Editing DNA (section)

== Uses in technology ==

=== Genetic engineering ===
{{further|Molecular biology|Nucleic acid methods|Genetic engineering}}
Methods have been developed to purify DNA from organisms, such as [[phenol-chloroform extraction]], and to manipulate it in the laboratory, such as [[restriction digest]]s and the [[polymerase chain reaction]]. Modern [[biology]] and [[biochemistry]] make intensive use of these techniques in recombinant DNA technology. [[Recombinant DNA]] is a man-made DNA sequence that has been assembled from other DNA sequences. They can be [[transformation (genetics)|transformed]] into organisms in the form of [[plasmid]]s or in the appropriate format, by using a [[viral vector]].<ref>{{cite journal | vauthors = Goff SP, Berg P | s2cid = 41788896 | title = Construction of hybrid viruses containing SV40 and lambda phage DNA segments and their propagation in cultured monkey cells | journal = Cell | volume = 9 | issue = 4 PT 2 | pages = 695–705 | date = December 1976 | pmid = 189942 | doi = 10.1016/0092-8674(76)90133-1 }}</ref> The [[genetic engineering|genetically modified]] organisms produced can be used to produce products such as recombinant [[protein]]s, used in [[medical research]],<ref>{{cite book | vauthors = Houdebine LM | title = Target Discovery and Validation Reviews and Protocols | chapter = Transgenic animal models in biomedical research | series = Methods in Molecular Biology | volume = 360 | pages = 163–202 | year = 2007 | pmid = 17172731 | doi = 10.1385/1-59745-165-7:163 | isbn = 978-1-59745-165-9 }}</ref> or be grown in [[agriculture]].<ref>{{cite journal | vauthors = Daniell H, Dhingra A | title = Multigene engineering: dawn of an exciting new era in biotechnology | journal = Current Opinion in Biotechnology | volume = 13 | issue = 2 | pages = 136–41 | date = April 2002 | pmid = 11950565 | pmc = 3481857 | doi = 10.1016/S0958-1669(02)00297-5 }}</ref><ref>{{cite journal | vauthors = Job D | title = Plant biotechnology in agriculture | journal = Biochimie | volume = 84 | issue = 11 | pages = 1105–10 | date = November 2002 | pmid = 12595138 | doi = 10.1016/S0300-9084(02)00013-5 }}</ref>

=== DNA profiling ===
{{further|DNA profiling}}

[[Forensic science|Forensic scientists]] can use DNA in [[blood]], [[semen]], [[skin]], [[saliva]] or [[hair]] found at a [[crime scene]] to identify a matching DNA of an individual, such as a perpetrator.<ref>{{Cite news|url=https://theconversation.com/from-the-crime-scene-to-the-courtroom-the-journey-of-a-dna-sample-82250|title=From the crime scene to the courtroom: the journey of a DNA sample| vauthors = Curtis C, Hereward J |date=29 August 2017 |work=The Conversation |access-date=22 October 2017 |archive-url=https://web.archive.org/web/20171022033110/http://theconversation.com/from-the-crime-scene-to-the-courtroom-the-journey-of-a-dna-sample-82250 |archive-date=22 October 2017 |url-status=live }}</ref> This process is formally termed [[DNA profiling]], also called ''DNA fingerprinting''. In DNA profiling, the lengths of variable sections of repetitive DNA, such as [[short tandem repeat]]s and [[minisatellite]]s, are compared between people. This method is usually an extremely reliable technique for identifying a matching DNA.<ref>{{cite journal | vauthors = Collins A, Morton NE | title = Likelihood ratios for DNA identification | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 91 | issue = 13 | pages = 6007–11 | date = June 1994 | pmid = 8016106 | pmc = 44126 | doi = 10.1073/pnas.91.13.6007 | bibcode = 1994PNAS...91.6007C | doi-access = free }}</ref> However, identification can be complicated if the scene is contaminated with DNA from several people.<ref>{{cite journal | vauthors = Weir BS, Triggs CM, Starling L, Stowell LI, Walsh KA, Buckleton J | title = Interpreting DNA mixtures | journal = Journal of Forensic Sciences | volume = 42 | issue = 2 | pages = 213–22 | date = March 1997 | doi = 10.1520/JFS14100J | pmid = 9068179 | s2cid = 14511630 }}</ref> DNA profiling was developed in 1984 by British geneticist Sir [[Alec Jeffreys]],<ref>{{cite journal | vauthors = Jeffreys AJ, Wilson V, Thein SL | title = Individual-specific 'fingerprints' of human DNA | journal = Nature | volume = 316 | issue = 6023 | pages = 76–79 | year = 1985 | pmid = 2989708 | doi = 10.1038/316076a0 | bibcode = 1985Natur.316...76J | s2cid = 4229883 | doi-access = free }}</ref> and first used in forensic science to convict Colin Pitchfork in the 1988 [[Colin Pitchfork|Enderby murders]] case.<ref>{{Cite web|date=2006-12-14|title=Colin Pitchfork|url=http://www.forensic.gov.uk/forensic_t/inside/news/list_casefiles.php?case=1|access-date=2023-03-27|archive-url=https://web.archive.org/web/20061214004903/http://www.forensic.gov.uk/forensic_t/inside/news/list_casefiles.php?case=1 |archive-date=14 December 2006 }}</ref>

