Arrest of DNA replication inReplication forks approaching from the non-permissive side of the Tus-Ter complex are arrested, but replisomes approaching from the permissive side can pass through the complex. The Ter sites are oriented in the chromosome to permit DNA replication in the origin-to-terminus direction, but restrict replication forks traveling in the terminus-to-origin direction. Thus, the Tus-Ter complexes form a replication fork trap and prevent DNA replication forks from meeting in regions other than in the chromosomal terminus.The functional polarity demonstrated by Tus is reflected in the asymmetry of the protein-DNA complex, whose crystal structure has been recently solved (2). Tus binds as a monomer (3, 4) and contacts both strands of the Ter site on the nonpermissive of the complex, but only a single strand on the permissive side (2, 5). The Ter site DNA is nestled into a cleft formed by the two primary domains of Tus (amino and carboxyl domains) and the interstrand -sheets that connect the two domains (2). The primary determinants of base pair recognition and binding are mediated by the main two interstrand -sheets, which penetrate deeply into the major groove of the Ter site, making both polar and hydrophobic contacts with the bases. Binding is also enhanced by extensive contacts between Tus and the phosphates in the DNA backbone. A total of 42 amino acid residues stretched along the length of the protein make contacts with the DNA.Tus binds to the chromosomal Ter sites with a very high affinity. The K obs for Tus binding to the TerB site ranges between 3.4 ϫ 10 Ϫ13 M and 7.5 ϫ 10 Ϫ13 M, depending on the buffer conditions used (5, 6). Half-lives (t1 ⁄2 ) of the protein-DNA complex were determined to be 550 to 149 min, respectively, in these studies. The high affinity of the Tus-Ter interaction in conjunction with the distribution of protein-DNA contacts has been used to suggest that Tus can arrest DNA replication by functioning as a clamp on the DNA and preventing the unwinding activity of the DnaB helicase (2,5,7,8). Alternately, protein-protein interactions between Tus and the DnaB helicase have been postulated to mediate replication arrest. This latter model is based upon the specificity of Tus function (9, 10), differential ability of Tus to halt helicase unwinding when presented with different templates (11), and mutational studies on Tus (6,12).Ter sequences were originally identified as 22-23 base pairs in length, based on sequence identity between TerA, TerB, and TerC (13,14). As additional sites were identified both in the chromosome and in plasmid replicons, it became apparent that the essential conserved elements of the Ter site were an 11-base pair "core" sequence (positions 9 -19) and an upstream G-C base pair at position 6 (Fig. 1). Nucleoside analogs have been used to partially map the determinants of Tus binding (15,16) and it was shown that (i) the G residues at positions 10, 13, and 17 within the core sequence contributed both major and minor groove interactions, (ii) the c...