasmid gives n. A mutation that destroys a site (RFLP) changes the banding pattern. A 4-bp site occurs about once per 256 bp by chance (4⁴), a 6-bp site about once per 4096.

Common confusion: Palindromic here does not mean one strand reads the same left to right: GAATTC backward is CTTAAG. It means the complementary strand also reads GAATTC when read 5′→3′. Also, restriction enzymes cut DNA; ligase joins it.