The  vaccinia virus  ( VACV  or  VV ) [ a ]  is a large, complex,  enveloped   virus  belonging to the  poxvirus  family. [ 3 ]  It has a  linear ,  double-stranded   DNA   genome  approximately 190  kbp  in length, which encodes approximately 250  genes . The dimensions of the  virion  are roughly 360 × 270 × 250  nm , with a mass of approximately 5–10  fg . [ 4 ]  The vaccinia virus is the source of the modern  smallpox vaccine , which the  World Health Organization  (WHO) used to eradicate smallpox in a global vaccination campaign in 1958–1977. Although  smallpox  no longer exists in the wild,  vaccinia  virus is still studied widely by scientists as a tool for  gene therapy  and  genetic engineering .


Smallpox  had been an endemic human disease that had a 30% fatality rate. In 1796, the British doctor  Edward Jenner  proved that an infection with the relatively mild  cowpox  virus would also confer immunity to the deadly smallpox. Jenner referred to cowpox as  variolae vaccinae  (smallpox of the cow). However, the origins of the smallpox vaccine became murky over time, [ 5 ]  especially after  Louis Pasteur  developed laboratory techniques for creating vaccines in the 19th century.  Allan Watt Downie  demonstrated in 1939 that the modern smallpox vaccine was serologically distinct from cowpox, [ 6 ]  and  vaccinia  was subsequently recognized as a separate viral species. Whole-genome sequencing has revealed that  vaccinia  is most closely related to  horsepox , and the cowpox strains found in Great Britain are the  least  closely related to  vaccinia . [ 7 ]


In addition to the morbidity of uncomplicated primary vaccination, transfer of infection to other sites by scratching, and  post-vaccinial  encephalitis , other complications of vaccinia infections may be divided into the following types: [ 8 ] : 391


Vaccinia virus is closely related to the virus that causes  cowpox ; historically the two were often considered to be one and the same. [ 9 ]  The precise origin of vaccinia virus is unknown due to the lack of record-keeping, as the virus was repeatedly cultivated and  passaged  in research laboratories for many decades. [ 10 ]  The most common notion is that vaccinia virus, cowpox virus, and  variola  virus (the causative agent of smallpox) were all derived from a common ancestral virus. There is also speculation that vaccinia virus was originally isolated from  horses , [ 9 ]  and analysis of DNA from an early (1902) sample of smallpox vaccine showed that it was 99.7% similar to horsepox virus. [ 11 ]


Poxviruses are unique among  DNA viruses  because they  replicate  only in the  cytoplasm  of the  host cell , outside of the  nucleus . [ 12 ]  Therefore, the large genome is required for encoding various  enzymes  and proteins involved in viral DNA replication and gene  transcription . During its replication cycle, VV produces four infectious forms which differ in their outer  membranes : intracellular mature virion (IMV), the intracellular enveloped virion (IEV), the cell-associated enveloped virion (CEV) and the extracellular enveloped virion (EEV). [ 13 ]  Although the issue remains contentious, the prevailing view is that the IMV consists of a single  lipoprotein  membrane, while the CEV and EEV are both surrounded by two membrane layers and the IEV has three envelopes. The IMV is the most abundant infectious form and is thought to be responsible for spread between hosts. On the other hand, the CEV is believed to play a role in cell-to-cell spread and the EEV is thought to be important for long range dissemination within the host organism. [ citation needed ]


Vaccinia virus is able to undergo multiplicity reactivation (MR). [ 14 ]  MR is the process by which two, or more, virus genomes containing otherwise lethal damage interact within an infected cell to form a viable virus genome.  Abel [ 14 ]  found that vaccinia viruses  exposed to doses of UV light sufficient to prevent progeny formation when single virus particles infected host chick embryo cells, could still produce viable progeny viruses when host cells were infected by two or more of these inactivated viruses; that is, MR could occur.  Kim and Sharp demonstrated MR of vaccinia virus after treatment with UV-light, [ 15 ]  nitrogen mustard, [ 16 ]  and X-rays or gamma rays. [ 17 ]   Michod et al. [ 18 ]  reviewed numerous examples of MR in different viruses, and suggested that MR is a common form of sexual interaction in viruses that provides the advantage of recombinational repair of genome damages. [ additional citation(s) needed ]


Vaccinia contains within its genome genes for several  proteins  that give the virus resistance to  interferons :


Vaccinia virus infection is typically very mild and often does not cause symptoms in healthy individuals, although it may cause rash and  fever . Immune responses generated from a vaccinia virus infection protects the person against a lethal  smallpox  infection. For this reason, vaccinia virus was, and still is, being used as a live-virus vaccine against smallpox. Unlike vaccines that use weakened forms of the virus being vaccinated against, the vaccinia virus vaccine cannot cause a smallpox infection because it does not contain the smallpox virus. However, certain complications and/or vaccine adverse effects occasionally arise. The chance of this happening is significantly increased in people who are  immunocompromised . Approximately 1 to 2 people out of every 1 million people vaccinated could die as a result of life-threatening reactions to the  vaccination . [ 22 ]  The rate of myopericarditis with ACAM2000 is 5.7 per 1,000 of primary vaccinees. [ 23 ]


On September 1, 2007, the U.S.  Food and Drug Administration  (FDA) licensed a new  vaccine   ACAM2000  against  smallpox  which can be produced quickly upon need. Manufactured by  Sanofi Pasteur , the U.S.  Centers for Disease Control and Prevention  stockpiled 192.5 million doses of the new vaccine (see list of common strains below). [ 24 ]


A smallpox vaccine,  Imvanex , which is based on the  Modified vaccinia Ankara  strain, was approved by the  European Medicines Agency  (EMA) in 2013. [ 25 ]  This strain has been used in vaccines during the  2022 monkeypox outbreak . [ citation needed ]


Vaccinia  is also used in recombinant  vaccines , as a vector for expression of foreign genes within a host, in order to generate an immune response. Other  poxviruses  are also used as live recombinant vaccines. [ 26 ]


The original vaccine for smallpox, and the origin of the idea of vaccination, was  Cowpox , described by  Edward Jenner  in 1798. The  Latin  term used for Cowpox was  Variolae vaccinae ,  Jenner's own translation of "smallpox of the cow".  That term lent its name to the whole idea of vaccination. [ 27 ]   When it was realized that the virus used in smallpox vaccination was not, or was no longer, the same as cowpox virus, the name 'vaccinia' was used for the virus in smallpox vaccine. (See OED.) Vaccine potency and efficacy prior to the invention of refrigerated methods of transportation was unreliable. The vaccine would be rendered impotent by heat and sunlight, and the method of drying samples on quills and shipping them to countries in need often resulted in an inactive vaccine. Another method employed was the "arm to arm" method. This involved vaccinating an individual then transferring it to another as soon as the infectious pustule forms, then to another, etc. This method was used as a form of living transportation of the vaccine, and usually employed orphans as carriers. However, this method was problematic due to the possibility of spreading other blood diseases, such as hepatitis and syphilis, as was the case in 1861, when 41 Italian children contracted syphilis after being vaccinated by the "arm to arm" method. [ 28 ]   Henry Austin Martin  introduced a method for vaccine production from calves. [ 29 ]


In 1913, E. Steinhardt, C. Israeli, and R. A. Lambert grew vaccinia virus in fragments of pig  corneal   tissue culture . [ 30 ]


A paper published in 1915 by Fredrick W. Twort, a student of Willian Bulloch, is considered to be the beginning of modern phage research. He was attempting to grow vaccinia virus on agar media in the absence of living cells when he noted that many colonies of contaminating micrococci grew up and appeared mucoid, watery or glassy, and this transformation could be induced in other colonies by inoculation of the fresh colony with material from the watery colony. Using a microscope, he observed that bacteria had degenerated into small granules that stained red with  Giemsa stain . He concluded that "...it [the agent of transformation] might almost be considered as an acute infectious disease of micrococci." [ 32 ]


In 1939   Allan Watt Downie  showed that the smallpox vaccines being used in the 20th century and cowpox virus were not the same, but were immunologically related. [ 6 ] [ 33 ]


In March 2007, a 2-year-old Indiana boy and his mother contracted a life-threatening vaccinia infection from the boy's father. [ 34 ]  The boy developed the telltale rash over 80 percent of his body after coming into close contact with his father, who was vaccinated for smallpox before being deployed overseas by the  United States Army . The United States military resumed smallpox vaccinations in 2002. The child acquired the infection due to  eczema , which is a known risk factor for vaccinia infection. The boy was treated with  intravenous immunoglobulin ,  cidofovir , and  Tecovirimat  (ST-246), a (then) experimental drug developed by  SIGA Technologies . [ 35 ]  On April 19, 2007, he was sent home with no after effects except for possible scarring of the skin. [ 34 ]


In 2010, the  Centers for Disease Control and Prevention  (CDC) reported that a woman in Washington had contracted vaccinia virus infection after digital vaginal contact with her boyfriend, a military member who had recently been vaccinated for smallpox. The woman had a history of childhood eczema, but she had not been symptomatic as an adult. The CDC indicated that it was aware of four similar cases in the preceding 12 months of vaccinia infection after sexual contact with a recent military vaccinee. [ 36 ]  Further cases—also in patients with a history of eczema—occurred in 2012. [ 37 ]


This is a list of some of the well-characterized vaccinia strains used for research and vaccination. [ citation needed ]


In September 2021,  Synthetic Genomics Inc.  ( SGI ),  a private company located in  La Jolla , California, changed its name to Viridos. [ 1 ]  The company is focused on the field of  synthetic biology , especially harnessing photosynthesis with micro algae to create alternatives to fossil fuels. [ 2 ]  Viridos designs and builds  biological systems  to address  global   sustainability  problems.


Synthetic biology  is an interdisciplinary branch of  biology  and engineering, combining fields such as  biotechnology ,  evolutionary biology ,  molecular biology ,  systems biology ,  biophysics ,  computer engineering , and  genetic engineering . Synthetic Genomics uses techniques such as  software engineering ,  bioprocessing ,  bioinformatics , biodiscovery,  analytical chemistry ,  fermentation , cell  optimization , and  DNA synthesis  to design and build biological systems. The company produces or performs research in the fields of sustainable  bio-fuels , insect resistant crops,  transplantable organs , targeted medicines, DNA synthesis  instruments  as well as a number of biological  reagents .


SGI mainly operates in three  end markets : research, bioproduction and applied products. The  research  segment focuses on genomics solutions for academic and  commercial research organizations . The commercial products and services include  instrumentation ,  reagents ,  DNA synthesis  services, and  bioinformatics  services and  software . In 2015, the company launched the BioXP 3200 system, [ 3 ]  a fully automated benchtop instrument that produces DNA fragments from many different sources for genomic data.


The company's efforts in bio-based production are intended to improve both existing production  hosts  and develop entirely new synthetic production hosts with the goal of more efficient routes to  bioproducts .


