Editing DNA replication (section)

=== 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 |last=Koonin |first=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>