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Acronym

Acronym

Acronyms and initialisms are abbreviations such as NATO, laser, or DNA, written as the initial letter or letters of words, and pronounced based on this abbreviated written form. Of the two words, acronym is the much more frequently used and known, and many dictionaries, speakers and writers refer to all abbreviations formed from initial letters as acronyms. However, some still differentiate between acronyms and initialisms: an acronym was originally a pronounceable word formed from the initial letter or letters of the constituent words, such as NATO /neɪtoʊ/ or RADAR /reɪdɑɹ/, from RAdio Detection And Ranging, while an initialism referred to an abbreviation pronounced as the names of the individual letters, such as TLA /ti.ɛl.eɪ/ or XHTML.

History

Acronyms and initialisms are a relatively new linguistic phenomenon, having only become popular during the 20th century. As literacy rates rose, the practice of referring to words by their first letters became increasingly convenient. The first recorded use of the word initialism in the Oxford English Dictionary (OED) is in 1899, and the first for acronym is in 1943. The word acronym comes from Greek: ακρος, akros, "topmost, extreme" + ονομα, onoma, "name". Nonetheless, earlier examples of acronyms exist. The early Christians in Rome used a fish as a symbol for Jesus in part because of an acronym—fish in Greek is ΙΧΘΥΣ (ichthus), which was said to stand for Ιησους Χριστος Θεου Υιος Σωτηρ (Iesous CHristos THeou (h)Uios Soter: Jesus Christ, Son of God, Saviour). Evidence of this interpretation dates from the second and third centuries and is preserved in the catacombs of Rome. Initialisms are known to have been used in Rome dating back even earlier than the Christian era. For example, the official name for the Roman Empire (and the Republic before it) was abbreviated as SPQR (Senatus Populusque Romanus), showing a clear precedent. Acronyms have been widely used in Hebrew since at least the Middle Ages. Several important rabbis are referred to with acronyms of their names. For example, Baal Shem Tov is called Besht. The word Tanakh is also an acronym. Acronyms and initialisms often occur in jargon or as names of organizations because they often serve as abbreviations of long terms that are frequently referenced, so a shortened form is desirable. Militaries and government agencies frequently employ acronyms and initialisms, perhaps most famously the US Government and the so-called alphabet agencies of Franklin D. Roosevelt's New Deal. The correct meaning of an acronym is frequently domain-specific knowledge, and many acronyms have different meanings in different domains. This has led some to use them to obfuscate meaning from those without such domain-specific knowledge.