SGI has a number of commercial as well as research and development stage programs across a variety of industries. Some of these  research partnerships  include:


Synthetic Genomics was founded in the spring of 2005 by  J. Craig Venter , Nobel Laureate  Hamilton O. Smith , Juan Enriquez, and David Kiernan. Venter (and Smith)'s previous company,  Celera Genomics , was a driving force in the race to sequence the  human genome . [ 9 ]
The firm takes its name from the phrase  synthetic genomics  which is a scientific discipline of  synthetic biology  related to the generation of organisms artificially using genetic material. [ 10 ] [ 11 ]


Many of SGI's collaborations have been with energy companies. In 2007, SGI worked with BP to commercialize microbial-based processes for increasing the conversion and recovery of subsurface hydrocarbons. [ 12 ]  In 2009, SGI received funding from  ExxonMobil  to produce  biofuels  on an industrial-scale using recombinant  algae  and other microorganisms. [ 13 ] [ 14 ]  The company purchased an 81-acre  site (33 ha) in the  Imperial Valley  in  Southern California  to produce  algae fuel  for their collaboration with Exxon Mobil. [ 15 ]  They also signed a collaborative agreement with  New England Biolabs  to Launch Gibson Assembly Master Mix Product for Synthetic and Molecular Biology Applications in 2012. [ 16 ]


In 2010, Synthetic Genomics spun off a new subsidiary, Synthetic Genomics Vaccines Inc., to develop next generation  vaccines [ 17 ]


In 2014 SGI expanded into the field of  organ transplantation  with a collaborative agreement with  United Therapeutics  valued at $50M [ 18 ]  and brought in Oliver Fetzer as  CEO . [ 19 ]


Vision rehabilitation  (often called  vision rehab ) is a term for a  medical rehabilitation  to improve vision or  low vision . In other words, it is the process of restoring functional ability and improving quality of life and independence in an individual who has lost visual function through illness or injury. [ 1 ] [ 2 ]  Most visual rehabilitation services are focused on low vision, which is a  visual impairment  that cannot be fully corrected by regular eyeglasses, contact lenses, medication, or surgery. Low vision interferes with the ability to perform everyday activities. [ 3 ]  Visual impairment is caused by factors including  brain damage ,  vision loss , and others. [ 4 ]  Of the vision rehabilitation techniques available, most center on neurological and physical approaches. According to the American Academy of Ophthalmology, "Provision of, or referral to, vision rehabilitation is now the standard of care for all who experience vision loss.." [ 5 ]


Rehabilitation (literally, the act of making able again) helps patients achieve physical, social, emotional, spiritual independence and quality of life. [ 6 ]  Rehabilitation does not undo or reverse the cause of damage; it seeks to promote function and independence through adaptation. Individuals can seek rehabilitation in different domains, such as  motor rehabilitation  after a stroke or physical rehabilitation after a car accident. [ 7 ]  Low vision can be caused by many diseases. [ 6 ]


There are many treatments and therapies to slow degradation of vision loss or improve the vision using neurological approaches. Studies have found that low vision can be restored to good vision. [ 4 ] [ 8 ]  In some cases, vision cannot be restored to normal levels but progressive visual loss can be stopped through interventions. [ 6 ]


In general, chemical treatments are designed to slow the process of vision loss. Some research is done with  neuroprotective treatment  that will slow the progression of vision loss. [ 9 ]  Despite other approaches existing, neuroprotective treatments seem to be most common among all chemical treatments.


Gene therapy  uses DNA as a delivery system to treat visual impairments. In this approach, DNA is modified through a viral vector, and then cells related to vision cease translating faulty proteins. [ 10 ]  Gene therapy seems to be the most prominent field that might be able to restore vision through therapy. However, research indicates gene therapy may worsen symptoms, cause them to last longer or lead to further complications.


For physical approaches to vision rehabilitation, most of the training is focused on ways to make environments easier to deal with for those with low vision.  Occupational therapy  is commonly suggested for these patients. [ 11 ]  Also, there are devices that help patients achieve higher standards of living. These include video magnifiers, peripheral prism glasses,  transcranial direct current stimulation  (tDCS),  closed-circuit television  (CCTV),  RFID  devices, electronic badges with emergency alert systems, virtual sound systems, and smart wheelchairs.


Mobility training  improves the ability for patients with visual impairment to live independently by training patients to become more mobile. [ 12 ]  For low vision patients, there are multiple mobility training methods and devices available including the 3D sound virtual reality system, talking  braille , and RFID floors.


The 3D sound virtual reality system transforms sounds into locations and maps the environment. [ 13 ]  This system alerts patients to avoid possible dangers. The talking braille is a device that helps low vision patients to read braille by detecting light and transmitting this information through Bluetooth technology. [ 14 ]  RFID floors are GPS-like navigation systems which help patients to detect building interiors, which ultimately allow them to detour around obstacles. [ 15 ]


Home skills training  allows patients to improve communication skills, self-care skills, cognitive skills, socialization skills, vocational training, psychological testing, and education. [ 16 ]  One study indicates that multicomponent group interventions for older adults with low vision as an effective approach related to home training. [ 17 ]  The multicomponent group interventions include learning new knowledge or skills each week, having multiple sessions to allow participants to apply learned knowledge or skills in their living environment, and building relationships with their health care providers. [ 18 ]  The most important factor in this intervention is support from family, which includes assistance with changes in lifestyles, financial concerns, and future planning. [ 19 ]


The field of  vision rehabilitation therapy  is made up of professionals who provide specialized services to individuals who are blind or who have a vision loss that cannot be corrected with prescription lenses, medication, or surgery. Professionals who work in this field are called Vision Rehabilitation Therapists [ 20 ]   (VRTs) or Rehabilitation Teachers [ 20 ]  (RTs). A vision rehabilitation therapist, VRT, is a professional who provides specialized instruction and guidance to individuals who are blind or have low vision. Best practice recommends professionals who work in this field be nationally certified. [ 21 ]  To obtain certification as a VRT, professionals must complete a course of study through a  university program , complete a 350-hour internship, and pass a certification examination. [ 22 ]  The certifying body for VRTs is the Academy for Certification of Vision Rehabilitation and Education Professionals, ACVREP. [ 20 ]  The ACVREP certification for a VRT is called Certified Vision Rehabilitation Therapist and the certified professional uses the letters CVRT indicating this credential. Scope of Practice A VRT works within the scope of practice outlined by ACVREP. [ 22 ]  The VRT provides Instruction in the use of adaptive skills and strategies to help individuals with vision loss to safely meet their personal goals for employment, education, and independence in the workplace, home, and community. Training from a VRT may include:


The VRT serves individuals of any age, whether vision loss is present at birth or if acquired later in life. Individuals with any level of visual impairment, whether partial or total, may benefit from services provided by the VRT. Services provided by a VRT are comprehensive taking into consideration visual abilities, other physical limitations, social supports, and emotional adjustment to vision loss. Instruction with a VRT often uses strategies which include other senses to complete tasks, use of devices that enhance low vision or increase accessibility, and problem-based learning.


Vision Rehabilitation Therapists are hired by state vocational rehabilitation programs, non-profit agencies, veterans’ administration (VA) hospitals, [ 23 ]  or they may choose to be self-employed, working as private contractors. A VRT may provide their services one-on-one or in a group setting. Many services are provided in the home of the client with vision loss, so that environmental factors can be assessed, and specific strategies practiced in the location where tasks need to be completed. Services might also be provided in the client’s workplace or educational institution, a community center, rehab residential facility, or in the community. The vision rehabilitation therapist may also work as part of a rehabilitation team, which may include an  Orientation and Mobility (O&M) Specialist  (COMS),  Certified Assistive Technology Instructional Specialist (CATIS) , and  Low Vision Therapist (CLVT)  to provide comprehensive rehabilitation services.


Occupational therapists can assess how low vision affects day-to-day function. [ 24 ]  They can promote independence in daily activities through home assessments and modifications, problem solving training, home exercise programs and finding compensatory strategies. [ 25 ] [ 24 ]  For example, an occupational therapist can suggest adding lighting and contrast to a room to improve visibility. [ 24 ]


The  William Allan Award , given by the  American Society of Human Genetics , was established in 1961 in memory of  William Allan  (1881–1943), one of the first American physicians to conduct extensive research in human genetics. [ 1 ]


The William Allan Award is presented annually to recognize substantial and far-reaching scientific contributions to human genetics carried out over a sustained period of scientific inquiry and productivity. An award of $25,000 and an engraved medal are presented at the Annual Meeting.


Source:  ASHG


The  Bateson Lecture  is an annual genetics lecture held as a part of the John Innes Symposium since 1972, in honour of the first Director of the  John Innes Centre ,  William Bateson .  [ 1 ]


Source:  John Innes Centre


The  Biffen Lecture  is a  lectureship  organised by the  John Innes Centre , named after  Rowland Biffen . [ 1 ]


The  Francis Crick Medal and Lecture [ 1 ] [ 2 ]  is  a prize lecture of the  Royal Society  established in 2003 with an endowment from  Sydney Brenner , the late Francis Crick's close friend and former colleague. It is delivered annually in  biology , particularly the areas which  Francis Crick [ 3 ]  worked ( genetics ,  molecular biology  and  neurobiology ), and also to theoretical work.  The medal is also intended for young scientists, i.e. under 40, or at career stage corresponding to being under 40 should their career have been interrupted.


Laureates include:  [ 4 ]


The  Darlington Lecture  is a lectureship of the  John Innes Centre  named after its former director, the  geneticist   C. D. Darlington . [ 1 ] [ 2 ]


The  Edward Novitski Prize  is awarded by the  Genetics Society of America  (GSA) to recognize an extraordinary level of creativity and intellectual ingenuity in solving significant problems in genetics research. [ 1 ]


Named in honor of  Drosophila  geneticist  Edward Novitski  (1918-2006), the award recognizes scientific achievement that stands out from the body of innovative work, that is deeply impressive to creative masters in the field, and that solves a difficult problem in genetics. It recognizes the beautiful and intellectually ingenious experimental design and execution involved in genetics scientific discovery.


The prize, established by the Novitski family, includes an engraved medal.


Source:  [ 2 ]


The  Elizabeth W. Jones Award for Excellence in Education  is awarded annually by the  Genetics Society of America  to recognize individuals who have made noteworthy contributions to  genetics   education . It was founded in 2007 as the  Genetics Society of America Award for Excellence in Education . Its first recipient was  Elizabeth W. Jones , after whom the award was renamed following her death in 2008. [ 1 ] [ 2 ]


Source:  Genetics Society of America


This science awards article is a  stub . You can help Wikipedia by  expanding it .


The  Genetics Society of American Medal  is a medal awarded by the  Genetics Society of America  (GSA) for outstanding contributions to the field of  genetics  in the last 15 years.


The Medal was established by the society in 1981 and recognizes members who have made recent contributions to the field. [ 1 ]


The  George W. Beadle Award  is a scientific prize given by the  Genetics Society of America  to individuals who have made “outstanding contributions” to  Genetics . The Award was established in 1999 and named in honor of  George Wells Beadle , [ 1 ]  who won the  Nobel Prize in Physiology or Medicine  in 1958.


