User:Chloe Paul/Sandbox 1: Difference between revisions

RTP has been of interest in terms of its specific binding to DNA because it doesn’t use the common DNA structural motifs such as a basic leucine zipper, zinc finger or helix-turn-helix motif. It has been established that RTP like Tus, is sequence specific, as it binds as the Ter sites (comprising of two sequences that are imperfect inverted repeats <ref name="bussiere" /><ref name=”vivian”>PMID:17521668</ref>). This means that RTP needs to be able to recognise specific bases in the helical DNA structure by reading the exposed edges of the bases located in the major and minor grooves of DNA not involved in pairing. Structurally RTP interacts with DNA through its alpha helices in the major grooves, its anti-parallel β-strands in the minor grooves and the flexible N-terminal regions wrapping with non-specific ionic interactions around the DNA <ref name=“wilce”>PMID:11224562</ref>.  

As previously noted the role of RTP is to terminate replication of the bacterial chromosome. It was originally assumed that the role of RTP was simply to arrest the replication fork allowing the DNA to cleanly separate <ref name=“wake”>PMID: 9271849</ref>. The proposed mechanism noted that the replication fork is only able to disrupt the RTP/ter interaction when approaching the A-site. This explains the polarity of the mechanism. However recent research has indicated a more complex mechanism involving interactions between the bound RTP and the replication fork helicase. The results of this research have confirmed a RTP/DnaB interaction in vivo, further suggesting this interaction plays an important role in replication fork arrest <ref name=“gautam”>PMID:11124956</ref>. This has lead to the development of a new helicase-specific model involving protein-protein interactions between the replication fork helicase and RTP which arrests the replication fork when it approaches from the appropriate direction <ref name=“kaplan”>PMID:19298368</ref>.