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Noti cut site12/18/2023 The BamHI enzyme is capable of making a large number of contacts with DNA. Sites of Recognition Between BamHI and DNA 1 Sites of Recognition Between BamHI and DNA.This bundle marks the BamHI dimer interface, and it is thought that the dipole moments of the NH2-terminal atoms on this bundle may contribute to electrostatic stabilization. Major groove contacts are formed by atoms residing on the amino-terminus of a parallel 4 helix bundle. The protein binds the bases through either direct hydrogen bonds or water-mediated H-bonds between the protein and every H-bond donor/acceptor group in the major groove. 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. DNA is bound in a large cleft that is formed between dimers the enzyme binds in a "crossover" manner. This allows the DNA to maintain its normal B-DNA conformation without distorting to facilitate enzyme binding. In its unbound form, BamHI displays a central b sheet, which resides in between α-helices.īamHI undergoes a series of unconventional conformational changes upon DNA recognition. This cleavage results in sticky ends which are 4 bp long. BamHI binds at the recognition sequence 5'-GGATCC-3', and cleaves these sequences just after the 5'-guanine on each strand. This exhibit focuses on the structure-function relations of BamHI as described by Newman, et al. Restriction endonuclease BamHI bound to a non-specific DNA.īamHI (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.
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