The  Haldane Lecture  is an award lecture given at the  John Innes Centre  in the United Kingdom since 2001. [ 1 ]  The lecture is named in honour of  J.B.S. Haldane , who was employed by the John Innes Trustees from 1927 to 1937 [ 2 ]  under the directorship of  Alfred Daniel Hall . [ 1 ] [ 3 ]


All Haldane Lecturers are presented with a print of a work of art by Leonie Woolhouse, wife of  Harold Woolhouse . [ 1 ]  During their visit to the John Innes Centre, Haldane Lecturers are given the opportunity to have their portrait painted by  Enrico Coen  as a memento. [ 1 ] [ 7 ]


The McClintock Prize for Plant Genetics and Genome Studies  is a prize awarded in genetics and genomics.  The Prize is awarded by the Maize Genetics Executive Committee, [ 1 ]  and is presented to the Prize winner each spring at the Annual Maize Genetics Conference.   [ 2 ]


Named in honour of  Barbara McClintock  the award was founded in 2013 by  Jeffrey Bennetzen , and funded by his royalties from the book  Handbook of Maize  by Bennetzen and  Sarah Hake .  McClintock received the  Physiology or Medicine Nobel Prize  in 1983 for her work on maize genome structure, function and evolution, especially for her discovery and study of mobile DNA elements (aka  jumping genes ).


Laureates of the award include: [ 3 ]


The  Ruth Stephens Gani Medal  is awarded annually by the  Australian Academy of Science  to recognise research in human genetics. [ 1 ]


The award honours the contributions by  Ruth Stephens Gani  to human  cytogenetics . [ 1 ]


It is an early career award normally for Australian resident nominees up to ten years work post doctorate. [ 1 ]


Below are a list of recipients from 2008-2018 in the field:


Source:  Australian Academy of Science


The  ASHG Scientific Achievement Award  was established in 2001 and is presented annually by the  American Society of Human Genetics  (ASHG) for outstanding scientific achievements in  human genetics  that have occurred in the last 10 years. [ 1 ]


The award was formerly known as the Curt Stern Award, or the Stern Award, named in honor of  Curt Stern  (1902–1981), a pioneering human geneticist. [ 1 ]  It was renamed in 2023 along with several other ASHG awards in a new organizational policy that removed individual's names from awards in favor of descriptive names. [ 2 ]


Source:  American Society of Human Genetics


The  Thomas Hunt Morgan Medal  is awarded by the  Genetics Society of America  (GSA) for lifetime contributions to the field of  genetics .


The medal is named after  Thomas Hunt Morgan , the 1933  Nobel Prize  winner, who received this award for his work with  Drosophila  and his "discoveries concerning the role played by the chromosome in heredity."  Morgan recognized that Drosophila, which could be bred quickly and inexpensively, had large quantities of offspring and a short life cycle, would make an excellent organism for genetic studies. His studies of the white-eye mutation and discovery of sex-linked inheritance provided the first experimental evidence that chromosomes are the carriers of genetic information.  Subsequent studies in his laboratory led to the discovery of recombination and the first genetic maps.


In 1981 the GSA established the Thomas Hunt Morgan Medal for lifetime achievement to honor this classical geneticist who was among those who laid the foundation for modern genetics.


Nucleotide bases [ 1 ]  (also  nucleobases ,  nitrogenous bases ) are  nitrogen -containing biological compounds that form  nucleosides , which, in turn, are components of  nucleotides , with all of these  monomers  constituting the basic building blocks of  nucleic acids . The ability of nucleobases to form  base pairs  and to stack one upon another leads directly to long-chain helical structures such as  ribonucleic acid  (RNA) and  deoxyribonucleic acid  (DNA). Five nucleobases— adenine  (A),  cytosine  (C),  guanine  (G),  thymine  (T), and  uracil  (U)—are called  primary  or  canonical . They function as the fundamental units of the  genetic code , with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. [ 2 ] [ page needed ]
In addition, some viruses have  aminoadenine  (Z) instead of adenine. It differs in having an extra  amine  group, creating a more stable bond to thymine. [ 3 ]


Adenine and guanine have a  fused-ring  skeletal structure derived of  purine , hence they are called  purine bases . [ 4 ]  The purine nitrogenous bases are characterized by their single  amino group  ( −NH 2 ), at the C6 carbon in adenine and C2 in guanine. [ 5 ]  Similarly, the simple-ring structure of cytosine, uracil, and thymine is derived of  pyrimidine , so those three bases are called the  pyrimidine bases . [ 6 ]


Each of the base pairs in a typical double- helix  DNA comprises a purine and a pyrimidine: either an A paired with a T or a C paired with a G. These purine-pyrimidine pairs, which are called  base complements , connect the two strands of the helix and are often compared to the rungs of a ladder. Only pairing purine with pyrimidine ensures a constant width for the DNA. The A–T pairing is based on two  hydrogen bonds , while the C–G pairing is based on three. In both cases, the hydrogen bonds are between the  amine  and  carbonyl  groups on the complementary bases.


Nucleobases such as adenine, guanine,  xanthine ,  hypoxanthine , purine,  2,6-diaminopurine , and 6,8-diaminopurine may have formed in outer space as well as on earth. [ 7 ] [ 8 ] [ 9 ]


The origin of the term  base  reflects these compounds' chemical properties in  acid–base reactions , but those properties are not especially important for understanding most of the biological functions of nucleobases.


At the sides of nucleic acid structure, phosphate molecules successively connect the two sugar-rings of two adjacent nucleotide monomers, thereby creating a long chain  biomolecule . These chain-joins of phosphates with sugars ( ribose  or  deoxyribose ) create the "backbone" strands for a single- or double helix biomolecule. In the double helix of DNA, the two strands are oriented chemically in opposite directions, which permits base pairing by providing  complementarity  between the two bases, and which is essential for  replication  of or  transcription  of the encoded information found in DNA. [ citation needed ]


DNA and RNA also contain other (non-primary) bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is  5-methylcytosine  (m 5 C). In RNA, there are many modified bases, including those contained in the nucleosides  pseudouridine  (Ψ),  dihydrouridine  (D),  inosine  (I), and  7-methylguanosine  (m 7 G). [ 10 ] [ 11 ]


Hypoxanthine  and  xanthine  are two of the many bases created through  mutagen  presence, both of them through  deamination  (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced from adenine, xanthine from guanine, [ 12 ]  and uracil results from deamination of cytosine.


These are examples of modified adenosine or guanosine.


These are examples of modified cytidine, thymidine or uridine.


A vast number of nucleobase analogues exist.
The most common applications are used as fluorescent probes, either directly or indirectly, such as  aminoallyl nucleotide , which are used to label cRNA or cDNA in  microarrays . Several groups are working on alternative "extra" base pairs to extend the genetic code, such as  isoguanine  and  isocytosine  or the fluorescent  2-amino-6-(2-thienyl)purine  and  pyrrole-2-carbaldehyde . [ 13 ] [ 14 ]


In medicine, several  nucleoside analogues  are used as anticancer and antiviral agents. The viral polymerase incorporates these compounds with non-canonical bases. These compounds are activated in the cells by being converted into nucleotides; they are administered as  nucleosides  as charged nucleotides cannot easily cross cell membranes. [ citation needed ]  At least one set of new base pairs has been announced as of May 2014. [ 15 ]


In order to understand  how life arose , knowledge is required of chemical pathways that permit formation of the key building blocks of  life  under plausible  prebiotic conditions . According to the  RNA world  hypothesis, free-floating  ribonucleotides  were present in the  primordial soup . These were the fundamental molecules that combined in series to form  RNA . Molecules as complex as RNA must have arisen from small molecules whose reactivity was governed by physico-chemical processes. RNA is composed of  purine  and  pyrimidine  nucleotides, both of which are necessary for reliable information transfer, and thus  Darwinian   evolution . Nam et al. [ 16 ]  demonstrated the direct condensation of nucleobases with ribose to give ribonucleosides in aqueous microdroplets, a key step leading to RNA formation. Similar results were obtained by Becker et al. [ 17 ]


Adenine  ( / ˈ æ d ɪ n ɪ n / ) ( symbol   A  or  Ade ) is a   purine   nucleotide base . It is one of the four nucleobases in the  nucleic acids  of  DNA , the other three being  guanine  (G),  cytosine  (C), and  thymine  (T). Adenine derivatives have various roles in  biochemistry  including  cellular respiration , in the form of both the energy-rich  adenosine triphosphate  (ATP) and the  cofactors   nicotinamide adenine dinucleotide  (NAD),  flavin adenine dinucleotide  (FAD) and  Coenzyme A . It also has functions in  protein synthesis  and as a chemical component of  DNA  and  RNA . [ 2 ]  The shape of adenine is complementary to either  thymine  in  DNA  or  uracil  in  RNA .


The adjacent image shows pure adenine, as an independent molecule. When connected into DNA, a  covalent bond  is formed between  deoxyribose  sugar and the bottom left nitrogen (thereby removing the existing hydrogen atom). The remaining structure is called an  adenine residue , as part of a larger molecule.  Adenosine  is adenine reacted with  ribose , as used in  RNA  and ATP;  Deoxyadenosine  is adenine attached to  deoxyribose , as used to form DNA.


Adenine forms several  tautomers , compounds that can be rapidly interconverted and are often considered equivalent. However, in isolated conditions, i.e. in an inert gas matrix and in the gas phase, mainly the 9H-adenine tautomer is found. [ 3 ] [ 4 ]


Purine metabolism  involves the formation of adenine and  guanine . Both adenine and guanine are derived from the nucleotide  inosine monophosphate  (IMP), which in turn is synthesized from a pre-existing  ribose phosphate  through a complex pathway using atoms from the  amino acids   glycine ,  glutamine , and  aspartic acid , as well as the coenzyme  tetrahydrofolate .


Patented Aug. 20, 1968, the current recognized method of industrial-scale production of adenine is a modified form of the formamide method. This method heats up  formamide  under 120 degree Celsius conditions within a sealed flask for 5 hours to form adenine. The reaction is heavily increased  in quantity by using a phosphorus oxychloride ( phosphoryl chloride ) or  phosphorus pentachloride  as an acid catalyst and sunlight or ultraviolet conditions. After the 5 hours have passed and the formamide-phosphorus oxychloride-adenine solution cools down, water is put into the flask containing the formamide and now-formed adenine. The water-formamide-adenine solution is then poured through a filtering column of activated charcoal. The water and formamide molecules, being small molecules, will pass through the charcoal and into the waste flask; the large adenine molecules, however, will attach or "adsorb" to the charcoal due to the  van der Waals forces  that interact between the adenine and the carbon in the charcoal. Because charcoal has a large surface area, it's able to capture the majority of molecules that pass a certain size (greater than water and formamide) through it. To extract the adenine from the charcoal-adsorbed adenine, ammonia gas dissolved in water ( aqua ammonia ) is poured onto the activated charcoal-adenine structure to liberate the adenine into the ammonia-water solution. The solution containing water, ammonia, and adenine is then left to air dry, with the adenine losing solubility due to the loss of ammonia gas that previously made the solution basic and capable of dissolving adenine, thus causing it to crystallize into a pure white powder that can be stored. [ 5 ]


Adenine is one of the two purine  nucleobases  (the other being  guanine ) used in forming  nucleotides  of the  nucleic acids . In DNA, adenine binds to  thymine  via two  hydrogen bonds  to assist in stabilizing the nucleic acid structures. In RNA, which is used for  protein synthesis , adenine binds to  uracil .


Adenine forms  adenosine , a  nucleoside , when attached to  ribose , and  deoxyadenosine  when attached to  deoxyribose . It forms  adenosine triphosphate  (ATP), a  nucleoside triphosphate , when three  phosphate groups  are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the basic methods of transferring  chemical energy  between  chemical reactions . ATP is thus a derivative of adenine,  adenosine ,  cyclic adenosine monophosphate , and  adenosine diphosphate .


