Abstract
The local separation of duplex DNA strands (strand opening) is necessary for initiating basic transactions on DNA such as transcription, replication, and homologous recombination. Strand opening is commonly a stage at which these processes are regulated. Many different mechanisms are used to open the DNA duplex, the details of which are of great current interest. In this review, we focus on a few well-studied cases of DNA replication origin opening in bacteria. In particular, we discuss the opening of origins that support the theta (θ) mode of replication, which is used by all chromosomal origins and many extra-chromosomal elements such as plasmids and phages. Although the details of opening can vary among different origins, a common theme is binding of the initiator to multiple sites at the origin, causing stress that opens an adjacent and intrinsically unstable A+T rich region. The initiator stabilizes the opening by capturing one of the open strands. How the initiator binding energy is harnessed for strand opening remains to be understood.
Highlights
A remarkable feature of double stranded DNA is its ability to undergo denaturation, whereby its strands can be completely separated into single strands, and renaturation, whereby the two complementary strands can be annealed back to form dsDNA
Strand opening usually refers to situations where the stability of duplex DNA is altered locally and for a limited period by DNA binding proteins
The opening was demonstrated in vitro at a time when DNA replication could be separated into discrete stages, with each step dependent on the previous one: initiator binding to the origin, strand opening at DUE, loading of the helicase, and loading of the primase and the rest of the replisome (Figure 1; Bramhill and Kornberg, 1988b; O’Donnell, 2006)
Summary
A remarkable feature of double stranded DNA (dsDNA) is its ability to undergo denaturation, whereby its strands can be completely separated into single strands, and renaturation, whereby the two complementary strands can be annealed back to form dsDNA. The binding of the initiator allows site-specific opening, which enables helicase loading. It is worth emphasizing that in vivo the aggregate of the A+T rich DUE, NAPs and negative supercoiling are not enough, and that the initiator binding to the origin provides an essential contribution to the energetics of opening.
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