Written usage

Abbreviations have been traditionally written using a full stop/period to mark the part that was deleted. In the case of most acronyms and initialisms, each letter is its own abbreviation, and in theory should get its own full stop/period. This usage is becoming less common as the presence of all capital letters is sufficient to indicate the word is an abbreviation; nevertheless some influential American style guides still insist on the many-periods treatment, such as the one used by The New York Times (which recommends periods after unpronounceable abbreviations such as "K.G.B." but not for pronounceable ones (acronyms), such as "NATO" [http://www.nytimes.com/2004/02/07/opinion/07KRIS.html?ex=1391490000&en=f887afd296d59e2f&ei=5007&partner=GOOGLE]), but other style guides, such as that of the BBC, no longer require this. Larry Trask, American author of the Penguin Guide to Punctuation, states categorically that, in British English, "this tiresome and unnecessary practice is now obsolete"[http://www.informatics.susx.ac.uk/doc/punctuation/node28.html]. Some acronyms undergo assimilation into ordinary words, when technical terms become commonplace with non-technical people: often they are then written in lower case, and eventually it is widely forgotten that the word was derived from the initials of others: scuba (Self-Contained Underwater Breathing Apparatus) and laser (Light Amplification by Stimulated Emission of Radiation), for instance. The term anacronym has been coined as a portmanteau of the words anachronism and acronym to describe acronyms whose original meaning is not known to most speakers. While typically abbreviations exclude the initials of short function words (such as "and", "or", "of", or "to"), they are sometimes included in acronyms to make them pronounceable. Numbers (both cardinal and ordinal) in names are often represented by digits rather than initial letters; e.g. 4GL (Fourth generation language) or G77 (Group of 77). The traditional style of pluralizing single letters with "'s" ("there are two Q's in that word") was naturally extended to acronyms when they were commonly written with periods, and is still preferred by some people for initialisms. It is, however, very common to inflect them like ordinary words; thus the usual plural of "CD" is "CDs," with "CD's" being reserved for the possessive. When an acronym is part of a computer function that is conventionally written in lowercase letters, it is common to use an apostrophe to pluralize or otherwise conjugate the token (in computer lingo, it is not uncommon to use the name of a computer program, format, or function, acronym or no, as a verb, e.g., "John zipped the files" or "John zip'ed the files" means that John used the program zip on the files to conglomerate them), resulting in sentences like "be sure to remove any extraneous dll's after the program finishes uninstalling." In some languages, the convention of doubling the letters in the initialism is used to indicate plural words, for example the Spanish acronym EE.UU. for Estados Unidos ("United States"). This convention is followed for a limited number of English abbreviations, such as pp. for "pages". In some cases, an acronym or initialism has been turned into a name. The letters making up the name of the SAT college entrance test, for example, no longer officially stand for anything. This trend has been common with many companies hoping to retain their brand recognition while simultaneously moving away from what they saw as an outdated image: American Telephone and Telegraph is now simply AT&T, the company formerly named Kentucky Fried Chicken changed its name to "KFC". British Petroleum changed its name to "BP" to emphasize that it was no longer only an oil company (captured by the motto "beyond petroleum"); and Silicon Graphics, Incorporated changed its name to "SGI" to emphasize that it was no longer only a computer graphics company. DVD, curiously enough, has become bereft of official meaning, as some of its advocates decided the original "Digital Video Disc" moniker was too limiting and wanted to change it to "Digital Versatile Disc" yet were unable to bring all members on board. The initialism now has "no official meaning." Initialisms may have advantages in international markets; for example, some national affiliates of International Business Machines are legally incorporated as "IBM" (or, for example, "IBM Canada") to avoid translating the full name into local languages. This rebranding can lead to RAS syndrome, as when Trustee Savings Bank became "TSB Bank." A few high tech companies have taken the redundant acronym to the extreme such as ISM Information Systems Management Corp. and SHL Systemhouse Ltd.. Another very common example is RAM memory. This is redundant since RAM already stands for Random Access Memory. Sometimes, the initials are kept but the meaning is changed. SADD, for instance, originally Students Against Driving Drunk, changed the full form of its name to Students Against Destructive Decisions. YM originally stood for Young Miss, and later Young & Modern, but now stands for simply Your Magazine. When initialisms are defined in print, especially in the case of industry-specific jargon, the words forming the abbreviation are often capitalized for clarity. While this would be perfectly acceptable for proper nouns like Kentucky Fried Chicken, some usage writers have argued that it is technically incorrect for other terms like storage area network. Correct or not, such usage is widespread in English publications.

Nomenclature

Initialism originally referred to abbreviations formed from initials, without reference to pronunciation, but during the middle portion of the twentieth century, when acronyms and initialisms saw more use than ever before, the word acronym was coined for abbreviations which are pronounced as a word, like "NATO" or "AIDS". The term initialism is now typically taken to refer to abbreviations which are pronounced by sounding out the name of each constituent letter (e.g. HTML). In general usage, the term acronym is commonly used to describe all abbreviations made from initial letters, regardless of pronunciation. Many writers and speakers do not observe any difference between acronyms and initialisms. There is no agreement as to what to call abbreviations that contain single letters, but can otherwise be pronounced as a word, such as JPEG (Jay-Peg). These abbreviations are sometimes referred to as acronym-initialism hybrids, although they are grouped by most under the broad meaning of acronym.