In older literature, adenine was sometimes called  Vitamin B 4 . [ 6 ]  Due to it being synthesized by the body and not essential to be obtained by diet, it does not meet the definition of  vitamin  and is no longer part of the  Vitamin B  complex. However, two B vitamins,  niacin  and  riboflavin , bind with adenine to form the essential cofactors  nicotinamide adenine dinucleotide  (NAD) and  flavin adenine dinucleotide  (FAD), respectively.  Hermann Emil Fischer  was one of the early scientists to study adenine.


It was named in 1885 by  Albrecht Kossel  after  Greek   ἀδήν  aden "gland", in reference to the pancreas, from which Kossel's sample had been extracted. [ 7 ] [ 8 ]


Experiments performed in 1961 by  Joan Oró  have shown that a large quantity of adenine can be synthesized from the  polymerization  of  ammonia  with five  hydrogen cyanide  (HCN) molecules in aqueous solution; [ 9 ]  whether this has implications for the  origin of life  on  Earth  is under debate. [ 10 ]


On August 8, 2011, a report, based on  NASA  studies with  meteorites  found on  Earth , was published suggesting building blocks of  DNA  and  RNA  (adenine,  guanine  and related  organic molecules ) may have been formed extraterrestrially in  outer space . [ 11 ] [ 12 ] [ 13 ]  In 2011, physicists reported that adenine has an "unexpectedly variable range of ionization energies along its reaction pathways" which suggested that "understanding experimental data on how adenine survives exposure to  UV light  is much more complicated than previously thought"; these findings have implications for  spectroscopic  measurements of  heterocyclic  compounds, according to one report. [ 14 ]


6-Amino-5-nitropyridin-2-one  or  6-amino-5-nitro-2(1H)-pyridinone  is a  pyridine  base.  It is used as a  nucleobase  of  hachimoji DNA , in which it  pairs with   5-aza-7-deazaguanine . [ 1 ]


2-Aminopurine , a  purine analog  of  guanine  and  adenine , is a fluorescent molecular marker used in nucleic acid research. [ 1 ]   It most commonly pairs with  thymine  as an adenine-analogue, but can also pair with  cytosine  as a guanine-analogue. [ 2 ]   For this reason it is sometimes used in the laboratory for mutagenesis.


5-Aza-7-deazaguanine  or  2-aminoimidazo[1,2-a][1,3,5]triazin-4(1H)-one  is a  5-Aza-7-deazapurine  base that is an  isomer  of  guanine . It is used as a  nucleobase  of  hachimoji DNA , in which it  pairs with   6-Amino-5-nitropyridin-2-one . [ 1 ]


β- D -Glucopyranosyloxymethyluracil  or  base J  is a hypermodified  nucleobase  found in the  DNA  of  kinetoplastids  including the human  pathogenic   trypanosomes . It was discovered in 1993, in the trypanosome  Trypanosoma brucei  and was the first hypermodified nucleobase found in eukaryotic DNA; it has since been found in other kinetoplastids, including  Leishmania . [ 1 ]
Within these organisms Base J acts as a  RNA polymerase II  transcription terminator, with its removal in  knockout cells  being accompanied by a massive read-through at RNA polymerase II termination sites, which ultimately proves lethal to the cell. [ 2 ] [ 3 ]


Base J is formed by the initial  hydroxylation  of  thymidine  and the subsequent  glycosylation  by an as yet unidentified  glycosyltransferase . [ 1 ]


A  base pair  ( bp ) is a fundamental unit of double-stranded  nucleic acids  consisting of two  nucleobases  bound to each other by  hydrogen bonds .  They form the building blocks of the  DNA  double helix and contribute to the folded structure of both DNA and  RNA . Dictated by specific  hydrogen bonding  patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs ( guanine – cytosine  and  adenine – thymine ) [ 1 ]  allow the DNA helix to maintain a regular helical structure that is subtly dependent on its  nucleotide sequence . [ 2 ]  The  complementary  nature of this based-paired structure provides a  redundant  copy of the  genetic information  encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which  DNA polymerase  replicates DNA and  RNA polymerase  transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes.


Intramolecular base pairs can occur within single-stranded nucleic acids. This is particularly important in RNA molecules (e.g.,  transfer RNA ), where Watson–Crick base pairs (guanine–cytosine and adenine– uracil ) permit the formation of short double-stranded helices, and a wide variety of non–Watson–Crick interactions (e.g., G–U or A–A) allow RNAs to fold into a vast range of specific three-dimensional  structures . In addition, base-pairing between  transfer RNA  (tRNA) and  messenger RNA  (mRNA) forms the basis for the  molecular recognition  events that result in the nucleotide sequence of mRNA becoming  translated  into the amino acid sequence of  proteins  via the  genetic code .


The size of an individual  gene  or an organism's entire  genome  is often measured in base pairs because DNA is usually double-stranded. Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of  telomeres ). The  haploid   human genome  (23  chromosomes ) is estimated to be about 3.2 billion base pairs long and to contain 20,000–25,000 distinct protein-coding genes. [ 3 ] [ 4 ] [ 5 ] [ 6 ]  A  kilobase  (kb) is a unit of measurement in  molecular biology  equal to 1000 base pairs of DNA or RNA. [ 7 ]  The total number of  DNA  base pairs on Earth is estimated at 5.0 × 10 37  with a weight of 50 billion  tonnes . [ 8 ]  In comparison, the total  mass  of the  biosphere  has been estimated to be as much as 4  TtC  (trillion tons of  carbon ). [ 9 ]


Hydrogen bonding  is the chemical interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. DNA with high  GC-content  is more stable than DNA with low GC-content. Crucially, however,  stacking interactions  are primarily responsible for stabilising the double-helical structure; Watson-Crick base pairing's contribution to global structural stability is minimal, but its role in the specificity underlying complementarity is, by contrast, of maximal importance as this underlies the template-dependent processes of the  central dogma  (e.g.  DNA replication ). [ 10 ]


The bigger  nucleobases , adenine and guanine, are members of a class of double-ringed chemical structures called  purines ; the smaller nucleobases, cytosine and thymine (and uracil), are members of a class of single-ringed chemical structures called  pyrimidines . Purines are complementary only with pyrimidines: pyrimidine–pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine–purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion. Purine–pyrimidine base-pairing of AT or GC or UA (in RNA) results in proper duplex structure. The only other purine–pyrimidine pairings would be AC and GT and UG (in RNA); these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two hydrogen bonds, does occur fairly often in  RNA  (see  wobble base pair ).


Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a  melting point  that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. Higher GC content results in higher melting temperatures; it is, therefore, unsurprising that the genomes of  extremophile  organisms such as  Thermus thermophilus  are particularly GC-rich. On the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often- transcribed  genes — are comparatively GC-poor (for example, see  TATA box ). GC content and melting temperature must also be taken into account when designing   primers  for  PCR  reactions. [ citation needed ]


The following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the  5′-end  to the  3′-end ; thus, the bottom strand is written 3′ to 5′.


Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors (mostly  point mutations ) in  DNA replication  and  DNA transcription . This is due to their  isosteric  chemistry. One common mutagenic base analog is  5-bromouracil , which resembles thymine but can base-pair to guanine in its  enol  form. [ 11 ]


Other chemicals, known as  DNA intercalators , fit into the gap between adjacent bases on a single strand and induce  frameshift mutations  by "masquerading" as a base, causing the DNA replication machinery to skip or insert additional nucleotides at the intercalated site. Most intercalators are large  polyaromatic  compounds and are known or suspected  carcinogens . Examples include  ethidium bromide  and  acridine . [ 12 ] [ citation needed ]


Mismatched base pairs can be generated by errors of  DNA replication  and as intermediates during  homologous recombination . The process of mismatch repair ordinarily must recognize and correctly repair a small number of base mispairs within a long sequence of normal DNA base pairs.  To repair mismatches formed during DNA replication, several distinctive repair processes have evolved to distinguish between the template strand and the newly formed strand so that only the newly inserted incorrect nucleotide is removed (in order to avoid generating a mutation). [ 13 ]   The proteins employed in mismatch repair during DNA replication, and the clinical significance of defects in this process are described in the article  DNA mismatch repair .  The process of mispair correction during recombination is described in the article  gene conversion .


The following abbreviations are commonly used to describe the length of a D/R NA molecule :


For single-stranded DNA/RNA, units of  nucleotides  are used—abbreviated nt (or knt, Mnt, Gnt)—as they are not paired.
To distinguish between units of  computer storage  and bases, kbp, Mbp, Gbp, etc. may be used for base pairs.


The  centimorgan  is also often used to imply distance along a chromosome, but the number of base pairs it corresponds to varies widely. In the human genome, the centimorgan is about 1 million base pairs. [ 15 ] [ 16 ]


An unnatural base pair (UBP) is a designed subunit (or  nucleobase ) of  DNA  which is created in a laboratory and does not occur in nature.  DNA sequences have been described which use newly created nucleobases to form a third base pair, in addition to the two base pairs found in nature, A-T ( adenine  –  thymine ) and G-C ( guanine  –  cytosine ).  A few research groups have been searching for a third base pair for DNA, including teams led by  Steven A. Benner ,  Philippe Marliere ,  Floyd E. Romesberg  and  Ichiro Hirao . [ 17 ]  Some new base pairs based on alternative hydrogen bonding, hydrophobic interactions and metal coordination have been reported. [ 18 ] [ 19 ] [ 20 ] [ 21 ]


In 1989 Steven Benner (then working at the  Swiss Federal Institute of Technology  in Zurich) and his team led with modified forms of cytosine and guanine into DNA molecules  in vitro . [ 22 ]  The nucleotides, which encoded RNA and proteins, were successfully replicated  in vitro . Since then, Benner's team has been trying to engineer cells that can make foreign bases from scratch, obviating the need for a feedstock. [ 23 ]


In 2002, Ichiro Hirao's group in Japan developed an unnatural base pair between 2-amino-8-(2-thienyl)purine (s) and pyridine-2-one (y) that functions in transcription and translation, for the site-specific incorporation of non-standard amino acids into proteins. [ 24 ]  In 2006, they created 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) as a third base pair for replication and transcription. [ 25 ]  Afterward, Ds and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (Px) was discovered as a high fidelity pair in PCR amplification. [ 26 ] [ 27 ]  In 2013, they applied the Ds-Px pair to DNA aptamer generation by  in vitro  selection (SELEX) and demonstrated the genetic alphabet expansion significantly augment DNA aptamer affinities to target proteins. [ 28 ]


In 2012, a group of American scientists led by Floyd Romesberg, a chemical biologist at the  Scripps Research Institute  in San Diego, California, published that his team designed an unnatural base pair (UBP). [ 20 ]   The two new artificial nucleotides or  Unnatural Base Pair  (UBP) were named  d5SICS  and  dNaM . More technically, these artificial  nucleotides  bearing hydrophobic  nucleobases , feature two fused  aromatic rings  that form a (d5SICS–dNaM) complex or base pair in DNA. [ 23 ] [ 29 ]  His team designed a variety of  in vitro  or "test tube" templates containing the unnatural base pair and they confirmed that it was efficiently replicated with high fidelity in virtually all sequence contexts using the modern standard  in vitro  techniques, namely  PCR amplification of DNA  and PCR-based applications. [ 20 ]  Their results show that for PCR and PCR-based applications, the d5SICS–dNaM unnatural base pair is functionally equivalent to a natural base pair, and when combined with the other two natural base pairs used by all organisms, A–T and G–C, they provide a fully functional and expanded six-letter "genetic alphabet". [ 29 ]


