Editing DNA replication (section)

== Replication process ==
{{Main|Prokaryotic DNA replication|Eukaryotic DNA replication}}

[[File:Asymmetry in the synthesis of leading and lagging strands.svg|thumb|left|Overview of the steps in DNA replication]]
[[File:Steps in DNA synthesis.svg|thumb|Steps in DNA synthesis]]

DNA replication, like all biological polymerization processes, proceeds in three enzymatically catalyzed and coordinated steps: initiation, elongation and termination.

=== Initiation ===
[[File:Figure Role of initiators for initiation of DNA replication.png|thumb|200px|right|Role of initiators for initiation of DNA replication]]
[[File:EukPreRC.jpg|thumb|200px|Formation of pre-replication complex]]
For a [[cell division|cell to divide]], it must first replicate its DNA.<ref>{{Cite book |title=Molecular Biology of the Cell |vauthors=Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P |publisher=Garland Science |year=2002 |isbn=0-8153-3218-1 |chapter=Chapter 5: DNA Replication Mechanisms |chapter-url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.section.754}}</ref> DNA replication is an all-or-none process; once replication begins, it proceeds to completion. Once replication is complete, it does not occur again in the same cell cycle. This is made possible by the division of initiation of the [https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/pre-replication-complex pre-replication complex].{{cn|date=November 2024}}

=== Pre-replication complex ===
{{Main|Pre-replication complex}}

In late [[mitosis]] and early [[G1 phase]], a large complex of initiator proteins assembles into the pre-replication complex at particular points in the DNA, known as "[[origin of replication|origins]]".<ref name="origins" /><ref name="Hu 352–372" /> In ''[[Escherichia coli|E. coli]]'' the primary initiator protein is [[DnaA|Dna A]]; in [[yeast]], this is the [[origin recognition complex]].<ref>{{Cite journal |vauthors=Weigel C, Schmidt A, Rückert B, Lurz R, Messer W |date=November 1997 |title=DnaA protein binding to individual DnaA boxes in the Escherichia coli replication origin, oriC |journal=The EMBO Journal |volume=16 |issue=21 |pages=6574–6583 |doi=10.1093/emboj/16.21.6574 |pmc=1170261 |pmid=9351837}}</ref>  Sequences used by initiator proteins tend to be "AT-rich" (rich in adenine and thymine bases), because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair) and thus are easier to strand-separate.<ref>{{Cite book |url=https://archive.org/details/molecularcellbio00lodi |title=Molecular Cell Biology |vauthors=Lodish H, Berk A, Zipursky LS, Matsudaira P, Baltimore D, Darnell J |publisher=W. H. Freeman and Company |year=2000 |isbn=0-7167-3136-3}}[https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.3163#3179 12.1.  General Features of Chromosomal Replication: Three Common Features of Replication Origins]</ref>  In eukaryotes, the origin recognition complex catalyzes the assembly of initiator proteins into the pre-replication complex. In addition, a recent report suggests that budding yeast ORC dimerizes in a cell cycle dependent manner to control licensing.<ref>{{Cite journal |vauthors=Lin YC, Prasanth SG |date=July 2021 |title=Replication initiation: Implications in genome integrity |journal=DNA Repair |volume=103 |page=103131 |doi=10.1016/j.dnarep.2021.103131 |pmc=8296962 |pmid=33992866 |doi-access=free}}</ref><ref>{{Cite journal |display-authors=6 |vauthors=Amin A, Wu R, Cheung MH, Scott JF, Wang Z, Zhou Z, Liu C, Zhu G, Wong CK, Yu Z, Liang C |date=March 2020 |title=An Essential and Cell-Cycle-Dependent ORC Dimerization Cycle Regulates Eukaryotic Chromosomal DNA Replication |journal=Cell Reports |volume=30 |issue=10 |pages=3323–3338.e6 |doi=10.1016/j.celrep.2020.02.046 |pmid=32160540 |doi-access=free}}</ref> In turn, the process of ORC dimerization is mediated by a cell cycle-dependent Noc3p dimerization cycle in vivo, and this role of Noc3p is separable from its role in ribosome biogenesis. [https://www.life-science-alliance.org/content/6/3/e202201594.full An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing] ORC and Noc3p are continuously bound to the chromatin throughout the cell cycle.<ref>{{Cite journal |vauthors=Zhang Y, Yu Z, Fu X, Liang C |date=June 2002 |title=Noc3p, a bHLH protein, plays an integral role in the initiation of DNA replication in budding yeast |journal=Cell |volume=109 |issue=7 |pages=849–860 |doi=10.1016/s0092-8674(02)00805-x |pmid=12110182 |doi-access=free}}</ref>  [[CDC6|Cdc6]] and [[DNA replication factor CDT1|Cdt1]] then associate with the bound origin recognition complex at the origin in order to form a larger complex necessary to load the [[Minichromosome maintenance|Mcm complex]] onto the DNA. In eukaryotes, the Mcm complex is the helicase that will split the DNA helix at the replication forks and origins. The Mcm complex is recruited at late G1 phase and loaded by the ORC-Cdc6-Cdt1 complex onto the DNA via ATP-dependent protein remodeling. The loading of the MCM complex onto the origin DNA marks the completion of pre-replication complex formation.<ref name="Morgan-2007">{{Cite book |title=The cell cycle: principles of control |vauthors=Morgan DO |date=2007 |publisher=New Science Press |isbn=978-0-19-920610-0 |location=London |pages=64–75 |oclc=70173205}}</ref>

