Editing Genetic code (section)

==History==
[[File:GeneticCode21-version-2.svg|thumb|upright=1.5|The genetic code]]{{Further|Adaptor hypothesis}}
Efforts to understand how proteins are encoded began after [[Nucleic acid double helix|DNA's structure]] was discovered in 1953. The key discoverers, English biophysicist [[Francis Crick]] and American biologist [[James Watson]], working together at the [[Cavendish Laboratory]] of the University of Cambridge, hypothesied that information flows from DNA and that there is a link between DNA and proteins.<ref>{{Cite journal |last1=Watson |first1=J. D. |last2=Crick |first2=F. H. |date=1953-05-30 |title=Genetical implications of the structure of deoxyribonucleic acid |url=https://pubmed.ncbi.nlm.nih.gov/13063483 |journal=Nature |volume=171 |issue=4361 |pages=964–967 |doi=10.1038/171964b0 |issn=0028-0836 |pmid=13063483 |bibcode=1953Natur.171..964W |s2cid=4256010}}</ref> Soviet-American physicist [[George Gamow]] was the first to give a workable scheme for protein synthesis from DNA.<ref name=":3">{{Cite journal |last=Stegmann |first=Ulrich E. |date=2016-09-01 |title='Genetic Coding' Reconsidered: An Analysis of Actual Usage |journal=The British Journal for the Philosophy of Science |language=en |volume=67 |issue=3 |pages=707–730 |doi=10.1093/bjps/axv007 |issn=0007-0882 |pmc=4990703 |pmid=27924115}}</ref> He postulated that sets of three bases (triplets) must be employed to encode the 20 standard amino acids used by living cells to build proteins, which would allow a maximum of {{nowrap|4{{smallsup|3}} {{=}} 64}} amino acids.<ref name="isbn0-465-09138-5">{{cite book|first=Francis|last=Crick|title=What Mad Pursuit: A Personal View of Scientific Discovery|authorlink=Francis Crick|chapter-url={{google books|plainurl=y |id=awoXBQAAQBAJ|page=89}}|date=10 July 1990|publisher=Basic Books|oclc=1020240407|pages=89–101|isbn=9780465091386|chapter=Chapter 8: The Genetic Code}}{{Dead link|date=May 2024 |bot=InternetArchiveBot |fix-attempted=yes }}</ref> He named this DNA–protein interaction (the original genetic code) as the "diamond code".<ref name=":6">{{Cite journal |last=Hayes |first=Brian |date=1998 |title=Computing Science: The Invention of the Genetic Code |url=https://www.jstor.org/stable/27856930 |journal=American Scientist |volume=86 |issue=1 |pages=8–14 |doi=10.1511/1998.17.3338 |jstor=27856930 |s2cid=121907709 |issn=0003-0996|url-access=subscription }}</ref>

In 1954, Gamow created an informal scientific organisation the [[RNA Tie Club]], as suggested by Watson, for scientists of different persuasions who were interested in how [[Translation (biology)|proteins were synthesised]] from genes. However, the club could have only 20 permanent members to represent each of the 20 amino acids; and four additional honorary members to represent the four nucleotides of DNA.<ref name=":5">{{Cite journal |last=Strauss |first=Bernard S |date=2019-03-01 |title=Martynas Yčas: The "Archivist" of the RNA Tie Club |url=https://doi.org/10.1534/genetics.118.301754 |journal=Genetics |volume=211 |issue=3 |pages=789–795 |doi=10.1534/genetics.118.301754 |issn=1943-2631 |pmc=6404253 |pmid=30846543}}</ref>

