Editing DNA (section)

== Biological functions ==
[[File:Eukaryote DNA-en.svg|thumb|upright=1.45|Location of eukaryote [[nuclear DNA]] within the chromosomes]]
DNA usually occurs as linear [[chromosome]]s in [[eukaryote]]s, and [[circular prokaryote chromosome|circular chromosomes]] in [[prokaryote]]s. The set of chromosomes in a cell makes up its [[genome]]; the [[human genome]] has approximately 3 billion base pairs of DNA arranged into 46 chromosomes.<ref name="Venter_2001" /> The information carried by DNA is held in the [[DNA sequence|sequence]] of pieces of DNA called [[gene]]s. [[Transmission (genetics)|Transmission]] of genetic information in genes is achieved via complementary base pairing. For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching [[Peptide sequence|protein sequence]] in a process called [[Translation (biology)|translation]], which depends on the same interaction between RNA nucleotides. In an alternative fashion, a cell may copy its genetic information in a process called [[DNA replication]]. The details of these functions are covered in other articles; here the focus is on the interactions between DNA and other molecules that mediate the function of the genome.

=== Genes and genomes ===
{{further|Cell nucleus|Chromatin|Chromosome|Gene|Noncoding DNA}}
Genomic DNA is tightly and orderly packed in the process called [[DNA condensation]], to fit the small available volumes of the cell. In eukaryotes, DNA is located in the [[cell nucleus]], with small amounts in [[mitochondrion|mitochondria]] and [[chloroplast]]s. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the [[nucleoid]].<ref>{{cite journal | vauthors = Thanbichler M, Wang SC, Shapiro L | title = The bacterial nucleoid: a highly organized and dynamic structure | journal = Journal of Cellular Biochemistry | volume = 96 | issue = 3 | pages = 506–21 | date = October 2005 | pmid = 15988757 | doi = 10.1002/jcb.20519 | doi-access = free }}</ref> The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its [[genotype]]. A gene is a unit of [[heredity]] and is a region of DNA that influences a particular characteristic in an organism. Genes contain an [[open reading frame]] that can be transcribed, and [[regulatory sequence]]s such as [[promoter (biology)|promoters]] and [[enhancer (genetics)|enhancers]], which control transcription of the open reading frame.

In many [[species]], only a small fraction of the total sequence of the [[genome]] encodes protein. For example, only about 1.5% of the human genome consists of protein-coding [[exon]]s, with over 50% of human DNA consisting of non-coding [[repeated sequence (DNA)|repetitive sequences]].<ref>{{cite journal | vauthors = Wolfsberg TG, McEntyre J, Schuler GD | title = Guide to the draft human genome | journal = Nature | volume = 409 | issue = 6822 | pages = 824–26 | date = February 2001 | pmid = 11236998 | doi = 10.1038/35057000 | bibcode = 2001Natur.409..824W | url = https://zenodo.org/record/1233093 | doi-access = free }}</ref> The reasons for the presence of so much [[noncoding DNA]] in eukaryotic genomes and the extraordinary differences in [[genome size]], or ''[[C-value]]'', among species, represent a long-standing puzzle known as the "[[C-value enigma]]".<ref>{{cite journal | vauthors = Gregory TR | title = The C-value enigma in plants and animals: a review of parallels and an appeal for partnership | journal = Annals of Botany | volume = 95 | issue = 1 | pages = 133–46 | date = January 2005 | pmid = 15596463 | doi = 10.1093/aob/mci009 | pmc = 4246714 }}</ref> However, some DNA sequences that do not code protein may still encode functional [[non-coding RNA]] molecules, which are involved in the [[regulation of gene expression]].<ref name="Birney_2007" />
[[File:T7 RNA polymerase.jpg|thumb|[[T7 RNA polymerase]] (blue) producing an [[Messenger RNA|mRNA]] (green) from a DNA template (orange)<ref>{{Cite web| vauthors = Yin YW, Steitz TA |title=RCSB PDB – 1MSW: Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase|url=https://www.rcsb.org/structure/1MSW|access-date=2023-03-27|website=www.rcsb.org|language=en-US}}</ref>]]