If environmental conditions are right in late G1 phase, the G1 and G1/S [[cyclin]]-[[Cyclin-dependent kinase|Cdk]] complexes are activated, which stimulate expression of genes that encode components of the DNA synthetic machinery. G1/S-Cdk activation also promotes the expression and activation of S-Cdk complexes, which may play a role in activating replication origins depending on species and cell type. Control of these Cdks vary depending on cell type and stage of development. This regulation is best understood in [[budding yeast]], where the S cyclins [[Clb 5,6 (Cdk1)|Clb5]] and [[Clb 5,6 (Cdk1)|Clb6]] are primarily responsible for DNA replication.<ref>{{Cite journal |vauthors=Donaldson AD, Raghuraman MK, Friedman KL, Cross FR, Brewer BJ, Fangman WL |date=August 1998 |title=CLB5-dependent activation of late replication origins in S. cerevisiae |journal=Molecular Cell |volume=2 |issue=2 |pages=173–182 |doi=10.1016/s1097-2765(00)80127-6 |pmid=9734354 |doi-access=free}}</ref> Clb5,6-Cdk1 complexes directly trigger the activation of replication origins and are therefore required throughout S phase to directly activate each origin.<ref name="Morgan-2007" />

In a similar manner, [[Cell division cycle 7-related protein kinase|Cdc7]] is also required through [[S phase]] to activate replication origins. Cdc7 is not active throughout the cell cycle, and its activation is strictly timed to avoid premature initiation of DNA replication. In late G1, Cdc7 activity rises abruptly as a result of association with the regulatory subunit [[DBF4]], which binds Cdc7 directly and promotes its protein kinase activity. Cdc7 has been found to be a rate-limiting regulator of origin activity. Together, the G1/S-Cdks and/or S-Cdks and Cdc7 collaborate to directly activate the replication origins, leading to initiation of DNA synthesis.<ref name="Morgan-2007" />

=== Preinitiation complex ===

In early S phase, S-Cdk and Cdc7 activation lead to the assembly of the preinitiation complex, a massive protein complex formed at the origin. Formation of the preinitiation complex displaces Cdc6 and Cdt1 from the origin replication complex, inactivating and disassembling the pre-replication complex. Loading the preinitiation complex onto the origin activates the Mcm helicase, causing unwinding of the DNA helix. The preinitiation complex also loads [[DNA polymerase alpha|α-primase]] and other DNA polymerases onto the DNA.<ref name="Morgan-2007" />