The development of forensic science and the ability to now obtain genetic matching on minute samples of blood, skin, saliva, or hair has led to re-examining many cases. Evidence can now be uncovered that was scientifically impossible at the time of the original examination. Combined with the removal of the [[double jeopardy]] law in some places, this can allow cases to be reopened where prior trials have failed to produce sufficient evidence to convince a jury. People charged with serious crimes may be required to provide a sample of DNA for matching purposes. The most obvious defense to DNA matches obtained forensically is to claim that cross-contamination of evidence has occurred. This has resulted in meticulous strict handling procedures with new cases of serious crime.

DNA profiling is also used successfully to positively identify victims of mass casualty incidents,<ref>{{cite web|url=http://massfatality.dna.gov/Introduction/ |title=DNA Identification in Mass Fatality Incidents |date=September 2006 |publisher=National Institute of Justice |url-status=dead |archive-url=https://web.archive.org/web/20061112000837/http://massfatality.dna.gov/Introduction/ |archive-date=12 November 2006 }}</ref> bodies or body parts in serious accidents, and individual victims in mass war graves, via matching to family members.

DNA profiling is also used in [[DNA paternity testing]] to determine if someone is the biological parent or grandparent of a child with the probability of parentage is typically 99.99% when the alleged parent is biologically related to the child. Normal [[DNA sequencing]] methods happen after birth, but there are new methods to test paternity while a mother is still pregnant.<ref>{{Cite news| vauthors = Pollack A |date=2012-06-19|title=Before Birth, Dad's ID|language=en-US|work=The New York Times|url=https://www.nytimes.com/2012/06/20/health/paternity-blood-tests-that-work-early-in-a-pregnancy.html|access-date=2023-03-27|issn=0362-4331|archive-url=https://web.archive.org/web/20170624231639/http://www.nytimes.com/2012/06/20/health/paternity-blood-tests-that-work-early-in-a-pregnancy.html|archive-date=2017-06-24|url-status=live}}</ref>

=== DNA enzymes or catalytic DNA ===
{{further|Deoxyribozyme}}
[[Deoxyribozyme]]s, also called DNAzymes or catalytic DNA, were first discovered in 1994.<ref name="Breaker 223–229">{{cite journal | vauthors = Breaker RR, Joyce GF | title = A DNA enzyme that cleaves RNA | journal = Chemistry & Biology | volume = 1 | issue = 4 | pages = 223–29 | date = December 1994 | pmid = 9383394 | doi = 10.1016/1074-5521(94)90014-0 }}</ref> They are mostly single stranded DNA sequences isolated from a large pool of random DNA sequences through a combinatorial approach called [[in vitro]] selection or [[systematic evolution of ligands by exponential enrichment]] (SELEX). DNAzymes catalyze variety of chemical reactions including RNA-DNA cleavage, RNA-DNA ligation, amino acids phosphorylation-dephosphorylation, carbon-carbon bond formation, etc. DNAzymes can enhance catalytic rate of chemical reactions up to 100,000,000,000-fold over the uncatalyzed reaction.<ref>{{cite journal | vauthors = Chandra M, Sachdeva A, Silverman SK | title = DNA-catalyzed sequence-specific hydrolysis of DNA | journal = Nature Chemical Biology | volume = 5 | issue = 10 | pages = 718–20 | date = October 2009 | pmid = 19684594 | pmc = 2746877 | doi = 10.1038/nchembio.201 }}</ref> The most extensively studied class of DNAzymes is RNA-cleaving types which have been used to detect different metal ions and designing therapeutic agents. Several metal-specific DNAzymes have been reported including the GR-5 DNAzyme (lead-specific),<ref name="Breaker 223–229" /> the CA1-3 DNAzymes (copper-specific),<ref>{{cite journal | vauthors = Carmi N, Shultz LA, Breaker RR | title = In vitro selection of self-cleaving DNAs | journal = Chemistry & Biology | volume = 3 | issue = 12 | pages = 1039–46 | date = December 1996 | pmid = 9000012 | doi = 10.1016/S1074-5521(96)90170-2 | doi-access = free }}</ref> the 39E DNAzyme (uranyl-specific) and the NaA43 DNAzyme (sodium-specific).<ref>{{cite journal | vauthors = Torabi SF, Wu P, McGhee CE, Chen L, Hwang K, Zheng N, Cheng J, Lu Y | title = In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 19 | pages = 5903–08 | date = May 2015 | pmid = 25918425 | pmc = 4434688 | doi = 10.1073/pnas.1420361112 | bibcode = 2015PNAS..112.5903T | doi-access = free }}</ref> The NaA43 DNAzyme, which is reported to be more than 10,000-fold selective for sodium over other metal ions, was used to make a real-time sodium sensor in cells.

