Editing DNA replication (section)

=== Elongation ===
DNA polymerase has 5′–3′ activity.
All known DNA replication systems require a free 3′ [[hydroxyl]] group before synthesis can be initiated (note: the DNA template is read in 3′ to 5′ direction whereas a new strand is synthesized in the 5′ to 3′ direction—this is often confused). Four distinct mechanisms for DNA synthesis are recognized:{{cn|date=November 2024}}
# All cellular life forms and many DNA [[virus]]es, [[phage]]s and [[plasmid]]s use a [[primase]] to synthesize a short RNA primer with a free 3′ OH group which is subsequently elongated by a DNA polymerase.
# The retroelements (including [[retrovirus]]es) employ a transfer RNA that primes DNA replication by providing a free 3′ OH that is used for elongation by the [[reverse transcriptase]].
# In the [[adenovirus]]es and the φ29 family of [[bacteriophage]]s, the 3′ OH group is provided by the side chain of an amino acid of the genome attached protein (the terminal protein) to which nucleotides are added by the DNA polymerase to form a new strand.
# In the single stranded DNA viruses—a group that includes the [[circovirus]]es, the [[geminivirus]]es, the [[parvovirus]]es and others—and also the many phages and [[plasmid]]s that use the rolling circle replication (RCR) mechanism, the RCR endonuclease creates a nick in the genome strand (single stranded viruses) or one of the DNA strands (plasmids). The 5′ end of the nicked strand is transferred to a [[tyrosine]] residue on the nuclease and the free 3′ OH group is then used by the DNA polymerase to synthesize the new strand.

Cellular organisms use the first of these pathways since it is the most well-known. In this mechanism, once the two strands are separated, [[primase]] adds RNA primers to the template strands. The leading strand receives one RNA primer while the lagging strand receives several. The leading strand is continuously extended from the primer by a DNA polymerase with high [[processivity]], while the lagging strand is extended discontinuously from each primer forming [[Okazaki fragments]]. [[RNase]] removes the primer RNA fragments, and a low processivity DNA polymerase distinct from the replicative polymerase enters to fill the gaps. When this is complete, a single nick on the leading strand and several nicks on the lagging strand can be found. [[Ligase]] works to fill these nicks in, thus completing the newly replicated DNA molecule.{{cn|date=November 2024}}

The primase used in this process differs significantly between [[bacteria]] and [[archaea]]/[[eukaryote]]s. Bacteria use a primase belonging to the [[DnaG]] protein superfamily which contains a catalytic domain of the TOPRIM fold type.<ref>{{Cite journal |vauthors=Aravind L, Leipe DD, Koonin EV |date=September 1998 |title=Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins |journal=Nucleic Acids Research |volume=26 |issue=18 |pages=4205–4213 |doi=10.1093/nar/26.18.4205 |pmc=147817 |pmid=9722641}}</ref> The TOPRIM fold contains an α/β core with four conserved strands in a [[Rossmann fold|Rossmann-like]] topology. This structure is also found in the catalytic domains of [[topoisomerase]] Ia, topoisomerase II, the OLD-family nucleases and DNA repair proteins related to the RecR protein.{{cn|date=November 2024}}

The primase used by archaea and eukaryotes, in contrast, contains a highly derived version of the [[RNA recognition motif]] (RRM). This primase is structurally similar to many viral RNA-dependent RNA polymerases, reverse transcriptases, cyclic nucleotide generating cyclases and DNA polymerases of the A/B/Y families that are involved in DNA replication and repair.  In eukaryotic replication, the primase forms a complex with Pol α.<ref>{{Cite journal |vauthors=Frick DN, Richardson CC |date=July 2001 |title=DNA primases |journal=Annual Review of Biochemistry |volume=70 |pages=39–80 |doi=10.1146/annurev.biochem.70.1.39 |pmid=11395402 |s2cid=33197061}}</ref>

Multiple DNA polymerases take on different roles in the DNA replication process. In ''[[Escherichia coli|E. coli]]'', [[Pol III|DNA Pol III]] is the polymerase enzyme primarily responsible for DNA replication. It assembles into a replication complex at the replication fork that exhibits extremely high processivity, remaining intact for the entire replication cycle. In contrast, [[Pol I|DNA Pol I]] is the enzyme responsible for replacing RNA primers with DNA. DNA Pol I has a 5′ to 3′ [[exonuclease]] activity in addition to its polymerase activity, and uses its exonuclease activity to degrade the RNA primers ahead of it as it extends the DNA strand behind it, in a process called [[nick translation]]. Pol I is much less processive than Pol III because its primary function in DNA replication is to create many short DNA regions rather than a few very long regions.{{cn|date=November 2024}}

In [[eukaryote]]s, the low-processivity enzyme, Pol α, helps to initiate replication because it forms a complex with primase.<ref>{{Cite journal |vauthors=Barry ER, Bell SD |date=December 2006 |title=DNA replication in the archaea |journal=Microbiology and Molecular Biology Reviews |volume=70 |issue=4 |pages=876–887 |doi=10.1128/MMBR.00029-06 |pmc=1698513 |pmid=17158702}}</ref>  In eukaryotes, leading strand synthesis is thought to be conducted by Pol ε; however, this view has recently been  challenged, suggesting a role for Pol δ.<ref>{{Cite journal |vauthors=Stillman B |date=July 2015 |title=Reconsidering DNA Polymerases at the Replication Fork in Eukaryotes |journal=Molecular Cell |volume=59 |issue=2 |pages=139–141 |doi=10.1016/j.molcel.2015.07.004 |pmc=4636199 |pmid=26186286}}</ref>  Primer removal is completed Pol δ<ref>{{Cite thesis |title=Distinguishing the pathways of primer removal during Eukaryotic Okazaki fragment maturation |date=February 2009 |degree=Ph.D. |publisher=School of Medicine and Dentistry, University of Rochester |vauthors=Rossi ML |hdl=1802/6537}}</ref> while repair of DNA during replication is completed by Pol ε.

As DNA synthesis continues, the original DNA strands continue to unwind on each side of the bubble, forming a [[replication fork]] with two prongs. In bacteria, which have a single origin of replication on their circular chromosome, this process creates a "[[theta structure]]" (resembling the Greek letter theta: θ). In contrast, eukaryotes have longer linear chromosomes and initiate replication at multiple origins within these.<ref>{{Cite journal |vauthors=Huberman JA, Riggs AD |date=March 1968 |title=On the mechanism of DNA replication in mammalian chromosomes |journal=Journal of Molecular Biology |volume=32 |issue=2 |pages=327–341 |doi=10.1016/0022-2836(68)90013-2 |pmid=5689363}}<!--|access-date=7 April 2016--></ref>