After α-primase synthesizes the first primers, the primer-template junctions interact with the clamp loader, which loads the sliding clamp onto the DNA to begin DNA synthesis. The components of the preinitiation complex remain associated with replication forks as they move out from the origin.<ref name="Morgan-2007" />

=== 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>

=== Replication fork ===
[[File:Replication fork.svg|right|thumb|Scheme of the replication fork.<br />a: template, b: leading strand, c: lagging strand, d: replication fork, e: primer, f: [[Okazaki fragments]]]]
[[File:Eukaryotic DNA replication.svg|thumb|437x437px|Many enzymes are involved in the DNA replication fork.]]
The replication fork is a structure that forms within the long helical DNA during DNA replication. It is produced by enzymes called helicases that break the hydrogen bonds that hold the DNA strands together in a helix. The resulting structure has two branching "prongs", each one made up of a single strand of DNA. These two strands serve as the template for the leading and lagging strands, which will be created as DNA polymerase matches complementary nucleotides to the templates; the templates may be properly referred to as the leading strand template and the lagging strand template.{{cn|date=November 2024}}

'''DNA is read by DNA polymerase in the 3′ to 5′ direction, meaning the new strand is synthesized in the 5' to 3' direction.''' Since the leading and lagging strand templates are oriented in opposite directions at the replication fork, a major issue is how to achieve synthesis of new lagging strand DNA, whose direction of synthesis is opposite to the direction of the growing replication fork.{{cn|date=November 2024}}

==== Leading strand ====
The leading strand is the strand of new DNA which is synthesized in the same direction as the growing replication fork. This sort of DNA replication is continuous.{{cn|date=November 2024}}

==== Lagging strand ====
The lagging strand is the strand of new DNA whose direction of synthesis is opposite to the direction of the growing replication fork. Because of its orientation, replication of the lagging strand is more complicated as compared to that of the leading strand.  As a consequence, the DNA polymerase on this  strand is seen to "lag behind" the other strand.{{cn|date=November 2024}}

The lagging strand is synthesized in short, separated segments. On the lagging strand ''template'', a [[primase]] "reads" the template DNA and initiates synthesis of a short complementary [[RNA]] primer. A DNA polymerase extends the primed segments, forming [[Okazaki fragment]]s. The RNA primers are then removed and replaced with DNA, and the fragments of DNA are joined by [[DNA ligase]].{{cn|date=November 2024}}

==== Dynamics at the replication fork ====
[[File:1axc tricolor.png|thumb|200px|The assembled human DNA clamp, a [[trimer (biochemistry)|trimer]] of the protein [[PCNA]]]]

In all cases the helicase is composed of six polypeptides that wrap around only one strand of the DNA being replicated. The two polymerases are bound to the helicase hexamer. In eukaryotes the helicase wraps around the leading strand, and in prokaryotes it wraps around the lagging strand.<ref name="replisome-in-Science">{{Cite journal |display-authors=6 |vauthors=Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W |date=February 2019 |title=Structures and operating principles of the replisome |journal=Science |volume=363 |issue=6429 |page=835 |doi=10.1126/science.aav7003 |pmc=6681829 |pmid=30679383}}</ref>

As helicase unwinds DNA at the replication fork, the DNA ahead is forced to rotate. This process results in a build-up of twists in the DNA ahead.<ref>{{Cite book |title=Molecular Biology of the Cell |vauthors=Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P |publisher=Garland Science |year=2002 |isbn=0-8153-3218-1 |chapter=DNA Replication Mechanisms: DNA Topoisomerases Prevent DNA Tangling During Replication |chapter-url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.section.754#787}}</ref> This build-up creates a torsional load that would eventually stop the replication fork. Topoisomerases are enzymes that temporarily break the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix; topoisomerases (including [[DNA gyrase]]) achieve this by adding negative [[DNA supercoil|supercoils]] to the DNA helix.<ref>{{Cite journal |vauthors=Reece RJ, Maxwell A |date=26 September 2008 |title=DNA gyrase: structure and function |journal=Critical Reviews in Biochemistry and Molecular Biology |volume=26 |issue=3–4 |pages=335–375 |doi=10.3109/10409239109114072 |pmid=1657531}}<!--|access-date=7 April 2016--></ref>

