Question

What are the advantages and disadvantages of using EcoRI vs BamHI as the restriction enzyme for the digest? Thank and happy easter!

Answer 1

EcoRI:

1. EcoRI produces 4 nucleotide ends (sticky end) with 5' end AATT overhangs. The nucleic acid recognition sequence is G/AATTC.
2. EcoRI exhibits star activity which means it shows non-specific cutting, in low salt concentration, high pH, high glycerol.
3. Widely used in cloning.
4. Type IIP enzyme.

BamHI:

1. Produces 5' overhang with sticky ends.
2. EcoRI and BamHI have extremely similar dimerization module, two ?-helices which form a four-helix bundle. EcoRI, in addition, has a small two-stranded antiparallel ?-sheet, which interacts with the symmetry-related ?-sheet of the other subunit. Altogether, BamHI has a considerably smaller subunit interface than EcoRI (800 versus 2600 Å2).
3. Shows star activity at low ionic strength, high glycerol, Mn2+ and DMSO.
4. Reaction temp: 30 ^oC