The first scientific contribution of the club, later recorded as "one of the most important unpublished articles in the history of science"<ref>{{Cite web |title=Francis Crick - Profiles in Science Search Results |url=https://profiles.nlm.nih.gov/spotlight/sc/catalog?f%5breadonly_nlm-id_ssim%5d%5b%5d=101584582X73 |access-date=2022-07-21 |website=profiles.nlm.nih.gov}}</ref> and "the most famous unpublished paper in the annals of molecular biology",<ref name="auto">{{Cite journal |last=Fry |first=Michael |date=2022 |title=Crick's Adaptor Hypothesis and the Discovery of Transfer RNA: Experiment Surpassing Theoretical Prediction |url=https://journals.publishing.umich.edu/ptpbio/article/id/2628/ |journal=Philosophy, Theory, and Practice in Biology |volume=14 |doi=10.3998/ptpbio.2628 |issn=2475-3025 |s2cid=249112573|doi-access=free }}</ref> was made by Crick. Crick presented a type-written paper titled  "On Degenerate Templates and the Adaptor Hypothesis: A Note for the RNA Tie Club"<ref name=":02">{{Cite web |last=Crick |first=Francis |date=1955 |title=On Degenerate Templates and the Adaptor Hypothesis: A Note for the RNA Tie Club |url=https://collections.nlm.nih.gov/catalog/nlm:nlmuid-101584582X73-doc |access-date=2022-07-21 |website=National Library of Medicine}}</ref> to the members of the club in January 1955, which "totally changed the way we thought about protein synthesis", as Watson recalled.<ref name=":0">{{Cite book |last=Watson |first=James D. |url=https://books.google.com/books?id=mav7RvFfjDkC |title=Avoid Boring People: Lessons from a Life in Science |date=2007 |publisher=Oxford University Press |isbn=978-0-19-280273-6 |pages=112 |language=en |oclc=47716375}}</ref> The hypothesis states that the triplet code was not passed on to amino acids as Gamow thought, but carried by a different molecule, an adaptor, that interacts with amino acids.<ref name="auto"/> The adaptor was later identified as tRNA.<ref>{{Cite journal |last1=Barciszewska |first1=Mirosława Z. |last2=Perrigue |first2=Patrick M. |last3=Barciszewski |first3=Jan |date=2016 |title=tRNA--the golden standard in molecular biology |url=https://pubmed.ncbi.nlm.nih.gov/26549858 |journal=Molecular BioSystems |volume=12 |issue=1 |pages=12–17 |doi=10.1039/c5mb00557d |pmid=26549858}}</ref>

===Codons===
{{Redirect|Codon}}
{{See also|DNA and RNA codon tables#Translation table 1}}

The [[Crick, Brenner et al. experiment|Crick, Brenner, Barnett and Watts-Tobin experiment]] first demonstrated that '''codons''' consist of three DNA bases. 

[[Marshall Nirenberg]] and [[J. Heinrich Matthaei]] were the first to reveal the nature of a codon in 1961.<ref>{{cite journal|last=Yanofsky|first=Charles|date=9 March 2007|title=Establishing the Triplet Nature of the Genetic Code|journal=Cell|volume=128|issue=5|pages=815–818|doi=10.1016/j.cell.2007.02.029|pmid=17350564|s2cid=14249277|doi-access=free}}</ref> They used a [[cell-free system]] to [[translation (biology)|translate]] a poly-[[uracil]] RNA sequence (i.e., UUUUU...) and discovered that the [[polypeptide]] that they had synthesized consisted of only the amino acid [[phenylalanine]].<ref name="pmid14479932">{{cite journal | vauthors = Nirenberg MW, Matthaei JH | title = The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 47 | issue = 10 | pages = 1588–602 | date = Oct 1961 | pmid = 14479932 | pmc = 223178 | doi = 10.1073/pnas.47.10.1588 | bibcode = 1961PNAS...47.1588N | doi-access = free }}</ref> They thereby deduced that the codon UUU specified the amino acid phenylalanine.

This was followed by experiments in [[Severo Ochoa]]'s laboratory that demonstrated that the poly-[[adenine]] RNA sequence (AAAAA...) coded for the polypeptide poly-[[lysine]]<ref name="pmid13946552">{{cite journal | vauthors = Gardner RS, Wahba AJ, Basilio C, Miller RS, Lengyel P, Speyer JF | title = Synthetic polynucleotides and the amino acid code. VII | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 48 | issue = 12 | pages = 2087–94 | date = Dec 1962 | pmid = 13946552 | pmc = 221128 | doi = 10.1073/pnas.48.12.2087 | bibcode = 1962PNAS...48.2087G | doi-access = free }}</ref> and that the poly-[[cytosine]] RNA sequence (CCCCC...) coded for the polypeptide poly-[[proline]].<ref name="pmid13998282">{{cite journal | vauthors = Wahba AJ, Gardner RS, Basilio C, Miller RS, Speyer JF, Lengyel P | title = Synthetic polynucleotides and the amino acid code. VIII | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 49 | issue = 1 | pages = 116–22 | date = Jan 1963 | pmid = 13998282 | pmc = 300638 | doi = 10.1073/pnas.49.1.116 | bibcode = 1963PNAS...49..116W | doi-access = free }}</ref> Therefore, the codon AAA specified the amino acid [[lysine]], and the codon CCC specified the amino acid [[proline]]. Using various [[copolymers]] most of the remaining codons were then determined.

