All natural DNA polymerase enzymes are only able to carry out 5′→3′ synthesis, which adds significant complications to the process by which double-stranded DNA is replicated (Section 13.2) [1].

The Meselson-Stahl experiment proved that DNA replication in living cells follows the semiconservative scheme proposed by Watson and Crick [2].

Genome replication is made up of three phases - initiation, elongation and termination [3]

Sequence analysis of E. coli origin of replication shows that it contains two short repeat motifs, one of nine nucleotides and the other of 13 nucleotides ( Figure 13.8A ). The nine-nucleotide repeat, five copies of which are dispersed throughout oriC, is the binding site for a protein called DnaA.

The result of DnaA binding is that the double helix opens up (‘melts') within the tandem array of three AT-rich, 13-nucleotide repeats located at one end of the oriC sequence ( Figure 13.8B ) [3].

http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/genomes/ch13f8.gif

In Figure 13.11 is illustrated the need for a primer to initiate synthesis of each new polynucleotide. It is not known for certain why DNA polymerases cannot begin synthesis on an entirely single-stranded template, but it may relate to the proofreading activity of these enzymes, which is essential for the accuracy of replication [3].

Okazaki fragment – is one of the short segments of RNA-primed DNA synthesized during replication of the lagging strand of the double helix [3*].

DNA topoisomerases provide a solution to the topological problem [in DNA].

Helicase is an enzyme that breaks base pairs in a double-stranded DNA molecule.

In bacteria, primers are synthesized by primase, a special RNA polymerase unrelated to the transcribing enzyme, with each primer 4–15 nucleotides in length. The main replicating polymerase of E. coli is DNA polymerase III.

DNA polymerase α has an important function in DNA synthesis, being the enzyme that primes eukaryotic replication (see Figure 13.12B ). The main replicating enzyme in mammals is DNA polymerase δ [2].

There are two base-pair combinations in DNA - A base-paired with T, and G base-paired with C [1].

Type IA topoisomerases introduce a break in one polynucleotide and pass the second polynucleotide through the gap that is formed ( Figure 13.4A ). The two ends of the broken strand are then re-ligated. This mode of action results in the linking number (the number of times one strand crosses the other in a circular molecule) being changed by one.

Type IB topoisomerases act in a similar way to the Type IA enzymes, although the detailed mechanism is different [2].

Origins of replication in the yeast Saccharomyces cerevisiae are called autonomously replicating sequences or ARSs [3].