=== Bioinformatics ===
{{further|Bioinformatics}}
[[Bioinformatics]] involves the development of techniques to store, [[data mining|data mine]], search and manipulate biological data, including DNA [[nucleic acid sequence]] data. These have led to widely applied advances in [[computer science]], especially [[string searching algorithm]]s, [[machine learning]], and [[database theory]].<ref>{{cite book | vauthors = Baldi P, Brunak S |author1-link=Pierre Baldi |title=Bioinformatics: The Machine Learning Approach |publisher= MIT Press |year=2001| isbn=978-0-262-02506-5 |oclc=45951728}}</ref> String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, were developed to search for specific sequences of nucleotides.<ref>{{cite book | vauthors = Gusfield D | title = Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology | publisher = [[Cambridge University Press]] | date = 15 January 1997 | isbn = 978-0-521-58519-4 }}</ref> The DNA sequence may be [[sequence alignment|aligned]] with other DNA sequences to identify [[Sequence homology|homologous sequences]] and locate the specific [[mutation]]s that make them distinct. These techniques, especially [[multiple sequence alignment]], are used in studying [[phylogenetics|phylogenetic]] relationships and protein function.<ref>{{cite journal | vauthors = Sjölander K | title = Phylogenomic inference of protein molecular function: advances and challenges | journal = Bioinformatics | volume = 20 | issue = 2 | pages = 170–79 | date = January 2004 | pmid = 14734307 | doi = 10.1093/bioinformatics/bth021 | citeseerx = 10.1.1.412.943 }}</ref> Data sets representing entire genomes' worth of DNA sequences, such as those produced by the [[Human Genome Project]], are difficult to use without the annotations that identify the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by [[Gene prediction|gene finding]] algorithms, which allow researchers to predict the presence of particular [[gene product]]s and their possible functions in an organism even before they have been isolated experimentally.<ref name="Mount">{{cite book | vauthors = Mount DM |title=Bioinformatics: Sequence and Genome Analysis |edition= 2nd |publisher= Cold Spring Harbor Laboratory Press |year= 2004 |isbn= 0-87969-712-1|oclc= 55106399|location=Cold Spring Harbor, NY}}</ref> Entire genomes may also be compared, which can shed light on the evolutionary history of particular organism and permit the examination of complex evolutionary events.