Subsequent work by [[Har Gobind Khorana]] identified the rest of the genetic code. Shortly thereafter, [[Robert W. Holley]] determined the structure of [[transfer RNA]] (tRNA), the adapter molecule that facilitates the process of translating RNA into protein. This work was based upon Ochoa's earlier studies, yielding the latter the [[Nobel Prize in Physiology or Medicine]] in 1959 for work on the [[enzymology]] of RNA synthesis.<ref name="Nobel_1959">{{cite press release |url=http://nobelprize.org/nobel_prizes/medicine/laureates/1959/index.html |title=The Nobel Prize in Physiology or Medicine 1959 |quote=The Nobel Prize in Physiology or Medicine 1959 was awarded jointly to Severo Ochoa and Arthur Kornberg 'for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid'. |publisher=The Royal Swedish Academy of Science |date=1959 |access-date=2010-02-27}}</ref>

Extending this work, Nirenberg and [[Philip Leder]] revealed the code's triplet nature and deciphered its codons. In these experiments, various combinations of [[mRNA]] were passed through a filter that contained [[ribosome]]s, the components of cells that [[Translation (biology)|translate]] RNA into protein. Unique triplets promoted the binding of specific tRNAs to the ribosome. Leder and Nirenberg were able to determine the sequences of 54 out of 64 codons in their experiments.<ref name="pmid5330357">{{cite journal | vauthors = Nirenberg M, Leder P, Bernfield M, Brimacombe R, Trupin J, Rottman F, O'Neal C | title = RNA codewords and protein synthesis, VII. On the general nature of the RNA code | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 53 | issue = 5 | pages = 1161–8 | date = May 1965 | pmid = 5330357 | pmc = 301388 | doi = 10.1073/pnas.53.5.1161 | bibcode = 1965PNAS...53.1161N | doi-access = free }}</ref> Khorana, Holley and Nirenberg received the Nobel Prize (1968) for their work.<ref name="Nobel_1968">{{cite press release |url=http://nobelprize.org/nobel_prizes/medicine/laureates/1968/index.html |title=The Nobel Prize in Physiology or Medicine 1968 |quote=The Nobel Prize in Physiology or Medicine 1968 was awarded jointly to Robert W. Holley, Har Gobind Khorana and Marshall W. Nirenberg 'for their interpretation of the genetic code and its function in protein synthesis'. |publisher=The Royal Swedish Academy of Science |date=1968 |access-date=2010-02-27}}</ref>

The three stop codons were named by discoverers Richard Epstein and Charles Steinberg. "Amber" was named after their friend Harris Bernstein, whose last name means "amber" in German.<ref>{{cite journal|date=Oct 2004|title=The genome of bacteriophage T4: an archeological dig|journal=Genetics|volume=168|issue=2|pages=575–82|pmc=1448817|pmid=15514035|vauthors=Edgar B|doi=10.1093/genetics/168.2.575}}</ref> The other two stop codons were named "ochre" and "opal" in order to keep the "color names" theme.

=== Expanded genetic codes (synthetic biology) ===
{{Main|Expanded genetic code}}
{{See also|Nucleic acid analogues}}

In a broad academic audience, the concept of the evolution of the genetic code from the original and ambiguous genetic code to a well-defined ("frozen") code with the repertoire of 20 (+2) canonical amino acids is widely accepted.<ref>{{Cite book| title = The book at the Wiley Online Library
| doi = 10.1002/3527607188
| isbn = 9783527312436
|last1 = Budisa|first1 = Nediljko| date = 2005-12-23
}}</ref>
However, there are different opinions, concepts, approaches and ideas, which is the best way to change it experimentally.{{Clarify|reason=are the opinions differing on "which one method is the best to change the experiments"?|date=February 2025}} Even models are proposed that predict "entry points" for synthetic amino acid invasion of the genetic code.<ref>{{cite journal
| last1 = Kubyshkin | first1 = V.
| last2 = Budisa | first2 = N.
| year = 2018
| title = Synthetic alienation of microbial organisms by using genetic code engineering: Why and how?
| journal = Biotechnology Journal
| volume = 12
| issue = 8
| pages = 16000933
| doi = 10.1002/biot.201600097
| pmid = 28671771
}}</ref>

Since 2001, 40 non-natural amino acids have been added into proteins by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl&nbsp;– tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring [[protein structure]] and function or to create novel or enhanced proteins.<ref name="XieSchultz2005">{{cite journal | vauthors = Xie J, Schultz PG | title = Adding amino acids to the genetic repertoire | journal = Current Opinion in Chemical Biology | volume = 9 | issue = 6 | pages = 548–54 | date = December 2005 | pmid = 16260173 | doi = 10.1016/j.cbpa.2005.10.011 }}</ref><ref name="pmid19318213">{{cite journal | vauthors = Wang Q, Parrish AR, Wang L | title = Expanding the genetic code for biological studies | journal = Chemistry & Biology | volume = 16 | issue = 3 | pages = 323–36 | date = March 2009 | pmid = 19318213 | pmc = 2696486 | doi = 10.1016/j.chembiol.2009.03.001 }}</ref>