Examples

- pronounced as a word, containing only initial letters:
- NATO: North Atlantic Treaty Organisation
- FIFA: Fédération Internationale de Football Association
- laser: light amplification by stimulated emission of radiation
- scuba: self-contained underwater breathing apparatus
- RAM: random access memory
- pronounced as a word, containing non-initial letters:
- Interpol: International Criminal Police Organization
- Gestapo: Geheime Staatspolizei ("secret state police")
- radar: radio detection and ranging
- CONMEBOL: Confederación Sudamericana de Fútbol (South American Football Confederation)
- pronounced as a word or names of letters, depending on speaker or context:
- FAQ: (fack or ef-ay-kyu) Frequently asked questions
- SQL: (sequel or es-kyu-el) Structured Query Language
- VAT: (vat or vee-ay-tee): Value added tax
- IRA: (ira or eye-are-ay): When used for Irish Republican Army, always pronounced as letters; when used for Individual Retirement Account, can be pronounced as letters or as a word.
- pronounced as a combination of names of letters and a word:
- OPEC: (OH-pec) Organization of Petroleum Exporting Countries
- JPEG: (JAY-peg) Joint Photographic Experts Group
- IUPAC: (AYE-YOU-pac) International Union of Pure and Applied Chemistry
- UEFA: (You-EE-fa or You-AY-fa) Union of European Football Associations
- CPU: (cee-pee-you) central processment unit
- pronounced only as the names of letters
- BBC: British Broadcasting Corporation
- DNA: DeoxyriboNucleic Acid
- DNS: Domain Name System
- ICBM: Intercontinental Ballistic Missiles
- pronounced as the names of letters that also sound like words
- YRUU: (WHY-are-YOU-YOU?) Young Religious Unitarian Universalists
- pronounced as the names of letters but with a shortcut
- AAA: (triple-AY) American Automobile Association
- IEEE: (AYE-triple-EE) Institute of Electrical and Electronics Engineers
- NAACP: (EN-double-AY-SEE-PEA) National Association for the Advancement of Colored People
- NCAA: (EN-SEE-double-AY) National Collegiate Athletic Association
- shortcut incorporated into name
- 3M: originally Minnesota Mining and Manufacturing Company
- W3C: World Wide Web Consortium
- E³: Electronic Entertainment Exposition
- recursive acronyms, where the acronym itself is the expansion of one initial
- VISA: VISA International Service Association
- GNU: GNU's Not Unix
- WINE: Wine Is Not an Emulator
- GOD GOD Over Djinn, from Douglas Hofstadter's Godel, Escher, Bach

Trivia

The longest acronym, according to the 1965 edition of Acronyms, Initialisms and Abbreviations Dictionary, is ADCOMSUBORDCOMPHIBSPAC, a United States Navy term that stands for "Administrative Command, Amphibious Forces, Pacific Fleet Subordinate Command." The world's longest initialism, according to the Guinness Book of World Records is NIIOMTPLABOPARMBETZHELBETRABSBOMONIMONKONOTDTEKHSTROMONT. The 56-letter initialism (54 in Cyrillic) is from the Concise Dictionary of Soviet Terminology and means "The laboratory for shuttering, reinforcement, concrete and ferroconcrete operations for composite-monolithic and monolithic constructions of the Department of the Technology of Building-assembly operations of the Scientific Research Institute of the Organization for building mechanization and technical aid of the Academy of Building and Architecture of the USSR." Sometimes an acronym's official meaning is crafted to fit an acronym that actually means something that sounds less "official." For instance, the Massive Ordnance Air Blast (MOAB) weapon recently developed in the United States is popularly called the "mother of all bombs" since it is the largest conventional bomb in the world; it is widely assumed that the "mother of all wars" phrase was the true inspiration for the MOAB acronym. During the 1960s trend for action-adventure spy thrillers, it was a common practice for fictional spy organizations or their nemeses to employ names that were acronyms (or more accurately, backronyms). Sometimes these acronyms made sense but most of the time, they were words incongruously crammed together for the mere purpose of obtaining a catchy acronym, traditionally a heroic sounding one for the good guys and an appropriately menacing one for the bad guys. This has become one of the most commonly parodied clichés of the spy thriller genre. Some of the most popular were:
- C.O.N.T.R.O.L. and K.A.O.S. from the Get Smart series.
- F.I.R.M. from the 1980s TV series Airwolf
- M.A.S.K.: The Mobile Armored Strike Kommand, the mask-wearing cohort from 1980s saturday morning cartoon M.A.S.K.
- V.E.N.O.M. : The Vicious, Evil Network Of Mayhem, the evil mask-wearing cohort from 1980s saturday morning cartoon M.A.S.K.
- H.A.R.M. from the No One Lives Forever (NOLF) series of computer games, which were released in the 1990s, but were based in 1960s pop culture. What H.A.R.M actually stands for is never revealed, and speculation about its true meaning is the subject of several jokes in both games. (However, in the 1966 spy film Agent for H.A.R.M., it stands for Human Aetiological Relations Machine.)
- S.H.I.E.L.D. from the Nick Fury, Agent of S.H.I.E.L.D. Marvel comics.
- S.P.E.C.T.R.E. from the James Bond series.
- U.N.C.L.E. and T.H.R.U.S.H from The Man from U.N.C.L.E. (The meaning of T.H.R.U.S.H. was never revealed on the series, but in the novelizations, T.H.R.U.S.H. was stated to be "Technological Hierarchy for the Removal of Undesirables and the Subjugation of Humanity.)
- P.A.G.A.N. (People Against Goodness and Normalcy) from the film Dragnet.

