Phage attachment sites are regions of DNA required for site-specific recombination. This reaction is best characterized for phage lambda.
The primary attachment site on the E. coli chromosome, attB, consists of three regions designated BOB' and the attachment site on lambda, attP, consists of three corresponding regions designated POP'. The actual crossover occurs between the homologous 15 bp core regions (designated O) on the two sites.
Sequences from approximately 150 bp to the left of O on attP (the "P arm") and approximately 80 bp to the right of O (the "P' arm") are required for recombination. Integrase and IHF bind to specific sites within the arms and fold the DNA into a complex structure (an "intasome") that facilitates interaction with the BOB' site on the chromosome and subsequent recombination. Integrase is an enzyme made by lambda that catalyzes the recombination event.IHF (Integration host factor) is a protein made by the E. coli host that binds to the DNA and causes it to bend.
If the normal attB site is deleted from the chromosome, integrase can bind with lower affinity to secondary sites on the chromosome, resulting in integration of lambda at a different site. The frequency of integration into secondary sites is 100-1000 times rarer than integration into attB. The secondary att sites have sequence similarity to attB. The sequence of attP, attB, and some secondary att sites are shown in the following table:
|Site||Core DNA Sequence|
|attP||tCAGCTTt tTtatAc tAAGTTGg|
|attB||cCTGCTTt tTtatAc tAACTTGa|
|proB||tgcGCTaa tTtatAc gAgGCTac|
|trpC||gCgtaaTg tTtatAa atgGCgGc|
|galT||cgcctTTg tTttcAa aAACCTGc|
|thrA||cggGCTTt tTtctgt gtttCctg|
|rrnB||ttgGCTat tTtacca cgACTgtc|
Integrase binds to the left and right sides of the core site and cuts the DNA within the core site to inititate recombination. The upper case nucleotides represent identity with the consensus sequence for integrase-nucleotide interactions in the core region of the att sites.