User:Cameron Ball/Sandbox 1: Difference between revisions

RTP binds DNA as a dimer at Ter sites. These Ter sites are 29 base pairs in length comprise of two non-identical inverted repeats that share three highly conserved base pairs. The two sites are designated the A-site and the B-site and each have different affinities for RTP. It is now known that RTP binds to Ter site in a directional manner as a result of these non-identical sites, allowing polymerase units to pass by one way but blocking them in another. However, historically, the exact way in which symmetric RTP dimers blocked polymerases in a polar fashion was a source of great confusion. This was compounded by the fact that a symmetrical DNA sequence (designated sRB) was used in the first crystal structure of an <scene name='User:Cameron_Ball/Sandbox_1/Rtp_dna_complex/1'>RTP:DNA complex</scene>. <ref>Wilce, J. A., Vivian, J. P., Hastings, A. F., Otting, G., Folmer, R. H., Duggin, I. G., Wake, R. G. & Wilce, M. C., Structure of the RTP-DNA complex and the mechanism of polar replication fork arrest., (2001). Nature Struct. Biol.8, 206–210.</ref>

<scene name='User:Cameron_Ball/Sandbox_1/Rtp_dna_complex/1'>RTP binds DNA</scene> through interactions between the <scene name='User:Cameron_Ball/Sandbox_1/Rtp_alpha_helices_and_dna_/1'>alpha helices</scene> and the major groove of DNA. Two possible mechanisms were originally proposed to explain it's activity; The "clamp" model, where RTP physically blocks the approaching polymerase and the "interaction" model, where there is some protein-protein interaction between RTP and the approaching replisome unit. Recent data shows that RTP-Ter contact is not sufficient to cause arrest, suggesting the interaction model is the best approximation. <ref> Kaplan, D.L and Bastia, D, Mechanisms of polar arrest of a replication fork, Molecular Microbiology 2009|72|2), 279-285 </ref> For example, in 2006 Ian Duggin showed that the fork arrest efficiency of RTP can be lowered by attaching peptides that would block any protein-protein interaction from occurring while not affecting the RTP-DNA binding affinity<ref> Duggin, I.G., DNA replication fork arrest by the Bacillus subtilis RTP-DNA complex involves a mechanism that is independent of the affinity of RTP-DNA binding ''J Mol Biol'' '''361:'''1-6</ref>.