Bare single-stranded DNA tends to fold back on itself forming [[Biomolecular structure#Secondary structure|secondary structures]]; these structures can interfere with the movement of DNA polymerase. To prevent this, [[single-strand binding protein]]s bind to the DNA until a second strand is synthesized, preventing secondary structure formation.<ref>{{Cite book |title=Molecular Biology of the Cell |vauthors=Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P |publisher=Garland Science |year=2002 |isbn=0-8153-3218-1 |chapter=DNA Replication Mechanisms: Special Proteins Help to Open Up the DNA Double Helix in Front of the Replication Fork |chapter-url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.section.754#774}}</ref>

Double-stranded DNA is coiled around [[histone]]s that  play an important role in regulating gene expression so the replicated DNA must be coiled around histones at the same places as the original DNA.<ref>{{Cite journal |last1=Koonin |first1=Eugene V. |last2=Krupovic |first2=Mart |last3=Ishino |first3=Sonoko |last4=Ishino |first4=Yoshizumi |date=2020-06-09 |title=The replication machinery of LUCA: common origin of DNA replication and transcription |journal=BMC Biology |volume=18 |issue=1 |page=61 |doi=10.1186/s12915-020-00800-9 |issn=1741-7007 |pmc=7281927 |pmid=32517760 |doi-access=free}}</ref> To ensure this, histone [[Chaperone (protein)|chaperones]] disassemble the [[chromatin]] before it is replicated and replace the histones in the correct place. Some steps in this reassembly are somewhat speculative.<ref>{{Cite journal |vauthors=Ransom M, Dennehey BK, Tyler JK |date=January 2010 |title=Chaperoning histones during DNA replication and repair |journal=Cell |volume=140 |issue=2 |pages=183–195 |doi=10.1016/j.cell.2010.01.004 |pmc=3433953 |pmid=20141833}}<!--|access-date=24 July 2020--></ref>

Clamp proteins act as a sliding clamp on DNA, allowing the DNA polymerase to bind to its template and aid in processivity. The inner face of the clamp enables DNA to be threaded through it. Once the polymerase reaches the end of the template or detects double-stranded DNA, the sliding clamp undergoes a conformational change that releases the DNA polymerase. Clamp-loading proteins are used to initially load the clamp, recognizing the junction between template and RNA primers.<ref name="Alberts" /><sup>:274-5</sup>

=== DNA replication proteins ===
At the replication fork, many replication enzymes assemble on the DNA into a complex molecular machine called the [[replisome]]. The following is a list of major DNA replication enzymes that participate in the replisome:<ref>{{Cite book |title=Introduction to Genetic Analysis |vauthors=Griffiths AJ, Wessler SR, Lewontin RC, Carroll SB |publisher=W. H. Freeman and Company |year=2008 |isbn=978-0-7167-6887-6}}[Chapter 7: DNA: Structure and Replication. pg 283–290]</ref>