In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a  plasmid  containing natural T-A and C-G base pairs along with the best-performing UBP Romesberg's laboratory had designed and inserted it into cells of the common bacterium  E. coli  that successfully replicated the unnatural base pairs through multiple generations. [ 17 ]  The  transfection  did not hamper the growth of the  E. coli  cells and showed no sign of losing its unnatural base pairs to its natural  DNA repair  mechanisms. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations. [ 29 ] [ 30 ]  Romesberg said he and his colleagues created 300 variants to refine the design of nucleotides that would be stable enough and would be replicated as easily as the natural ones when the cells divide.  This was in part achieved by the addition of a supportive  algal gene  that expresses a  nucleotide triphosphate  transporter which efficiently imports the triphosphates of both d5SICSTP and dNaMTP into  E. coli  bacteria. [ 29 ]  Then, the natural bacterial replication pathways use them to accurately replicate a  plasmid  containing d5SICS–dNaM. Other researchers were surprised that the bacteria replicated these human-made DNA subunits. [ 31 ]


The successful incorporation of a third base pair is a significant breakthrough toward the goal of greatly expanding the number of  amino acids  which can be encoded by DNA, from the existing 20 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel  proteins . [ 17 ]  The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses. [ 32 ]  Experts said the synthetic DNA incorporating the unnatural base pair raises the possibility of life forms based on a different DNA code. [ 31 ] [ 32 ]


In addition to the canonical pairing, some conditions can also favour base-pairing with alternative base orientation, and number and geometry of hydrogen bonds. These pairings are accompanied by alterations to the local backbone shape. [ citation needed ]


The most common of these is the  wobble base pairing  that occurs between  tRNAs  and  mRNAs  at the third base position of many  codons  during  transcription [ 34 ]  and during the charging of tRNAs by some  tRNA synthetases . [ 35 ]  They have also been observed in the secondary structures of some RNA sequences. [ 36 ]


Additionally,  Hoogsteen base pairing  (typically written as A•U/T and G•C) can exist in some DNA sequences (e.g. CA and TA dinucleotides) in dynamic equilibrium with standard Watson–Crick pairing. [ 33 ]  They have also been observed in some protein–DNA complexes. [ 37 ]


In addition to these alternative base pairings, a wide range of base-base hydrogen bonding is observed in RNA secondary and tertiary structure. [ 38 ]  These bonds are often necessary for the precise, complex shape of an RNA, as well as its binding to interaction partners. [ 38 ]


Benzylthiouracil  ( BTU ) is an antithyroid preparation. It is a  thioamide , closely related to  propylthiouracil .


Benzylthiouracil has been associated with severe  adverse effects , notably  vasculitis  and subsequent  ANCA -positive  glomerulonephritis , as well as isolated  reports  of lung damage. [ 1 ] [ 2 ] [ 3 ] [ 4 ]


This  hormonal preparation  article is a  stub . You can help Wikipedia by  expanding it .


5-Bromouracil  ( 5-BrU ,  5BrUra , or  br5Ura [ 1 ] ) is a brominated derivative of  uracil  that acts as an  antimetabolite  or  base analog , substituting for  thymine  in  DNA , and can induce DNA  mutation  in the same way as  2-aminopurine . [ 2 ]  It is used mainly as an experimental  mutagen , but its deoxyriboside derivative ( 5-bromo-2-deoxy-uridine ) is used to treat  neoplasms .


5-BrU exists in three  tautomeric  forms that have different base pairing properties. The  keto  form (shown in the infobox) is complementary to  adenine , so it can be incorporated into DNA by aligning opposite adenine residues during DNA replication (see below left). Alternatively, the  enol  (below right) and ion forms are complementary to  guanine . This means that 5-BrU can be present in DNA either opposite adenine or guanine.


The three forms frequently interchange so base-pairing properties can become altered at any time. The result of this is that during a subsequent round of replication a different base is aligned opposite the 5-BrU residue. Further rounds of replication 'fix' the change by incorporating a normal nitrogen base into the complementary strand.


Thus 5-BrU induces a  point mutation  via base substitution. This base pair will change from an A-T to a G-C or from a G-C to an A-T after a number of replication cycles, depending on whether 5-BrU is within the DNA molecule or is an incoming base when it is enolized or ionized.


Cytosine  ( / ˈ s aɪ t ə ˌ s iː n ,   - ˌ z iː n ,   - ˌ s ɪ n / [ 2 ] [ 3 ] ) ( symbol   C  or  Cyt ) is one of the four  nucleotide bases  found in  DNA  and  RNA , along with  adenine ,  guanine , and  thymine  ( uracil  in RNA). It is a  pyrimidine  derivative, with a  heterocyclic   aromatic ring  and two substituents attached (an  amine  group at position 4 and a  keto  group at position 2). The  nucleoside  of cytosine is  cytidine .  In  Watson–Crick base pairing , it forms three  hydrogen bonds  with  guanine .


Cytosine was discovered and named by  Albrecht Kossel  and Albert Neumann in 1894 when it was hydrolyzed from calf  thymus  tissues. [ 4 ] [ 5 ]  A structure was proposed in 1903, and was synthesized (and thus confirmed) in the laboratory in the same year.


In 1998, cytosine was used in an early demonstration of  quantum information processing   when Oxford University researchers implemented the  Deutsch–Jozsa algorithm  on a two  qubit   nuclear magnetic resonance quantum computer (NMRQC) . [ 6 ]


In March 2015, NASA scientists reported the formation of cytosine, along with uracil and thymine, from  pyrimidine  under the space-like laboratory conditions, which is of interest because pyrimidine has been found in meteorites although its origin is unknown. [ 7 ]


Cytosine can be found as part of DNA, as part of RNA, or as a part of a  nucleotide . As  cytidine triphosphate  (CTP), it can act as a co-factor to enzymes, and can transfer a phosphate to convert  adenosine diphosphate  (ADP) to  adenosine triphosphate  (ATP).


In DNA and RNA, cytosine is paired with  guanine . However, it is inherently unstable, and can change into  uracil  ( spontaneous deamination ). This can lead to a  point mutation  if not repaired by the  DNA repair   enzymes  such as uracil glycosylase, which cleaves a uracil in DNA.


Cytosine can also be  methylated  into  5-methylcytosine  by an enzyme called  DNA methyltransferase  or be methylated and  hydroxylated  to make  5-hydroxymethylcytosine . The difference in rates of deamination of cytosine and 5-methylcytosine (to uracil and  thymine ) forms the basis of  bisulfite sequencing . [ 8 ]


When found third in a  codon  of  RNA , cytosine is synonymous with  uracil , as they are interchangeable as the third base.
When found as the second base in a codon, the third is always interchangeable. For example, UCU, UCC, UCA and UCG are all  serine , regardless of the third base.


Active enzymatic deamination of cytosine or 5-methylcytosine by the  APOBEC  family of cytosine deaminases could have both beneficial and detrimental implications on various cellular processes as well as on organismal evolution. [ 9 ]  The implications of deamination on 5-hydroxymethylcytosine, on the other hand, remains less understood.


Until October 2021, Cytosine had not been found in meteorites, which suggested the first strands of RNA and DNA had to look elsewhere to obtain this building block. Cytosine likely formed within some meteorite parent bodies, however did not persist within these bodies due to an effective  deamination  reaction into  uracil . [ 10 ]


In October 2021, Cytosine was announced as having been found in meteorites by researchers in a joint Japan/NASA project, that used novel methods of detection which avoided damaging nucleotides as they were extracted from meteorites. [ 11 ]


2,6-diaminopurine  ( 2,6-DAP , also known as  2-aminoadenine ) is a compound once used in the treatment of  leukemia . [ 1 ]  As the Z base, it is found instead of  adenine  (A) in the genetic material of some  bacteriophage  viruses. [ 2 ]


In August 2011, a report, based on  NASA  studies with  meteorites  found on  Earth , was published suggesting 2,6-diaminopurine and related  organic molecules , including the  DNA  and  RNA  components  adenine  and  guanine , may have been formed extraterrestrially in  outer space . [ 3 ] [ 4 ] [ 5 ]


In  cyanophage S-2L  ( Siphoviridae ), diaminopurine is used instead of adenine ( host evasion ). [ 6 ]  Diaminopurine base (Z) pairs perfectly with  thymine  (T) as it is identical to adenine (A) but has an amine group at position 2 forming 3 intermolecular hydrogen bonds, eliminating the major difference between the two types of basepairs (weak:A-T and strong:C-G). This improved stability affects protein-binding interactions that rely on those differences.


Four papers published April 2021 further describes the use and production of the Z-base. It is now known that: [ 7 ]


In August 2021, it was shown that DatZ, MazZ and PurZ are sufficient to replace some occurrence of A by Z in the bacterial genome of  E. coli ; expression of this system is toxic to the cell. The structures of MazZ (subtype 2) and PurZ are also determined, showing a possible link between PurZ and  archaeal  versions of PurA. [ 12 ]


2-aminoadenine is produced in two steps. The enzyme MazZ (homologous to MazG,  EC 3.6.1.8 ) first performs: [ 12 ]


The enzyme PurZ (homologous to PurA,  EC 6.3.4.4 ) then performs: [ 9 ]


The resulting dSMP is processed by host enzymes analogously to  adenylosuccinate  to produce dZTP.


2,6-DAP was used to treat  leukemia  since as early as 1951. [ 13 ]  It is known to arrest progression of  cell cycle  in mouse leukemia cells by 1989. [ 14 ]  Cancer cells are known to become resistant to DAP by losing their  adenine phosphoribosyltransferase  (APRT) function, [ 15 ]  a process shared with  E. coli . [ 16 ]


DAP derivatives are  in vitro   antivirals  useful against  pseudorabies  virus, a economically important livestock disease. [ 17 ]  This base, in its free form, is able to correct UGA  nonsense mutations  by encouraging  translational readthrough , through the inhibition of  FTSJ1 . [ 18 ]


In bioengineering,  anti-miRNA oligonucleotides  (specifically, the  serinol  nucleic acid [SNA] type) incorporating base Z instead of A show enhanced binding to RNA. [ 19 ]


DAP is used similarly to other nuclear acid analogues in the investigation of enzyme structures and mechanisms. [ 20 ]


2,4-Diaminopyrimidine  is a  diaminopyrimidine .


This article about an  aromatic  compound is a  stub . You can help Wikipedia by  expanding it .


Dihydrothymine  is an intermediate in the metabolism of  thymine .


Dihydrouracil  is an intermediate in the catabolism of  uracil . [ 1 ]  It is the base present in the  nucleoside   dihydrouridine .