External links

- [http://www.initialisms.com initialisms.com]— Acronyms, Abbreviations & Initialisms Directory
- [http://www.noslang.com Online Acronym Dictionary & Translator]— Lookup or translate slang and acronyms
- [http://www.acronymfinder.com Acronym Finder]— searchable database of acronyms and abbreviations (over 400,000 entries)
- [http://www.acronymsearch.com Acronym Search]—searchable acronyms and abbreviation database (over 50,000 entries)
- [http://lethargy.swmed.edu/argh/ARGH.asp Biomedical Acronym Database]
- [http://coombs.anu.edu.au/WWWVLPages/AsianPages/Acronyms.html Acronyms Used by Asian Studies' Scholars: a Dictionary]
- [http://www.siglas.com.br English and Portuguese acronyms searchable database (over 200,000 entries)] Category:Abbreviations Category:Types of words ko:두문자어 ja:頭字語 simple:Acronym

Abbreviation

Abbreviation (from Latin brevis "short") is strictly a shorter form of a word, but more particularly, an abbreviation is a letter or group of letters, taken from a word or words, and employed to represent them for the sake of brevity. For example, the word "abbreviation" can be abbreviated as "abbr." or "abbrev."

Types of abbreviations

Apart from the common form of shortening one word, there are other types of abbreviations. These include apocopations, syllabic abbreviations, acronyms, initialisms and portmanteaux.

Syllabic abbreviations (SAs)

A syllabic abbreviation is an abbreviation formed from (usually) initial syllables of several words, such as Interpol = International + police. Syllabic abbreviations are usually written using lower case, sometimes starting with a capital letter, and are always pronounced as words rather than letter by letter. Syllabic abbreviations should be distinguished from portmanteaus.