H. Murakami and M. Sisido extended some codons to have four and five bases. [[Steven A. Benner]] constructed a functional 65th (''[[in vivo]]'') codon.<ref name="isbn0-387-22046-1">{{cite book|first=Matthew |last=Simon | name-list-style = vanc | title = Emergent Computation: Emphasizing Bioinformatics|url={{google books |plainurl=y |id=Uxg51oZNkIsC|page=105}}|date=7 January 2005|publisher=Springer Science & Business Media|isbn=978-0-387-22046-8|pages=105–106}}</ref>

In 2015 [[Nediljko Budisa|N. Budisa]], [[Dieter Söll|D. Söll]] and co-workers reported the full substitution of all 20,899 [[tryptophan]] residues (UGG codons) with unnatural thienopyrrole-alanine in the genetic code of the [[Bacteria|bacterium]] ''[[Escherichia coli|E. coli]]''.<ref>{{cite journal | last1 = Hoesl | first1 = M. G. | last2 = Oehm | first2 = S. | last3 = Durkin | first3 = P. | last4 = Darmon | first4 = E. | last5 = Peil | first5 = L. | last6 = Aerni | first6 = H.-R. | last7 = Rappsilber | first7 = J. | author-link7=Juri Rappsilber | last8 = Rinehart | first8 = J. | last9 = Leach | first9 = D. | last10 = Söll | first10 = D. | last11 = Budisa | first11 = N. | year = 2015 | title = Chemical evolution of a bacterial proteome | journal = Angewandte Chemie International Edition | volume = 54 | issue = 34 | pages = 10030–10034 | doi = 10.1002/anie.201502868 | pmc = 4782924 | pmid=26136259 }} NIHMSID: NIHMS711205</ref>

In 2016 the first stable semisynthetic organism was created. It was a (single cell) bacterium with two synthetic bases (called X and Y). The bases survived cell division.<ref>{{cite web|url=http://www.kurzweilai.net/first-stable-semisynthetic-organism-created|title=First stable semisynthetic organism created {{!}} KurzweilAI|date=3 February 2017|website=www.kurzweilai.net|access-date=2017-02-09}}</ref><ref>{{cite journal | vauthors = Zhang Y, Lamb BM, Feldman AW, Zhou AX, Lavergne T, Li L, Romesberg FE | title = A semisynthetic organism engineered for the stable expansion of the genetic alphabet| journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 114 | issue = 6 | pages = 1317–1322 | date = February 2017 | pmid = 28115716 | doi = 10.1073/pnas.1616443114 | pmc=5307467| bibcode = 2017PNAS..114.1317Z| doi-access = free}}</ref>

In 2017, researchers in South Korea reported that they had engineered a mouse with an extended genetic code that can produce proteins with unnatural amino acids.<ref>{{cite journal | vauthors = Han S, Yang A, Lee S, Lee HW, Park CB, Park HS | title = Expanding the genetic code of Mus musculus | journal = Nature Communications | volume = 8 | pages = 14568 | date = February 2017 | pmid = 28220771 | doi = 10.1038/ncomms14568 | pmc=5321798| bibcode = 2017NatCo...814568H }}</ref>

In May 2019, researchers reported the creation of a new "Syn61" strain of the ''E. coli'' bacteria. This strain has a fully [[Synthetic biology#Synthetic life|synthetic]] genome that is refactored (all overlaps expanded), recoded (removing the use of three out of 64 codons completely), and further modified to remove the now unnecessary tRNAs and release factors. It is fully [[Genetic viability|viable]] and grows 1.6× slower than its wild-type counterpart "[[Escherichia coli#MDS42|MDS42]]".<ref name="NYT-20190515">{{cite news |last=Zimmer |first=Carl |author-link=Carl Zimmer |title=Scientists Created Bacteria With a Synthetic Genome. Is This Artificial Life? - In a milestone for synthetic biology, colonies of E. coli thrive with DNA constructed from scratch by humans, not nature. |url=https://www.nytimes.com/2019/05/15/science/synthetic-genome-bacteria.html |archive-url=https://ghostarchive.org/archive/20220102/https://www.nytimes.com/2019/05/15/science/synthetic-genome-bacteria.html |archive-date=2022-01-02 |url-access=limited |url-status=live |date=15 May 2019 |work=[[The New York Times]] |access-date=16 May 2019 }}{{cbignore}}</ref><ref name="NAT-20190515">{{cite journal |author=Fredens, Julius |s2cid=205571025 |display-authors=et al. |title=Total synthesis of Escherichia coli with a recoded genome |date=15 May 2019 |journal=[[Nature (journal)|Nature]] |volume=569 |issue=7757 |pages=514–518 |doi=10.1038/s41586-019-1192-5 |pmid=31092918 |pmc=7039709 |bibcode=2019Natur.569..514F }}</ref>