Editing DNA ligase (section)

== Types ==

=== ''E. coli'' ===
The ''[[Escherichia coli|E. coli]]'' DNA ligase is encoded by the ''lig'' gene.  DNA ligase in ''[[Escherichia coli|E. coli]]'', as well as most prokaryotes, uses energy gained by cleaving [[nicotinamide adenine dinucleotide]] (NAD) to create the phosphodiester bond.<ref name="foster"/>  It does not ligate blunt-ended DNA except under conditions of molecular crowding with [[polyethylene glycol]], and cannot join RNA to DNA efficiently.{{cn|date=January 2024}}

The activity of E. coli DNA ligase can be enhanced by [[DNA polymerase]] at the right concentrations. Enhancement only works when the concentrations of the DNA polymerase 1 are much lower than the DNA fragments to be ligated. When the concentrations of Pol I DNA polymerases are higher, it has an adverse effect on E. coli DNA ligase<ref name="pmid29409896">{{cite journal | vauthors = Yang Y, LiCata VJ | title = Pol I DNA polymerases stimulate DNA end-joining by Escherichia coli DNA ligase | journal = Biochemical and Biophysical Research Communications | volume = 497 | issue = 1 | pages = 13–18 | date = February 2018 | pmid = 29409896 | doi = 10.1016/j.bbrc.2018.01.165 | url = https://digitalcommons.lsu.edu/biosci_pubs/2422 | doi-access = free }}</ref>

=== T4 ===
The DNA ligase from [[bacteriophage T4]] (a [[bacteriophage]] that infects ''[[Escherichia coli]]'' bacteria). The T4 ligase is the most-commonly used in laboratory research.<ref name="url_www.promega.com">{{cite web | url = https://www.promega.com/~/media/files/resources/product%20guides/cloning%20enzymes/ligases.pdf?la=en+ | title = Ligases | work = Enzyme Resources Guide | publisher = Promega Corporation | pages = 8–14 }}</ref>  It can ligate either [[cohesive end|cohesive or blunt ends]] of DNA, oligonucleotides, as well as RNA and RNA-DNA hybrids, but not single-stranded nucleic acids. It can also ligate [[Sticky and blunt ends|blunt-ended DNA]] with much greater efficiency than ''[[Escherichia coli|E. coli]]'' DNA ligase.  Unlike ''E. coli'' DNA ligase, T4 DNA ligase cannot utilize NAD and it has an absolute requirement for ATP as a cofactor. Some engineering has been done to improve the ''in vitro'' activity of T4 DNA ligase; one successful approach, for example, tested T4 DNA ligase fused to several alternative DNA binding proteins and found that the constructs with either p50 or [[NF-kB]] as fusion partners were over 160% more active in blunt-end ligations for cloning purposes than wild type T4 DNA ligase.<ref name="pmid23754529">{{cite journal | vauthors = Wilson RH, Morton SK, Deiderick H, Gerth ML, Paul HA, Gerber I, Patel A, Ellington AD, Hunicke-Smith SP, Patrick WM | title = Engineered DNA ligases with improved activities in vitro | journal = Protein Engineering, Design & Selection | volume = 26 | issue = 7 | pages = 471–8 | date = July 2013 | pmid = 23754529 | doi = 10.1093/protein/gzt024 | doi-access = free }}</ref>  A typical reaction for inserting a fragment into a plasmid vector would use about 0.01 (sticky ends) to 1 (blunt ends) units of ligase.  The optimal incubation temperature for T4 DNA ligase is 37&nbsp;°C, a temperature at which T4 enzymes are most active. However, it is not uncommon to setup ligation reactions at 16&nbsp;°C, a trade-off temperature at which the ligase is active as well as one that is suitable for base-pairing of sticky ends. {{cn|date=January 2024}}