=== DNA nanotechnology ===
{{further|DNA nanotechnology}}
[[File:DNA nanostructures.png|thumb|upright=1.8|The DNA structure at left (schematic shown) will self-assemble into the structure visualized by [[Atomic force microscope|atomic force microscopy]] at right. [[DNA nanotechnology]] is the field that seeks to design nanoscale structures using the [[molecular recognition]] properties of DNA molecules.<ref>{{cite journal | vauthors = Strong M | title = Protein nanomachines | journal = PLOS Biology | volume = 2 | issue = 3 | pages = E73 | date = March 2004 | pmid = 15024422 | pmc = 368168 | doi = 10.1371/journal.pbio.0020073 | s2cid = 13222080 | doi-access = free }}</ref>]]
DNA nanotechnology uses the unique [[molecular recognition]] properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties.<ref>{{cite journal | vauthors = Rothemund PW | s2cid = 4316391 | title = Folding DNA to create nanoscale shapes and patterns | journal = Nature | volume = 440 | issue = 7082 | pages = 297–302 | date = March 2006 | pmid = 16541064 | doi = 10.1038/nature04586 | bibcode = 2006Natur.440..297R | url = https://authors.library.caltech.edu/22244/3/nature04586-s2.pdf }}</ref> DNA is thus used as a structural material rather than as a carrier of biological information. This has led to the creation of two-dimensional periodic lattices (both tile-based and using the ''[[DNA origami]]'' method) and three-dimensional structures in the shapes of [[Polyhedron|polyhedra]].<ref>{{cite journal | vauthors = Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W, Golas MM, Sander B, Stark H, Oliveira CL, Pedersen JS, Birkedal V, Besenbacher F, Gothelf KV, Kjems J | s2cid = 4430815 | title = Self-assembly of a nanoscale DNA box with a controllable lid | journal = Nature | volume = 459 | issue = 7243 | pages = 73–76 | date = May 2009 | pmid = 19424153 | doi = 10.1038/nature07971 | bibcode = 2009Natur.459...73A | hdl = 11858/00-001M-0000-0010-9362-B | hdl-access = free }}</ref> [[DNA machine|Nanomechanical devices]] and [[DNA computing|algorithmic self-assembly]] have also been demonstrated,<ref>{{cite journal | vauthors = Ishitsuka Y, Ha T | title = DNA nanotechnology: a nanomachine goes live | journal = Nature Nanotechnology | volume = 4 | issue = 5 | pages = 281–82 | date = May 2009 | pmid = 19421208 | doi = 10.1038/nnano.2009.101 | bibcode = 2009NatNa...4..281I }}</ref> and these DNA structures have been used to template the arrangement of other molecules such as [[Colloidal gold|gold nanoparticles]] and [[streptavidin]] proteins.<ref>{{cite journal | vauthors = Aldaye FA, Palmer AL, Sleiman HF | title = Assembling materials with DNA as the guide | journal = Science | volume = 321 | issue = 5897 | pages = 1795–99 | date = September 2008 | pmid = 18818351 | doi = 10.1126/science.1154533 | bibcode = 2008Sci...321.1795A | s2cid = 2755388 }}</ref> DNA and other nucleic acids are the basis of [[aptamers]], synthetic oligonucleotide ligands for specific target molecules used in a range of biotechnology and biomedical applications.<ref>{{cite journal | vauthors = Dunn MR, Jimenez RM, Chaput JC |title=Analysis of aptamer discovery and technology |journal=Nature Reviews Chemistry |date=2017 |volume=1 |issue=10 |doi=10.1038/s41570-017-0076 |url=https://www.nature.com/articles/s41570-017-0076 |access-date=30 June 2022}}</ref>

=== History and anthropology ===
{{further|Phylogenetics|Genetic genealogy}}
Because DNA collects mutations over time, which are then inherited, it contains historical information, and, by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their [[Phylogenetics|phylogeny]].<ref>{{cite journal | vauthors = Wray GA | title = Dating branches on the tree of life using DNA | journal = Genome Biology | volume = 3 | issue = 1 | pages = REVIEWS0001 | year = 2002 | pmid = 11806830 | pmc = 150454 | doi = 10.1186/gb-2001-3-1-reviews0001 | doi-access = free }}</ref> This field of phylogenetics is a powerful tool in [[evolutionary biology]]. If DNA sequences within a species are compared, [[population genetics|population geneticists]] can learn the history of particular populations. This can be used in studies ranging from [[ecological genetics]] to [[anthropology]].

=== Information storage ===
{{Main|DNA digital data storage}}

DNA as a [[data storage|storage device]] for information has enormous potential since it has much higher [[storage density]] compared to electronic devices. However, high costs, slow read and write times ([[memory latency]]), and insufficient [[data corruption|reliability]] has prevented its practical use.<ref name="pmid29744271">{{cite journal | vauthors = Panda D, Molla KA, Baig MJ, Swain A, Behera D, Dash M | title = DNA as a digital information storage device: hope or hype? | journal = 3 Biotech | volume = 8 | issue = 5 | pages = 239 | date = May 2018 | pmid = 29744271 | doi = 10.1007/s13205-018-1246-7 | pmc=5935598}}</ref><ref name="pmid30073589">{{cite journal | vauthors = Akram F, Haq IU, Ali H, Laghari AT | s2cid = 51905843 | title = Trends to store digital data in DNA: an overview | journal = Molecular Biology Reports | volume = 45 | issue = 5 | pages = 1479–1490 | date = October 2018 | pmid = 30073589 | doi = 10.1007/s11033-018-4280-y }}</ref>