Some noncoding DNA sequences play structural roles in chromosomes. [[Telomere]]s and [[centromere]]s typically contain few genes but are important for the function and stability of chromosomes.<ref name=Nugent /><ref>{{cite journal | vauthors = Pidoux AL, Allshire RC | title = The role of heterochromatin in centromere function | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 360 | issue = 1455 | pages = 569–79 | date = March 2005 | pmid = 15905142 | pmc = 1569473 | doi = 10.1098/rstb.2004.1611 }}</ref> An abundant form of noncoding DNA in humans are [[pseudogene]]s, which are copies of genes that have been disabled by mutation.<ref>{{cite journal | vauthors = Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M | title = Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 | journal = Genome Research | volume = 12 | issue = 2 | pages = 272–80 | date = February 2002 | pmid = 11827946 | pmc = 155275 | doi = 10.1101/gr.207102 }}</ref> These sequences are usually just molecular [[fossil]]s, although they can occasionally serve as raw [[Genome|genetic material]] for the creation of new genes through the process of [[gene duplication]] and [[divergent evolution|divergence]].<ref>{{cite journal | vauthors = Harrison PM, Gerstein M | title = Studying genomes through the aeons: protein families, pseudogenes and proteome evolution | journal = Journal of Molecular Biology | volume = 318 | issue = 5 | pages = 1155–74 | date = May 2002 | pmid = 12083509 | doi = 10.1016/S0022-2836(02)00109-2 }}</ref>

=== Transcription and translation ===
{{further|Genetic code|Transcription (genetics)|Protein biosynthesis}}
A gene is a sequence of DNA that contains genetic information and can influence the [[phenotype]] of an organism. Within a gene, the sequence of bases along a DNA strand defines a [[messenger RNA]] sequence, which then defines one or more protein sequences. The relationship between the nucleotide sequences of genes and the [[amino acid|amino-acid]] sequences of proteins is determined by the rules of [[Translation (biology)|translation]], known collectively as the [[genetic code]]. The genetic code consists of three-letter 'words' called ''codons'' formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT).

In transcription, the codons of a gene are copied into messenger RNA by [[RNA polymerase]]. This RNA copy is then decoded by a [[ribosome]] that reads the RNA sequence by base-pairing the messenger RNA to [[transfer RNA]], which carries amino acids. Since there are 4 bases in 3-letter combinations, there are 64 possible codons (4<sup>3</sup>&nbsp;combinations). These encode the twenty [[list of standard amino acids|standard amino acids]], giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAG, TAA, and TGA codons, (UAG, UAA, and UGA on the mRNA).

=== Replication ===
{{further|DNA replication}}
[[File:DNA replication en.svg|thumb|upright=1.78|right|DNA replication: The double helix is unwound by a [[helicase]] and [[topoisomerase|topo&shy;iso&shy;merase]]. Next, one [[DNA polymerase]] produces the [[Replication fork|leading strand]] copy. Another DNA polymerase binds to the [[Replication fork|lagging strand]]. This enzyme makes discontinuous segments (called [[Okazaki fragment]]s) before [[DNA ligase]] joins them together.]]
[[Cell division]] is essential for an organism to grow, but, when a cell divides, it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for [[DNA replication]]. Here, the two strands are separated and then each strand's [[complementary DNA]] sequence is recreated by an [[enzyme]] called [[DNA polymerase]]. This enzyme makes the complementary strand by finding the correct base through complementary base pairing and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix.<ref>{{cite journal | vauthors = Albà M | title = Replicative DNA polymerases | journal = Genome Biology | volume = 2 | issue = 1 | pages = REVIEWS3002 | year = 2001 | pmid = 11178285 | pmc = 150442 | doi = 10.1186/gb-2001-2-1-reviews3002 | doi-access = free }}</ref> In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.