Usage of syllabic abbreviations in different languages

Syllabic abbreviations are not widely used in English or French. On the other hand, they prevailed in Germany under the Nazis and in the Soviet Union for naming the plethora of new bureaucratic organizations. For example, Gestapo stands for Geheime Staats-Polizei, or "secret state police". Similarly, Comintern stands for the Communist International. This has caused syllabic abbreviations to have negative connotation, notwithstanding that such abbreviations were used in Germany even before the Nazis came to power, e.g., Schupo for Schutzpolizei. Syllabic abbreviations were also typical for the German language used in the German Democratic Republic, e.g. Stasi for Staatssicherheit ("state security", the secret police) or Vopo for Volkspolizist ("people's policeman"). East Asian languages whose writing uses Chinese-originated ideograms instead of an alphabet form abbreviations similarly by using key characters from a term or phrase. For example, in Japanese the term for the United Nations, kokusai rengō (国際連合) is often abbreviated to kokuren (国連). (Such abbreviations are called ryakugo (略語) in Japanese). The classic example is, of course, shogun. The syllabic abbreviation is frequently used for universities: for instance, Beida (北大, Běidà) for Peking University (Beijing) and Tōdai (東大) for the University of Tokyo.
Usage of syllabic abbreviations in organisations
Syllabic abbreviations are prefered by the US Navy as it increases readability amidst the large number of initialisms that would otherwise have to fit into the same acronyms. Hence DESRON 6 is used (in the full capital form) to mean "Destroyer Squadron 6," while COMNAVFORLANT would be "Commander, Naval Force (in the) Atlantic."
Style conventions
In modern English there are several conventions for abbreviations and the choice may be confusing. The only rule universally accepted is that one should be consistent, and to this end publishers express their preferences in a style guide. Questions which arise include the following:
- Use of upper or lower case letters. If the original word was capitalised, then the first letter of its abbreviation should retain the capital, for example Lev. for Leviticus. When abbreviating words spelt with lower case letters, there is no consistent rule.
- Use of periods (full stops) and spaces, for example when abbreviating United States, should one write "US", "U.S." or "U. S."? Spaces are generally not used between single letter abbreviations of words in the same phrase, so one almost never encounters "U. S.". In American English, the period is usually added if the abbreviation may be interpreted as a word, though some American writers do not use a period here. There is no stop/period between letters of the same word, for example St. and not S.t. for Saint. In modern British English abbreviations are written with full stops if the word has been cut at the point of abbreviation (e.g., "Street" – "St[reet]" – becomes "St."), but not otherwise (e.g., "Saint" – "S[ain]t" – becomes "St"). Thus in the United Kingdom, titles such as "Doctor", "Mister" and "Mistress" are abbreviated as "Dr", "Mr", and "Mrs" respectively, but in Canada and the U.S. as "Dr.", "Mr." and "Mrs." respectively.
- Acronyms that were originally capitalized (with or without periods) but have since "stood the test of time" by entering the vocabulary as generic words are no longer abbreviated with capital letters nor with any periods—e.g., sonar, radar, laser, and scuba.
- Whether to add an apostrophe for a plural where the plural is not formed by doubling up the last letter: should one write CDs or CD's? The apostrophe is not needed grammatically but sometimes is added to make it clear that the s is not part of the abbreviation. Because the apostrophe most often represents possession or a contraction, some style guides prefer that it not be used at all with abbreviations, but only with individual letters—"Dot all your i's and cross all your t's!" or "Mind your p's and q's!"—or numbers—"The dyslexic student mixes up his S's and 5's." Thus numbers, such as decades, that are understood to represent other concepts, are not written with apostrophes either—e.g., "The U.S. enjoyed an economic boom in the 1990s and the Roaring ’20s", referring to decades, or "I am going to the bank to exchange four 5's for two 10's", where the 5's and 10's refer to banknotes. Conventions followed by publications and newspapers:
- Publications based in the United States tend to follow the style guides of the Chicago Manual of Style and the Associated Press. The U.S. Government follows a style guide published by the U.S. Government Printing Office.
- There is some inconsistency in abbreviation styles, however, as they are not rigorously defined by style guides. Some two-word abbreviations, like "United Nations", are abbreviated with uppercase letters and periods, and others, like "personal computer" (PC) and "compact disc" (CD), are not; rather, they are typically abbreviated without periods and in uppercase letters. A third variation is to use lowercase letters with periods; this is used by Time Magazine in abbreviating "public relations" (p.r.). Moreover, even three-word abbreviations (most U.S. publications use uppercase abbreviations without periods) are sometimes not consistently abbreviated, even within the same article.
- The New York Times is unique in having a consistent style by always abbreviating with periods: P.C., I.B.M., P.R. This is in contrast with the trend of British publications to completely make do without periods for convenience.
- Many British publications follow some of these guidelines in abbreviation:
- For the sake of convenience, many British publications, including the BBC and The Guardian, have completely done away with the use of full stops or periods in all abbreviations. These include:
- Social titles, like Ms or Mr (though these would not have had full stops in any case — see above) Capt, Prof, etc.;
- Two-letter abbreviations for countries (US, not U.S.);
- Words are seldom abbreviated with lower case letters (PR, instead of p.r., or pr)
- Abbreviations beyond three letters (full caps for all except initialisms);
- Names (e.g., FW de Klerk, GB Whiteley, Park JS). A notable exception is the Economist (e.g., Mr F. W. de Klerk)
- Scientific units.
- Acronyms are referred to with only the first letter of the abbreviation capitalised. For instance, the North Atlantic Treaty Organisation can be abbreviated as Nato, and Severe Acute Respiratory Syndrome as Sars. Initialisms (which are similar to acronyms but which are not pronounced as words) are always written in capitals, for instance the British Broadcasting Corporation is abbreviated to BBC, never Bbc.
- When abbreviating scientific units, no space is added between the number and unit (e.g., 100mph, 100m, 10cm, 10ºC). Miscellaneous and general rules
- Plurals are often formed by doubling up the last letter of the abbreviation. Most of these deal with writing and publishing: MS=manuscript, MSS=manuscripts; l=line, ll=lines; p=page, pp=pages; s=section, ss=sections). This form, derived from Latin is used in Europe in many places: dd=didots. "The following (lines or pages)" is denoted by ff. One example that does not concern printing is hh=hands.
- A doubled letter also appears in abbreviations of some Welsh names, as in Welsh the double "l" is a separate sound: "Ll. George" for (late British prime minister) Lloyd George.
- Some titles, such as "Reverend" and "Honourable", are spelt out when preceded by "the", rather than as "Rev." or "Hon." respectively. This is true for most British publications, and some in the United States.
- It is usually advised to spell out the abbreviation where it is new or unfamiliar to the reader (e.g., UNESCO in a magazine about music, because it more frequently refers to another entity in another context, the United Nations Educational, Scientific and Cultural Organization).
History
After World War II, the British greatly reduced their use of the full stop and other punctuations after abbreviations in at least semi-formal writing, while the Americans more readily kept its use until more recently, and still maintain it more than Britons. The classic example, considered by their American counterparts quite curious, was the maintenance of the internal comma in a British organization of secret agents called the "Special Operations, Executive" – "S.O.,E." – which is not found in histories written after about 1960. But before that, many Britons were more scrupulous at maintaining the French form. In French, the period only follows an abbreviation if the last letter in the abbreviation is not the last letter of its antecedent: "M." is the abbreviation for "monsieur" while "Mme" is that for "Madame" and "Mlle" for "Mademoiselle". Like many other cross-channel linguistic acquisitions, many Britons readily took this up and followed this rule themselves, while the Americans took a simpler rule and applied it rigorously. Over the years, however, the lack of convention in some style guides has made it difficult to determine which two-word abbreviations should be abbreviated with periods and which should not. The U.S. media tend to abbreviate two-word abbreviations like United States (U.S.), but surprisingly, not personal computer (PC) or television (TV), which is a source of confusion. Many British publications have gradually done away with the use of periods in abbreviations completely.
Examples