{| class="wikitable"
|-
! Enzyme !! Function in DNA replication
|-
| [[DNA helicase]] || Also known as helix destabilizing enzyme. Helicase separates the two strands of DNA at the [[Replication Fork]] behind the topoisomerase.
|-
| [[DNA polymerase]] || The enzyme responsible for catalyzing the addition of nucleotide substrates to DNA in the 5′ to 3′ direction during DNA replication. Also performs proof-reading and error correction.  There exist many different types of DNA Polymerase, each of which perform different functions in different types of cells.
|-
| [[DNA clamp]] || A protein which prevents elongating DNA polymerases from dissociating from the DNA parent strand.
|-
| [[Single-strand DNA-binding protein]] || Bind to ssDNA and prevent the DNA double helix from re-annealing after DNA helicase unwinds it, thus maintaining the strand separation, and facilitating the synthesis of the new strand.
|-
| [[Topoisomerase]] || Relaxes the DNA from its super-coiled nature.
|-
| [[DNA gyrase]] || Relieves strain of unwinding by DNA helicase; this is a specific type of topoisomerase
|-
| [[DNA ligase]]|| Re-anneals the semi-conservative strands and joins [[Okazaki Fragments]] of the lagging strand.
|-
| [[Primase]] || Provides a starting point of RNA (or DNA) for DNA polymerase to begin synthesis of the new DNA strand.
|-
| [[Telomerase]] || Lengthens telomeric DNA by adding repetitive nucleotide sequences to the ends of '''[[Eukaryotic chromosome fine structure|eukaryotic chromosomes]]'''.  This allows germ cells and stem cells to avoid the [[Hayflick limit]] on cell division.<ref>{{Cite web |date=2009-05-11 |title=Will the Hayflick limit keep us from living forever? |url=http://science.howstuffworks.com/life/genetic/hayflick-limit.htm |access-date=January 20, 2015 |website=Howstuffworks |vauthors=Clark J}}</ref>
|}
''[[In vitro]]'' [[single-molecule experiment]]s (using [[optical tweezers]] and [[magnetic tweezers]]) have found synergetic interactions between the replisome enzymes ([[helicase]], [[polymerase]], and [[Single-strand DNA-binding protein]]) and with the DNA replication fork enhancing [[DNA unwinding element|DNA-unwinding]] and DNA-replication.<ref name="Jarillo-2021" /> These results lead to the development of kinetic models accounting for the synergetic interactions and their stability.<ref name="Jarillo-2021" />

=== Replication machinery ===

[[File:E. coli replisome.png|thumb|left|E. coli Replisome. Notably, the DNA on lagging strand forms a loop. The exact structure of replisome is not well understood.]]

'''Replication machineries''' consist of factors involved in DNA replication and appearing on template ssDNAs. Replication machineries include primosotors are replication enzymes; DNA polymerase, DNA helicases, DNA clamps and DNA topoisomerases, and replication proteins; e.g. single-stranded DNA binding proteins (SSB). In the replication machineries these components coordinate. In most of the bacteria, all of the factors involved in DNA replication are located on replication forks and the complexes stay on the forks during DNA replication. Replication machineries are also referred to as replisomes, or DNA replication systems. These terms are generic terms for proteins located on replication forks. In eukaryotic and some bacterial cells the replisomes are not formed.{{cn|date=November 2024}}

In an alternative figure, DNA factories are similar to projectors and DNAs are like as cinematic films passing constantly into the projectors. In the replication factory model, after both DNA helicases for leading strands and lagging strands are loaded on the template DNAs, the helicases run along the DNAs into each other. The helicases remain associated for the remainder of replication process. Peter Meister et al. observed directly replication sites in [[budding yeast]] by monitoring [[green fluorescent protein]] (GFP)-tagged DNA polymerases α. They detected DNA replication of pairs of the tagged loci spaced apart symmetrically from a replication origin and found that the distance between the pairs decreased markedly by time.<ref name="in&out">{{Cite journal |vauthors=Meister P, Taddei A, Gasser SM |date=June 2006 |title=In and out of the replication factory |journal=Cell |volume=125 |issue=7 |pages=1233–5 |doi=10.1016/j.cell.2006.06.014 |pmid=16814710 |s2cid=15397410 |doi-access=free}}</ref> This finding suggests that the mechanism of DNA replication goes with DNA factories. That is, couples of replication factories are loaded on replication origins and the factories associated with each other. Also, template DNAs move into the factories, which bring extrusion of the template ssDNAs and new DNAs. Meister's finding is the first direct evidence of replication factory model. Subsequent research has shown that DNA helicases form dimers in many eukaryotic cells and bacterial replication machineries stay in single intranuclear location during DNA synthesis.<ref name="watson237">{{Cite book |title=Molecular Biology of the Gene |vauthors=Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R, Inglis CH |date=2008 |publisher=Pearson/Benjamin Cummings |isbn=978-0-8053-9592-1 |edition=6th |location=San Francisco |page=237}}</ref>