Flucytosine , also known as  5-fluorocytosine  ( 5-FC ), is an  antifungal medication . [ 2 ]  It is specifically used, together with  amphotericin B , for serious  Candida  infections  and  cryptococcosis . [ 2 ]  It may be used by itself or with other antifungals for  chromomycosis . [ 2 ]  Flucytosine is used  by mouth  and by  injection into a vein . [ 2 ] [ 3 ]


Common side effects include  bone marrow suppression , loss of appetite,  diarrhea , vomiting, and  psychosis . [ 2 ]   Anaphylaxis  and other  allergic reactions  occasionally occur. [ 2 ]  It is unclear if use in  pregnancy  is safe for the baby. [ 4 ]  Flucytosine is in the fluorinated  pyrimidine analogue  family of medications. [ 2 ]  It works by being converted into  fluorouracil  inside the fungus, which impairs its ability to  make   protein . [ 2 ]


Flucytosine was first made in 1957. [ 5 ]  It is on the  World Health Organization's List of Essential Medicines . [ 6 ]  As of 2016, in the United States the medication cost about US$2,000 per day while in the United Kingdom it is about US$22 per day. [ 7 ]  It is not available in much of the  developing world . [ 8 ]


Flucytosine by mouth is used for the treatment of serious infections caused by susceptible strains of  Candida  or  Cryptococcus neoformans . It can also be used for the treatment of  chromomycosis  (chromoblastomycosis), if susceptible strains cause the infection. Flucytosine must not be used as a sole agent in life-threatening fungal infections due to relatively weak antifungal effects and fast development of resistance, but rather in combination with amphotericin B and/or  azole  antifungals such as  fluconazole  or  itraconazole . Minor infections such as candidal  cystitis  may be treated with flucytosine alone. In some countries, treatment with slow  intravenous infusions  for no more than a week is also a therapeutic option, particular if the disease is life-threatening. [ citation needed ]


Serious fungal infections may occur in those who are immunocompromised. These people benefit from combination therapy including flucytosine, but the incidence of side-effects of a combination therapy, particular with amphotericin B, may be higher. [ citation needed ]


In animal models (rats), flucytosine has been found to be  teratogenic . Sufficient human data does not exist.  Pregnant  women should be given flucytosine only if the potential benefits exceed the potential harm to the fetus. [ citation needed ]


It is not known if flucytosine is distributed in human breast milk. Given the potential risk to the child, the patient should not  breastfeed  during treatment with flucytosine. [ citation needed ]


The efficacy and safety in patients under 18 years of age has not been determined. [ citation needed ]


It is not known if flucytosine is a human  carcinogen . The issue has been raised because traces of  5-fluorouracil , which is a known carcinogen, are found in the colon resulting from the metabolization of flucytosine.


Flucytosine may increase the toxicity of  amphotericin B  and vice versa, although the combination may be life-saving and should be used whenever indicated (e.g.,  cryptococcal  meningitis). The cytostatic  cytarabine  inhibits the antimycotic activity of flucytosine. [ citation needed ]


Symptoms and their severities are unknown, because flucytosine is used under close medical supervision, but expected to be an excess of the usually encountered  side effects  on the  bone marrow , gastrointestinal tract,  liver  and  kidney  function. Vigorous hydration and  hemodialysis  may be helpful in removing the drug from the body. Hemodialysis is particular useful in patients with impaired renal function. [ citation needed ]


Two major mechanisms of action have been elucidated:


Flucytosine is active  in vitro  as well as  in vivo  against some strains of  Candida  and  Cryptococcus . Limited studies demonstrate that flucytosine may be of value against infections with  Sporothrix ,  Aspergillus ,  Cladosporium ,  Exophiala , and  Phialophora .
Resistance is quite commonly seen as well in treatment-naive patients and under current treatment with flucytosine. In different strains of  Candida  resistance has been noted to occur in 1 to 50% of all specimens obtained from patients. [ citation needed ]


Flucytosine is well absorbed (75 to 90%) from the  gastrointestinal tract . Intake with meals slows the absorption, but does not decrease the amount absorbed. Following an oral dose of 2 grams peak serum levels are reached after approximately 6 hours. The time to peak level decreases with continued therapy. After 4 days peak levels are measured after 2 hours. The drug is eliminated renally. In normal patients flucytosine has reportedly a half-life of 2.5 to 6 hours. In patients with impaired renal function higher serum levels are seen and the drug tends to accumulate. The drug is mainly excreted unchanged in the urine (90% of an oral dose) and only traces are metabolized and excreted in the feces. Therapeutic serum levels range from 25 to 100 μg/ml. Serum levels in excess of 100 μg are associated with a higher incidence of side effects. Periodic measurements of serum levels are recommended for all patients and are a must in patients with renal damage. [ citation needed ]


Although a generic, off patent medication in the U.S., as of January 2016, there was only one FDA-approved pharmaceutical supplier,  Valeant Pharmaceuticals . Due to this monopoly, the cost per 250 mg tablet was $70.46 per tablet for a daily treatment cost of ~$2110/day for a 75 kg adult (165 pounds) adult and $29,591 for a two-week treatment course as of December 2015. [ 7 ]   This cost of flucytosine is more than 100-fold higher in the U.S. than in the United Kingdom and Europe via  Meda AB  Pharmaceuticals.


In some countries, such as  Switzerland , flucytosine has been licensed to treat cats, dogs and birds (in most cases together with amphotericin B) for the same indications as in humans. [ citation needed ]


Fluorouracil  ( 5-FU ,  5-fluorouracil ), sold under the brand name  Adrucil  among others, is a  cytotoxic   chemotherapy  medication used to treat  cancer . [ 3 ]  By  intravenous injection  it is used for treatment of  colorectal cancer ,  oesophageal cancer ,  stomach cancer ,  pancreatic cancer ,  breast cancer , and  cervical cancer . [ 3 ]  As a cream it is used for  actinic keratosis ,  basal cell carcinoma , and skin  warts . [ 4 ] [ 5 ]


Side effects of use by injection are common. [ 3 ]  They may include inflammation of the mouth, loss of appetite,  low blood cell counts , hair loss, and inflammation of the skin. [ 3 ]  When used as a cream, irritation at the site of application usually occurs. [ 4 ]  Use of either form in  pregnancy  may harm the fetus. [ 3 ]  Fluorouracil is in the  antimetabolite  and  pyrimidine analog  families of medications. [ 6 ] [ 7 ]  How it works is not entirely clear, but it is believed to involve blocking the action of  thymidylate synthase  and thus stopping the production of  DNA . [ 3 ]


Fluorouracil was patented in 1956 and came into medical use in 1962. [ 8 ]  It is on the  World Health Organization's List of Essential Medicines . [ 9 ]  In 2022, it was the 270th most commonly prescribed medication in the United States, with more than 900,000 prescriptions. [ 10 ] [ 11 ]


Fluorouracil has been given systemically for  anal ,  breast ,  colorectal ,  oesophageal ,  stomach ,  pancreatic  and  skin cancers  (especially  head and neck cancers ). [ 12 ]  It has also been given topically (on the skin) for  actinic keratoses , skin cancers and  Bowen's disease [ 12 ]  (a type of  cutaneous squamous-cell carcinoma ), and as eye drops for treatment of  ocular surface squamous neoplasia . [ 13 ]  Other uses include ocular injections into a previously created  trabeculectomy   bleb  to inhibit healing and cause scarring of tissue, thus allowing adequate  aqueous humor  flow to reduce intraocular pressure.


Fluorouracil is contraindicated in patients who are severely debilitated and in patients with  bone marrow suppression  due to either radiotherapy or chemotherapy. [ 14 ]  It is likewise contraindicated in pregnant or breastfeeding women. [ 14 ]


Non-topical use, i.e.  administration by injection, should be avoided in patients who do not have malignant illnesses. [ 14 ]


in 2020, the EU and UK license was updated to state that fluorouracil was contra-indicated in patients that "have a known complete absence of dihydropyrimidine dehydrogenase (DPD) activity" [ 15 ] .  In US, as of 2024, there is no specific contraindication on the package inserts however, there is a cautionary warning: "Increased risk of serious or fatal adverse reactions in patients with low or absent Dipyrimidine Dehydrogenase activity: withhold or permanently discontinue fluorouracil in patients with evidence of acute early-onset or unusually severe toxicity, which may indicate near complete or total absence of dipyrimidine dehydrogenase (DPD) activity.


No fluorouracil dose has been proven safe in patients with absent DPD activity" [ 16 ]


Within the UK, DPYD testing to check for this contraindication is now routine practice [ 17 ] , this is not the case in the US [ 18 ] .


Adverse effects by frequency include: [ 12 ] [ 14 ] [ 19 ] [ 20 ] [ 21 ]


Common (> 1% frequency):


Uncommon (0.1–1% frequency):


Rare (< 0.1% frequency):


Diarrhea is severe and may be dose-limiting and is exacerbated by co-treatment with  calcium folinate . [ 12 ]   Neutropenia  tends to peak about 9–14 days after beginning treatment. [ 12 ]   Thrombocytopenia  tends to peak about 7–17 days after the beginning of treatment and tends to recover about 10 days after its peak. [ 12 ]   Cardiotoxicity  is a fairly common side effect, usually manifesting as  angina  or symptoms associated with  coronary artery spasm , but about 0.55% of those receiving the drug will develop life-threatening cardiotoxicity. [ 25 ]  Life-threatening cardiotoxicity includes:  arrhythmias ,  ventricular tachycardia  and  cardiac arrest , secondary to transmural ischaemia. [ 25 ]


Common (> 1% frequency): [ 12 ] [ 26 ]


The United States package insert warns that acute cerebellar syndrome has been observed following injection of fluorouracil and may persist after cessation of treatment. Symptoms include  ataxia ,  nystagmus , and  dysmetria . [ 27 ]


There is very little difference between the minimum effective dose and maximum tolerated dose of 5-FU, and the drug exhibits marked individual pharmacokinetic variability. [ 28 ] [ 29 ] [ 30 ]  Therefore, an identical dose of 5-FU may result in a therapeutic response with acceptable toxicity in some patients and unacceptable and possibly life-threatening toxicity in others. [ 28 ]  Both overdosing and underdosing are of concern with 5-FU, although several studies have shown that the majority of colorectal cancer patients treated with 5-FU are underdosed based on today's dosing standard, body surface area (BSA). [ 31 ] [ 32 ] [ 33 ] [ 34 ]  The limitations of BSA-based dosing prevent oncologists from being able to accurately titer the dosage of 5-FU for the majority of individual patients, which results in sub-optimal treatment efficacy or excessive toxicity. [ 31 ] [ 32 ]


Numerous studies have found significant relationships between concentrations of 5-FU in blood plasma and both desirable or undesirable effects on patients. [ 35 ] [ 36 ]  Studies have also shown that dosing based on the concentration of 5-FU in plasma can greatly increase desirable outcomes while minimizing negative side effects of 5-FU therapy. [ 31 ] [ 37 ]  One such test that has been shown to successfully monitor 5-FU plasma levels and which "may contribute to improved efficacy and safety of commonly used 5-FU-based chemotherapies" is the My5-FU test. [ 33 ] [ 38 ] [ 39 ]


Uridine Triacetate  is a potential antidote for cases of suspected overdose. [ 40 ]


The  US Food and Drug Administration  has highlighted the dangers of inadvertent administration to pets. [ 41 ]  While fluorouracil is sometimes used off label to treat horses, its administration to dogs in particular can be fatal.