[[Escherichia virus T4|Bacteriophage T4]] ligase [[mutant]]s have increased sensitivity to both [[ultraviolet|UV]] irradiation<ref name="pmid4891973">{{cite journal | vauthors = Baldy MW | title = Repair and recombination in phage T4. II. Genes affecting UV sensitivity | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 33 | pages = 333–8 | date = 1968 | pmid = 4891973 | doi = 10.1101/sqb.1968.033.01.038 }}</ref><ref name="pmid4909413">{{cite journal | vauthors = Baldy MW | title = The UV sensitivity of some early-function temperature-sensitive mutants of phage T4 | journal = Virology | volume = 40 | issue = 2 | pages = 272–87 | date = February 1970 | pmid = 4909413 | doi = 10.1016/0042-6822(70)90403-4 }}</ref> and the alkylating agent [[methyl methanesulfonate]]<ref name="pmid4927528">{{cite journal | vauthors = Baldy MW, Strom B, Bernstein H | title = Repair of alkylated bacteriophage T4 deoxyribonucleic acid by a mechanism involving polynucleotide ligase | journal = Journal of Virology | volume = 7 | issue = 3 | pages = 407–8 | date = March 1971 | pmid = 4927528 | pmc = 356131 | doi = 10.1128/JVI.7.3.407-408.1971 }}</ref> indicating that DNA ligase is employed in the [[DNA repair|repair]] of the [[DNA damage (naturally occurring)|DNA damages]] caused by these agents.

=== Mammalian ===
In mammals, there are four specific types of ligase.
# [[DNA ligase 1]]: ligates the nascent DNA of the [[DNA replication#Lagging strand|lagging strand]] after the [[RNase H|Ribonuclease H]] has removed the RNA primer from the [[Okazaki fragment]]s.
# [[DNA ligase 3]]: [[protein complex|complexes]] with [[DNA repair]] [[protein]] [[XRCC1]] to aid in sealing DNA during the process of [[DNA repair|nucleotide excision repair]] and recombinant fragments. Of the all known mammalian DNA ligases, only ligase 3 has been found to be present in mitochondria.
# [[DNA ligase 4]]: complexes with [[XRCC4]].  It catalyzes the final step in the [[non-homologous end joining]] DNA double-strand break repair pathway.  It is also required for [[V(D)J recombination]], the process that generates diversity in [[immunoglobulin]] and [[T-cell receptor]] loci during [[immune system]] development.
* DNA ligase 2: A purification artifact resulting from proteolytic degradation of DNA ligase 3. Initially, it has been recognized as another DNA ligase and it is the reason for the unusual nomenclature of DNA ligases.<ref>{{cite journal |last1=Tomkinson |first1=Alan E |last2=Sallmyr |first2=Annahita |title=Structure and function of the DNA ligases encoded by the mammalian LIG3 gene |journal=Gene |date=5 September 2013 |volume=531 |issue=2 |pages=150–157 |doi=10.1016/j.gene.2013.08.061 |pmid=24013086 |url= |ref=tomkinson_lig3_review|pmc=3881560 }}</ref>

DNA ligase from [[eukaryotes]] and some microbes uses [[adenosine triphosphate]] (ATP) rather than NAD.<ref name="foster">{{cite book | vauthors = Foster JB, Slonczewski J | title = Microbiology: An Evolving Science | edition = Second | publisher = W. W. Norton & Company | location = New York | year = 2010 | isbn = 978-0-393-93447-2 }}</ref>

===Thermostable===
Derived from a thermophilic bacterium, the enzyme is stable and active at much higher temperatures than conventional DNA ligases. Its half-life is 48 hours at 65&nbsp;°C and greater than 1&nbsp;hour at 95&nbsp;°C. Ampligase DNA Ligase has been shown to be active for at least 500 thermal cycles (94&nbsp;°C/80&nbsp;°C) or 16 hours of cycling.<sup>10</sup>&nbsp;This exceptional thermostability permits extremely high hybridization stringency and ligation specificity.<ref>{{cite web|url=http://www.epibio.com/enzymes/ligases-kinases-phosphatases/dna-ligases/ampligase-thermostable-dna-ligase?details|title=Ampligase- Thermostable DNA Ligase|website=www.epibio.com|access-date=2017-05-15|archive-date=2017-06-19|archive-url=https://web.archive.org/web/20170619152322/http://www.epibio.com/enzymes/ligases-kinases-phosphatases/dna-ligases/ampligase-thermostable-dna-ligase?details|url-status=dead}}</ref>