BamHI (pronounced "Bam H one") (from Bacillus amyloliquefaciens) is a type II restriction endonuclease, having the capacity for recognizing short sequences (6 bp) of DNA and specifically cleaving them at a target site.

This allows the DNA to maintain its normal B-DNA conformation without distorting to facilitate enzyme binding.

DNA is bound in a large cleft that is formed between dimers; the enzyme binds in a "crossover" manner.

Each BamHI subunit makes the majority of its backbone contacts with the phosphates of a DNA half site but base pair contacts are made between each BamHI subunit and nitrogenous bases in the major groove of the opposite DNA half site.

Major groove contacts are formed by atoms residing on the amino-terminus of a parallel 4 helix bundle.

Water-mediated hydrogen bonding, as well as both main-chain and side-chain interactions aid in binding of the BamHI recognition sequence.

Although a6 from each subunit does not enter the DNA major groove, it's preceding loops interact with the outer ends of the recognition site.

[1] As discussed above, the L and R subunits bind in a cross over manner, whereby the R-subunit of BamHI contacts the left DNA half-site of the recognition sequence.

The recognition site for BamHI has a palindromic sequence which can be cut in half for ease in showing bonds.