The FDA reports that it has received 20 reports of fatal outcomes in dogs following accidental ingestion of topical  fluorouracil. [ 42 ]


It may increase the INR and prothrombin times in people on  warfarin . [ 14 ]  Fluorouracil's efficacy is decreased when used alongside  allopurinol , which can be used to decrease fluorouracil induced stomatitis through use of allopurinol mouthwash. [ 43 ]


The  dihydropyrimidine dehydrogenase  (DPD) enzyme is responsible for the detoxifying metabolism of fluoropyrimidines, a class of drugs that includes 5-fluorouracil,  capecitabine , and  tegafur . [ 44 ]   Genetic variations  within the DPD gene ( DPYD ) can lead to reduced or absent DPD activity, and individuals who are  heterozygous  or  homozygous  for these variations may have partial or complete  DPD deficiency ; an estimated 0.2% of individuals have complete  DPD deficiency . [ 44 ] [ 45 ]  Those with partial or complete DPD deficiency have a significantly increased risk of severe or even fatal drug toxicities when treated with fluoropyrimidines; examples of toxicities include  myelosuppression ,  neurotoxicity  and  hand-foot syndrome . [ 44 ] [ 45 ]


5-FU acts in several ways, but principally as a  thymidylate synthase (TS) inhibitor . Interrupting the action of this enzyme blocks synthesis of the pyrimidine  thymidylate (dTMP) , which is a  nucleotide  required for  DNA replication .  Thymidylate synthase  methylates deoxyuridine monophosphate (dUMP) to form  thymidine monophosphate  (dTMP). Administration of 5-FU causes a scarcity in dTMP, so rapidly dividing cancerous cells undergo cell death via  thymineless death . [ 46 ]  Calcium folinate provides an exogenous source of reduced folinates and hence stabilises the 5-FU-TS complex, hence enhancing 5-FU's cytotoxicity. [ 47 ]


In 1954, Abraham Cantarow and Karl Paschkis found liver tumors absorbed radioactive  uracil  more readily than did normal liver cells.  Charles Heidelberger , who had earlier found that fluorine in  fluoroacetic acid  inhibited a vital enzyme, asked Robert Duschinsky and Robert Schnitzer at  Hoffmann-La Roche  to synthesize fluorouracil. [ 48 ]  Some credit Heidelberger and Duschinsky with the discovery that 5-fluorouracil markedly inhibited tumors in mice. [ 49 ]  The original 1957 report [ 50 ] [ 51 ]
In 1958, Anthony R. Curreri,  Fred J. Ansfield , Forde A. McIver, Harry A. Waisman, and Charles Heidelberger reported the first clinical findings of 5-FU's activity in cancer in humans. [ 52 ]


In 2003, scientists isolated 5-fluorouracil derivatives, closely related compounds, from the marine sponge,  Phakellia  fusca , collected around  Yongxing Island  of the  Xisha Islands  in the  South China Sea . This is significant because fluorine-containing  natural products  are extremely rare. [ 53 ]


The name "fluorouracil" is the  INN ,  USAN ,  USP  name, and  BAN . The form "5-fluorouracil" is often used; it shows that there is a fluorine atom on the 5th carbon of a  uracil  ring.


Guanine  ( / ˈ ɡ w ɑː n iː n /   ⓘ ) ( symbol   G  or  Gua ) is one of the four main  nucleotide bases  found in the  nucleic acids   DNA  and  RNA , the others being  adenine ,  cytosine , and  thymine  ( uracil  in RNA). In  DNA , guanine is paired with cytosine. The guanine  nucleoside  is called  guanosine .


With the formula C 5 H 5 N 5 O, guanine is a derivative of  purine , consisting of a fused  pyrimidine - imidazole  ring system with conjugated double bonds. This unsaturated arrangement means the  bicyclic molecule  is planar.


Guanine, along with adenine and cytosine, is present in both DNA and RNA, whereas thymine is usually seen only in DNA, and uracil only in RNA. Guanine has two  tautomeric  forms,  the major keto form (see figures) and rare enol form . [ citation needed ]


It binds to cytosine through three  hydrogen bonds . In cytosine, the amino group acts as the hydrogen bond donor and the C-2 carbonyl and the N-3 amine as the hydrogen-bond acceptors. Guanine has the C-6 carbonyl group that acts as the hydrogen bond acceptor, while a group at N-1 and the amino group at C-2 act as the hydrogen bond donors. [ citation needed ]


Guanine can be  hydrolyzed  with strong acid to  glycine ,  ammonia ,  carbon dioxide , and  carbon monoxide . First, guanine gets  deaminated  to become  xanthine . [ 2 ]  Guanine oxidizes more readily than adenine, the other purine-derivative base in DNA. Its high melting point of 350 °C reflects the intermolecular hydrogen bonding between the oxo and amino groups in the molecules in the crystal. Because of this intermolecular bonding, guanine is relatively insoluble in water, but it is soluble in dilute acids and bases.


The first isolation of guanine was reported in 1844 by the German chemist  Julius Bodo Unger  [ de ]  (1819–1885), who obtained it as a mineral formed from the excreta of sea birds, which is known as  guano  and which was used as a source of fertilizer; guanine was named in 1846. [ 3 ]  Between 1882 and 1906,  Emil Fischer  determined the structure and also showed that  uric acid  can be converted to guanine. [ 4 ]


Trace amounts of guanine form by the  polymerization  of  ammonium cyanide  ( NH 4 CN ). Two experiments conducted by Levy et al. showed that heating 10 mol·L −1   NH 4 CN  at 80 °C for 24 hours gave a yield of 0.0007%, while using 0.1 mol·L −1   NH 4 CN  frozen at −20 °C for 25 years gave a 0.0035% yield. These results indicate guanine could arise in frozen regions of the primitive earth. In 1984, Yuasa reported a 0.00017% yield of guanine after the electrical discharge of  NH 3 ,  CH 4 ,  C 2 H 6 , and 50 mL of water, followed by a subsequent acid hydrolysis. However, it is unknown whether the presence of guanine was not simply a resultant contaminant of the reaction. [ 5 ]


A  Fischer–Tropsch  synthesis can also be used to form guanine, along with  adenine ,  uracil , and  thymine . Heating an equimolar gas mixture of CO, H 2 , and NH 3  to 700 °C for 15 to 24 minutes, followed by quick cooling and then sustained reheating to 100 to 200 °C for 16 to 44 hours with an alumina catalyst, yielded guanine and uracil:


Another possible abiotic route was explored by quenching a 90% N 2 –10%CO–H 2 O gas mixture high-temperature plasma. [ 6 ]


Traube's synthesis  involves heating 2,4,5-triamino-1,6-dihydro-6-oxypyrimidine (as the sulfate) with  formic acid  for several hours.


Guanine is not synthesized  de novo [ clarification needed ] , instead it's split from the more complex molecule,  guanosine , by the enzyme  guanosine phosphorylase :


Guanine can be synthesized de novo, with the rate-limiting enzyme of  inosine monophosphate dehydrogenase .


The word guanine derives from the Spanish loanword  guano  ('bird/bat droppings'), which itself is from the  Quechua  word  wanu , meaning 'dung'. As the  Oxford English Dictionary  notes, guanine is "A white amorphous substance obtained abundantly from guano, forming a constituent of the excrement of birds". [ 7 ]


In 1656 in Paris, a Mr. Jaquin extracted from the scales of the fish  Alburnus alburnus  so-called "pearl essence", [ 8 ]  which is crystalline guanine. [ 9 ]  In the cosmetics industry, crystalline guanine is used as an additive to various products (e.g., shampoos), where it provides a pearly  iridescent  effect. It is also used in metallic paints and simulated pearls and plastics. It provides shimmering luster to eye shadow and  nail polish . Facial treatments using the droppings, or guano, from Japanese nightingales have been used in Japan and elsewhere, because the guanine in the  droppings  makes the skin look paler. [ 10 ]  Guanine crystals are rhombic platelets composed of multiple transparent layers, but they have a high index of refraction that partially reflects and transmits light from layer to layer, thus producing a pearly luster. It can be applied by spray, painting, or dipping. It may irritate the eyes. Its alternatives are  mica , faux pearl (from ground shells), [ 11 ]  and  aluminium  and  bronze  particles.


Guanine has a very wide variety of biological uses that include a range of functions ranging in both complexity and versatility. These include camouflage, display, and vision among other purposes. [ 12 ]


Spiders, scorpions, and some amphibians convert ammonia, as a product of protein metabolism in the cells, to guanine, as it can be excreted with minimal water loss. [ 12 ]


Guanine is also found in specialized skin cells of fish called  iridocytes  (e.g., the  sturgeon ), [ 13 ] [ 12 ]  as well as being present in the reflective deposits of the eyes of  deep-sea fish  and some  reptiles , such as  crocodiles  and  chameleons . [ 13 ]


On 8 August 2011, a report, based on  NASA  studies with  meteorites  found on Earth, was published suggesting building blocks of DNA and RNA (guanine,  adenine  and related  organic molecules ) may have been formed extra-terrestrially in outer space. [ 14 ] [ 15 ] [ 16 ]


5-Hydroxycytosine  is an oxidized form of  cytosine  that is associated with an increased frequency of C to T transition mutations, with some C to G transversions. [ 1 ]  It does not distort the DNA molecule and is readily bypassed by replicative  DNA polymerases . [ 2 ]


It has been shown in vitro to miscode for  adenine .


5-hydroxycytosine is imperative for parallel DNA triplex formation, explaining why parallel triplexes form only at pH 6 and below.


5-Formylcytosine  (5fC) is a  pyrimidine   nitrogen base  derived from  cytosine . In the context of nucleic acid chemistry and biology, it is regarded as an epigenetic marker. Discovered in 2011 in mammalian embryonic stem cells by  Thomas Carell 's research group [ 1 ]  the modified nucleoside was more recently confirmed to be relevant both as an intermediate in the active demethylation pathway and as a standalone epigenetic marker. [ 2 ]  In mammals, 5fC is formed by oxidation of  5-Hydroxymethylcytosine  (5hmC) a reaction mediated by  TET enzymes . [ 3 ]  Its molecular formula is C 5 H 5 N 3 O 2. [ 4 ]


Similarly to the related cytosine modifications  5-Methylcytosine  (5mC) and 5hmC, 5fC is broadly distributed across the mammalian genome, although it is much more rarely occurring. [ 5 ]  The specific concentration values vary significantly depending on the cell type. [ 6 ]  5fC can be aberrantly expressed in distinct sets of tissue that can indicate different tumor onsets and canceration. [ 7 ]


The exact functions of 5fC have not been yet precisely defined, although it is likely to play key roles in at least two distinct frameworks. Firstly, 5fC serves as an intermediate of the active  demethylation  pathway, a process that contributes to the DNA maintenance and integrity by replacing 5mC with canonical cytosine. A central dilemma regarding 5fC (and epigenetics in general) is how reader proteins recognise their substrates with such high specificity over the overwhelming background.  Thymine-DNA glycosylase  (TDG), a protein which is involved in the removal of 5fC from DNA in mammals, is especially interesting in this context. [ 8 ]  Secondly, 5fC can exist as an independent, stable modification, but its role in this context is still blurry.  [ 2 ]


The understanding of the impact of 5fC on DNA physical properties is to date limited. Recent studies have reported contradictory findings regarding the structural impact of 5fC on DNA. [ 9 ] [ 10 ]  On the other hand, several researchers working independently have identified 5fC to distinctly increase DNA flexibility. [ 11 ] [ 12 ]  5fC also curtails DNA double helix stability and increases base pair opening. [ 13 ]


5-Hydroxymethylcytosine  (5hmC) is a  DNA   pyrimidine   nitrogen base  derived from  cytosine . It is potentially important in  epigenetics , because the hydroxymethyl group on the cytosine can possibly switch a gene on and off. It was first seen in  bacteriophages  in 1952. [ 1 ] [ 2 ]  However, in 2009 it was found to be abundant in  human  and  mouse  brains, [ 3 ]  as well as in  embryonic stem cells . [ 4 ]  In mammals, it can be generated by oxidation of  5-methylcytosine , a reaction mediated by  TET enzymes .