Replication Factories Disentangle Sister Chromatids. The disentanglement is essential for distributing the chromatids into daughter cells after DNA replication. Because sister chromatids after DNA replication hold each other by '''[[Cohesin]]''' rings, there is the only chance for the disentanglement in DNA replication. Fixing of replication machineries as replication factories can improve the success rate of DNA replication. If replication forks move freely in chromosomes, catenation of nuclei is aggravated and impedes mitotic segregation.<ref name="in&out" />

=== Termination ===
Eukaryotes initiate DNA replication at multiple points in the chromosome, so replication forks meet and terminate at many points in the chromosome.  Because eukaryotes have linear chromosomes, DNA replication is unable to reach the very end of the chromosomes.  Due to this problem, DNA is lost in each replication cycle from the end of the chromosome.  [[Telomeres]] are regions of repetitive DNA close to the ends and help prevent loss of genes due to this shortening. Shortening of the telomeres is a normal process in [[somatic cell]]s.  This shortens the telomeres of the daughter DNA chromosome.  As a result, cells can only divide a certain number of times before the DNA loss prevents further division. (This is known as the [[Hayflick limit]].)  Within the [[germ cell]] line, which passes DNA to the next generation, [[telomerase]] extends the repetitive sequences of the telomere region to prevent degradation. Telomerase can become mistakenly active in somatic cells, sometimes leading to [[cancer]] formation. Increased telomerase activity is one of the hallmarks of cancer.<ref>{{Cite journal |last=Shay |first=Jerry W. |date=2016-06-01 |title=Role of Telomeres and Telomerase in Aging and Cancer |journal=Cancer Discovery |language=en |volume=6 |issue=6 |pages=584–593 |doi=10.1158/2159-8290.CD-16-0062 |pmid=27029895 |pmc=4893918 |issn=2159-8274}}</ref>

Termination requires that the progress of the DNA replication fork must stop or be blocked. Termination at a specific locus, when it occurs, involves the interaction between two components: (1) a termination site sequence in the DNA, and (2) a protein which binds to this sequence to physically stop DNA replication. In various bacterial species, this is named the DNA replication terminus site-binding protein, or [[Ter protein]].<ref>{{Cite journal |last1=Neylon |first1=Cameron |last2=Kralicek |first2=Andrew V. |last3=Hill |first3=Thomas M. |last4=Dixon |first4=Nicholas E. |date=September 2005 |title=Replication Termination in Escherichia coli : Structure and Antihelicase Activity of the Tus- Ter Complex |journal=Microbiology and Molecular Biology Reviews |language=en |volume=69 |issue=3 |pages=501–526 |doi=10.1128/MMBR.69.3.501-526.2005 |pmid=16148308 |pmc=1197808 |issn=1092-2172}}</ref>

Because bacteria have circular chromosomes, termination of replication occurs when the two replication forks meet each other on the opposite end of the parental chromosome. ''E. coli'' regulates this process through the use of termination sequences that, when bound by the [[Tus protein]], enable only one direction of replication fork to pass through. As a result, the replication forks are constrained to always meet within the termination region of the chromosome.<ref>{{Cite book |title=Genomes |vauthors=Brown TA |publisher=[[BIOS Scientific Publishers]] |year=2002 |isbn=1-85996-228-9 |chapter=Chapter 13.2.3. Termination of replication |chapter-url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes.section.8121#8156}}</ref>