Editing DNA replication (section)

== DNA polymerase ==
{{Main|DNA polymerase}}

[[File:DNA polymerase.svg|thumb|250px|right| DNA polymerases adds nucleotides to the 3′ end of a strand of DNA.<ref>{{Cite book |title=Fundamental Molecular Biology |vauthors=Allison L |date=2007 |publisher=Blackwell Publishing |isbn=978-1-4051-0379-4 |page=112}}</ref> If a mismatch is accidentally incorporated, the polymerase is inhibited from further extension. Proofreading removes the mismatched nucleotide and extension continues.]]

[[DNA polymerase]]s are a family of [[enzyme]]s that carry out all forms of DNA replication.<ref>{{Cite book |url=https://archive.org/details/biochemistrychap00jere |title=Biochemistry |vauthors=Berg JM, Tymoczko JL, Stryer L, Clarke ND |publisher=W.H. Freeman and Company |year=2002 |isbn=0-7167-3051-0}} [https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=stryer.section.3769 Chapter 27, Section 2: DNA Polymerases Require a Template and a Primer]</ref>  DNA polymerases in general cannot initiate synthesis of new strands but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a short fragment of RNA, called a [[primer (molecular biology)|primer]], must be created and paired with the template DNA strand.

DNA polymerase adds a new strand of DNA by extending the 3′ end of an existing nucleotide chain, adding new [[nucleotide]]s matched to the template strand, one at a time, via the creation of [[phosphodiester bond]]s. The energy for this process of DNA polymerization comes from hydrolysis of the [[high-energy phosphate]] (phosphoanhydride) bonds between the three phosphates attached to each unincorporated [[nucleotide|base]].  Free bases with their attached phosphate groups are called [[nucleotide]]s; in particular, bases with three attached phosphate groups are called [[nucleoside triphosphate]]s. When a nucleotide is being added to a growing DNA strand, the formation of a phosphodiester bond between the proximal phosphate of the nucleotide to the growing chain is accompanied by hydrolysis of a high-energy phosphate bond with release of the two distal phosphate groups as a [[pyrophosphate]]. Enzymatic hydrolysis of the resulting [[pyrophosphate]] into inorganic phosphate consumes a second high-energy phosphate bond and renders the reaction effectively irreversible.<ref group="Note">The [[Bioenergetics|energetics]] of this process may also help explain the directionality of synthesis—if DNA were synthesized in the 3′ to 5′ direction, the energy for the process would come from the 5′ end of the growing strand rather than from free nucleotides. The problem is that if the high energy triphosphates were on the growing strand and not on the free nucleotides, proof-reading by removing a mismatched terminal nucleotide would be problematic: Once a nucleotide is added, the triphosphate is lost and a single phosphate remains on the backbone between the new nucleotide and the rest of the strand. If the added nucleotide were mismatched, removal would result in a DNA strand terminated by a monophosphate at the end of the "growing strand" rather than a high energy triphosphate. So strand would be stuck and wouldn't be able to grow anymore. In actuality, the high energy triphosphates hydrolyzed at each step originate from the free nucleotides, not the polymerized strand, so this issue does not exist.</ref>

In general, DNA polymerases are highly accurate, with an intrinsic error rate of less than one mistake for every 10<sup>7</sup> nucleotides added.<ref name="pmid18166979">{{Cite journal |vauthors=McCulloch SD, Kunkel TA |date=January 2008 |title=The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases |journal=Cell Research |volume=18 |issue=1 |pages=148–161 |doi=10.1038/cr.2008.4 |pmc=3639319 |pmid=18166979}}</ref> Some DNA polymerases can also delete nucleotides from the end of a developing strand in order to fix mismatched bases. This is known as proofreading. Finally, post-replication mismatch repair mechanisms monitor the DNA for errors, being capable of distinguishing mismatches in the newly synthesized DNA Strand from the original strand sequence. Together, these three discrimination steps enable replication fidelity of less than one mistake for every 10<sup>9</sup> nucleotides added.<ref name="pmid18166979" />

The rate of DNA replication in a living cell was first measured as the rate of phage T4 DNA elongation in phage-infected ''E. coli''.<ref>{{Cite journal |vauthors=McCarthy D, Minner C, Bernstein H, Bernstein C |date=October 1976 |title=DNA elongation rates and growing point distributions of wild-type phage T4 and a DNA-delay amber mutant |journal=Journal of Molecular Biology |volume=106 |issue=4 |pages=963–981 |doi=10.1016/0022-2836(76)90346-6 |pmid=789903}}<!--|access-date=7 April 2016--></ref> During the period of exponential DNA increase at 37&nbsp;°C, the rate was 749 nucleotides per second.  The mutation rate per base pair per replication during phase T4 DNA synthesis is 1.7 per 10<sup>8</sup>.<ref>Drake JW (1970) ''The Molecular Basis of Mutation.'' Holden-Day, San Francisco {{ISBN|0-8162-2450-1}}  {{ISBN|978-0-8162-2450-0}}</ref>