Every mammalian cell seems to contain 5-Hydroxymethylcytosine, but the levels vary significantly depending on the cell type. The highest levels are found in neuronal cells of the  central nervous system . [ 5 ] [ 6 ] [ 7 ]  The amount of hydroxymethylcytosine increases with age, as shown in mouse  hippocampus  and  cerebellum . [ 5 ] [ 8 ]


The exact function of this nitrogen base is still not fully elucidated, but it is thought that it may regulate  gene  expression or prompt  DNA demethylation . This hypothesis is supported by the fact that artificial DNA that contains 5-hydroxymethylcytosines (5hmC) can be converted into unmodified cytosines once introduced into mammalian cells. [ 9 ]  Moreover, 5hmC is highly enriched  in  primordial germ cells , where it apparently plays a role in global DNA demethylation. [ 10 ]  Additionally, 5-Formylcytosine, an oxidation product of 5-Hydroxymethylcytosine and possible intermediate of an oxidative demethylation pathway was detected in DNA from embryonic stem cells, [ 11 ]  although no significant amounts of these putative demethylation intermediates could be detected in mouse tissue. [ 7 ]  5-Hydroxymethylcytosine may be especially important in the  central nervous system , as it is found in very high levels there. [ 7 ]  Reduction in the 5-Hydroxymethylcytosine levels have been found associated with impaired self-renewal in embryonic stem cells. [ 12 ]  5-Hydroxymethylcytosine is also associated with labile, unstable nucleosomes which are frequently repositioned during cell differentiation. [ 13 ]


The accumulation of 5-hydroxymethylcytosine (5hmC) in post-mitotic  neurons  is associated with “functional demethylation” that facilitates  transcription  and  gene expression . [ 14 ]   The term “ demethylation ,” as applied to neurons, ordinarily refers to the replacement of  5-methylcytosine  (5mC) by  cytosine  in  DNA  that can occur through a series of reactions involving a  TET enzyme  as well as enzymes of the DNA  base excision repair  pathway (see  Epigenetics in learning and memory ).  “Demethylation” of 5mC in DNA most often results in the promotion of expression of genes with neuronal activities.   “Functional demethylation” refers to the replacement of 5mC by 5hmC, ordinarily a single-step TET-mediated reaction, that also facilitates gene expression, an effect similar to that of “demethylation.”


Phages probably evolved to use 5hmC to avoid recognition by most restriction enzymes in bacteria. The  T4 phage  uses 5hmC exclusively during replication, adding  glycosylation  to the hydroxyl group to further complicate the moiety. [ 15 ]  Some bacteria have in turn evolved  restriction enzymes  specific for sites containing 5hmC. One prominent example is PvuRts1I, originally identified in 1994. [ 16 ]


5hmC in T4 is produced by genome protein 42, deoxycytidylate 5-hydroxymethyltransferase ( P08773 ;  EC 2.1.2.8 ). The glycosylation reactions are known as  EC 2.4.1.26 ,  EC 2.4.1.27 , and  EC 2.4.1.28 .


5-Hydroxymethylcytosine was observed by Skirmantas Kriaucionis, an associate at the Heintz lab, who was looking for levels of  5-methylcytosine  in two different neuron types. He discovered a significant amount of an unknown substance instead, and after conducting several tests, identified it as being 5-hydroxymethylcytosine. [ 17 ]


The lab of L. Aravind used bioinformatic tools to predict that the Tet family of enzymes would likely oxidize 5-methylcytosine to 5-hydroxymethylcytosine. [ 18 ]  This was demonstrated  in vitro  and in live human and mouse cells by scientists working in the labs of Anjana Rao and  David R. Liu .


5-Hydroxymethylcytosine was originally observed in  mammals  in 1972 by R. Yura, [ 19 ]  but this initial finding is dubious. Yura found 5-hmC present at extremely high levels in rat brain and liver, completely supplanting 5-methylcytosine. This contradicts all research conducted on mammalian DNA composition conducted before and since, including the Heintz and Rao papers, and another group was unable to reproduce Yura's result. [ 20 ]


With the discovery of 5-hydroxymethylcytosine some concerns have been raised regarding DNA methylation studies using the bisulfite sequencing technique. [ 21 ]  5-hydroxymethylcytosine has been shown to behave like its precursor, 5-methylcytosine, in  bisulfite conversion  experiments. [ 22 ]  Therefore, bisulfite sequencing data may need to be revisited to verify whether the detected modified base is 5-methylcytosine or 5-hydroxymethylcytosine. In 2012 the lab of  Chuan He  discovered a method to solve the problems of 5-hydroxymethylcytosine being detected as 5-methylcytosine in normal bisulfite conversion experiments using the oxidative properties of the Tet-family of enzymes, this method has been termed  TAB-seq . [ 23 ] [ 24 ]


In June 2020, Oxford Nanopore added a hydroxymethyl cytosine detection model to their research basecaller, rerio, allowing old signal-level data from any R9+ nanopore runs to be re-called to identify 5hmC.  [ 25 ]


As of 2024, methods to characterize the presence of 5-hmC include: [ 26 ]


5-Hydroxyuracil  is an oxidized form of  cytosine  that is produced by the oxidative  deamination  of cytosines by  reactive oxygen species . [ 1 ]  It does not distort the DNA molecule and is bypassed by replicative  DNA polymerases . It can miscode for adenine and is potentially mutagenic. [ 2 ]


Hypoxanthine  is a naturally occurring  purine  derivative. It is occasionally found as a constituent of  nucleic acids , where it is present in the  anticodon  of  tRNA  in the form of its nucleoside  inosine . It has a  tautomer  known as 6-hydroxypurine. Hypoxanthine is a necessary additive in certain cells, bacteria, and parasite cultures as a substrate and nitrogen source. For example, [ 1 ] [ 2 ]  it is commonly a required  reagent  in  malaria parasite cultures , since  Plasmodium falciparum  requires a source of hypoxanthine for nucleic acid synthesis and energy metabolism.


In August 2011, a report, based on  NASA  studies with  meteorites  found on Earth, was published suggesting hypoxanthine and related  organic molecules , including the  DNA  and  RNA  components  adenine  and  guanine , may have been formed extraterrestrially in outer space. [ 3 ] [ 4 ] [ 5 ]


The  Pheretima aspergillum  worm, used in Chinese medicine preparations, contains hypoxanthine. [ 6 ]


It is one of the products of the action of  xanthine oxidase  on  xanthine .  However, more frequently in  purine degradation , xanthine is formed from oxidation of hypoxanthine by  xanthine oxidoreductase .


Hypoxanthine-guanine phosphoribosyltransferase  converts hypoxanthine into  IMP  in  nucleotide salvage .


Hypoxanthine is also a spontaneous  deamination  product of  adenine .  Because of its resemblance to  guanine , the spontaneous deamination of adenine can lead to an error in  DNA transcription /replication, as it base pairs with  cytosine . Hypoxanthine is removed from DNA by base excision repair, initiated by N-methylpurine glycosylase (MPG), also known as alkyl adenine glycosylase (Aag). [ 7 ]


Isocytosine  or  2-aminouracil  is a  pyrimidine  base that is an  isomer  of  cytosine .  It is used in combination with  isoguanine  in studies of unnatural  nucleic acid analogues  of the normal  base pairs  in  DNA . [ 1 ]  In particular, it is used as a  nucleobase  of  hachimoji RNA . [ 2 ]


It can be synthesized from  guanidine  and  malic acid . [ 3 ]


It is also used in physical chemical studies involving metal complex binding,  hydrogen bonding , and  tautomerism  and  proton transfer  effects in nucleobases. [ 4 ]


Isoguanine  or  2-hydroxyadenine  is a  purine  base that is an  isomer  of  guanine .  It is a product of oxidative damage to DNA and has been shown to cause mutation. [ 1 ]   It is also used in combination with  isocytosine  in studies of unnatural  nucleic acid analogues  of the normal  base pairs  in DNA. [ 2 ] [ 3 ]


It is used as a  nucleobase  of  hachimoji nucleic acids . [ 4 ]  In hachimoji DNA, it  pairs with   1-methylcytosine , while in hachimoji RNA, it pairs with isocytosine.


1-Methylcytosine  is a  methylated  form of the  DNA  base  cytosine .


In 1-methylcytosine, a  methyl group  is attached to the 1st atom in the 6-atom ring. This methyl group distinguishes 1-methylcytosine from cytosine.


Miriam Rossi  worked on the refinement of 1-methylcytosine. [ 1 ]


1-Methylcytosine is used as a  nucleobase  of  hachimoji DNA , in which it  pairs with   isoguanine . [ 2 ]


5-Methylcytosine  is a  methylated  form of the  DNA  base  cytosine  (C) that regulates gene  transcription  and takes several other biological roles. [ 1 ]  When cytosine is methylated, the DNA maintains the same sequence, but the  expression of methylated genes  can be altered (the study of this is part of the field of  epigenetics ). 5-Methylcytosine is incorporated in the  nucleoside   5-methylcytidine .


In 5-methylcytosine, a  methyl group  is attached to the 5th atom in the 6-atom ring, counting counterclockwise from the NH-bonded  nitrogen  at the six o'clock position. This methyl group distinguishes 5-methylcytosine from cytosine.


While trying to isolate the bacterial  toxin  responsible for  tuberculosis , W.G. Ruppel isolated a novel  nucleic acid  named  tuberculinic acid  in 1898 from  Tubercle bacillus . [ 2 ]  The nucleic acid was found to be unusual, in that it contained in addition to  thymine ,  guanine  and  cytosine , a methylated nucleotide. In 1925,  Johnson  and Coghill successfully detected a minor amount of a methylated cytosine derivative as a product of  hydrolysis  of tuberculinic acid with  sulfuric acid . [ 3 ] [ 4 ]  This report was severely criticized because their identification was based solely on the optical properties of the crystalline  picrate , and other scientists failed to reproduce the same result. [ 5 ]   But its existence was ultimately proven in 1948, when  Hotchkiss  separated the nucleic acids of  DNA  from  calf   thymus  using  paper chromatography , by which he detected a unique methylated cytosine, quite distinct from conventional cytosine and  uracil . [ 6 ]  After seven decades, it turned out that it is also a common feature in different  RNA  molecules, although the precise role is uncertain. [ 7 ]


The function of this chemical varies significantly among species: [ 8 ]