=== Extracellular nucleic acids ===
Naked extracellular DNA (eDNA), most of it released by cell death, is nearly ubiquitous in the environment. Its concentration in soil may be as high as 2 μg/L, and its concentration in natural aquatic environments may be as high at 88 μg/L.<ref name=Tani_2010>{{cite book | vauthors = Tani K, Nasu M | veditors = Kikuchi Y, Rykova EY | title = Extracellular Nucleic Acids |url=https://archive.org/details/extracellularnuc00kiku |url-access=limited |publisher=Springer |date=2010 |pages=[https://archive.org/details/extracellularnuc00kiku/page/n35 25]–38 |chapter=Roles of Extracellular DNA in Bacterial Ecosystems |isbn=978-3-642-12616-1}}</ref> Various possible functions have been proposed for eDNA: it may be involved in [[horizontal gene transfer]];<ref name="Vlassov_2007">{{cite journal | vauthors = Vlassov VV, Laktionov PP, Rykova EY | title = Extracellular nucleic acids | journal = BioEssays | volume = 29 | issue = 7 | pages = 654–67 | date = July 2007 | pmid = 17563084 | doi = 10.1002/bies.20604 | s2cid = 32463239 }}</ref> it may provide nutrients;<ref name="pmid11591672">{{cite journal | vauthors = Finkel SE, Kolter R | title = DNA as a nutrient: novel role for bacterial competence gene homologs | journal = Journal of Bacteriology | volume = 183 | issue = 21 | pages = 6288–93 | date = November 2001 | pmid = 11591672 | pmc = 100116 | doi = 10.1128/JB.183.21.6288-6293.2001 }}</ref> and it may act as a buffer to recruit or titrate ions or antibiotics.<ref name=Mulcahy_2008>{{cite journal | vauthors = Mulcahy H, Charron-Mazenod L, Lewenza S | title = Extracellular DNA chelates cations and induces antibiotic resistance in Pseudomonas aeruginosa biofilms | journal = PLOS Pathogens | volume = 4 | issue = 11 | pages = e1000213 | date = November 2008 | pmid = 19023416 | pmc = 2581603 | doi = 10.1371/journal.ppat.1000213 | doi-access = free }}</ref> Extracellular DNA acts as a functional extracellular matrix component in the [[biofilm]]s of several bacterial species. It may act as a recognition factor to regulate the attachment and dispersal of specific cell types in the biofilm;<ref name=Berne_2010>{{cite journal | vauthors = Berne C, Kysela DT, Brun YV | title = A bacterial extracellular DNA inhibits settling of motile progeny cells within a biofilm | journal = Molecular Microbiology | volume = 77 | issue = 4 | pages = 815–29 | date = August 2010 | pmid = 20598083 | pmc = 2962764 | doi = 10.1111/j.1365-2958.2010.07267.x }}</ref> it may contribute to biofilm formation;<ref name=Whitchurch_2002>{{cite journal | vauthors = Whitchurch CB, Tolker-Nielsen T, Ragas PC, Mattick JS | title = Extracellular DNA required for bacterial biofilm formation | journal = Science | volume = 295 | issue = 5559 | pages = 1487 | date = February 2002 | pmid = 11859186 | doi = 10.1126/science.295.5559.1487 }}</ref> and it may contribute to the biofilm's physical strength and resistance to biological stress.<ref name=Hu_2012>{{cite journal | vauthors = Hu W, Li L, Sharma S, Wang J, McHardy I, Lux R, Yang Z, He X, Gimzewski JK, Li Y, Shi W | title = DNA builds and strengthens the extracellular matrix in Myxococcus xanthus biofilms by interacting with exopolysaccharides | journal = PLOS ONE | volume = 7 | issue = 12 | pages = e51905 | year = 2012 | pmid = 23300576 | pmc = 3530553 | doi = 10.1371/journal.pone.0051905 | bibcode = 2012PLoSO...751905H | doi-access = free }}</ref>

[[Cell-free fetal DNA]] is found in the blood of the mother, and can be sequenced to determine a great deal of information about the developing fetus.<ref name="Hui_2013">{{cite journal | vauthors = Hui L, Bianchi DW | title = Recent advances in the prenatal interrogation of the human fetal genome | journal = Trends in Genetics | volume = 29 | issue = 2 | pages = 84–91 | date = February 2013 | pmid = 23158400 | pmc = 4378900 | doi = 10.1016/j.tig.2012.10.013 }}</ref>

Under the name of [[environmental DNA]] eDNA has seen increased use in the natural sciences as a survey tool for [[ecology]], monitoring the movements and presence of species in water, air, or on land, and assessing an area's biodiversity.<ref>{{cite journal | vauthors = Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, Salling AB, Galatius A, Orlando L, Gilbert MT | display-authors = 6 | title = Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals | journal = PLOS ONE | volume = 7 | issue = 8 | pages = e41781 | year = 2012 | pmid = 22952587 | pmc = 3430683 | doi = 10.1371/journal.pone.0041781 | bibcode = 2012PLoSO...741781F | doi-access = free }}</ref><ref>{{Cite web | url=https://www.the-scientist.com/news-opinion/researchers-detect-land-animals-using-dna-in-nearby-water-bodies-67481 | title=Researchers Detect Land Animals Using DNA in Nearby Water Bodies}}</ref>

=== Neutrophil extracellular traps ===
{{Main|Neutrophil extracellular traps}}
Neutrophil extracellular traps (NETs) are networks of extracellular fibers, primarily composed of DNA, which allow [[neutrophils]], a type of white blood cell, to kill extracellular pathogens while minimizing damage to the host cells.