- List of classical abbreviations
- List of mediaeval abbreviations
- List of abbreviations in use in 1911
- List of acronyms and initialisms
- The abbreviations used in the 1913 edition of Webster's dictionary
Abbreviation types

- Acronym and initialism
- Apocopation
- TLA
- Syllabic abbreviation
- Portmanteau
See also

- List of syllabic abbreviations
- Neologism, word, term, or phrase which has been recently created
- Internet slang, list of computing and IT abbreviations, list of medical abbreviations, list of government and military acronyms, abbreviations used in CIA World Factbook,
- ISO language code, ISO country code.
- Ditloid
External links

- [http://www.abbreviationz.com/ AbbreviationZ] acronyms, abbreviations & Initialisms directory.
- [http://www.acronyma.com/ Acronyma]—large database of acronyms and abbreviations (over 450,000 entries)
- [http://www.acronymfinder.com/ Acronym Finder]—searchable acronyms and abbreviations site (over 400,000 entries) Category:Abbreviations ja:略語 simple:Abbreviation

NATO

:NATO is also an acronym for the National Association of Theatre Owners. National Association of Theatre Owners National Association of Theatre Owners The North Atlantic Treaty Organisation (NATO), sometimes called North Atlantic Alliance, Atlantic Alliance or the Western Alliance, is an international organisation for defence collaboration established in 1949, in support of the North Atlantic Treaty signed in Washington, D.C., on April 4, 1949. Its headquarters are located in Brussels, Belgium. Its other official name is the French equivalent, l'Organisation du Traité de l'Atlantique du Nord (OTAN).
Purpose
The core of NATO is Article V of the NATO Treaty, which states: :The Parties agree that an armed attack against one or more of them in Europe or North America shall be considered an attack against them all. Consequently they agree that, if such an armed attack occurs, each of them, in exercise of the right of individual or collective self-defence recognised by Article 51 of the Charter of the United Nations, will assist the Party or Parties so attacked by taking forthwith, individually and in concert with the other Parties, such action as it deems necessary, including the use of armed force, to restore and maintain the security of the North Atlantic area. This provision was intended so that if the USSR and its allies launched an attack against any of the NATO members, it would be treated as if it was an attack on all member states. This marked a significant change for the United States, which had traditionally favoured isolationist policies. However, the feared invasion of Western Europe never came. Instead, the provision was invoked for the first time in the treaty's history on September 12, 2001, in response to the September 11 attacks on the United States the day before. NATO Summit 2006 will take place in Latvia.
History

Chronology of events
Latvia
- March 17, 1948: The Benelux countries, France, and the United Kingdom sign the Treaty of Brussels, a precursor to the NATO Agreement.
- April 4, 1949: North Atlantic Treaty is signed in Washington, DC.
- May 14, 1955: Warsaw Pact treaty is signed in Warsaw by the Soviet Union and its satellite states as a formal response to NATO. Both organisations are opposing sides in the Cold War. After the fall of the Iron Curtain in 1989, the Warsaw Pact disintegrates.
- 1966: Charles de Gaulle removes French armed forces from NATO's integrated military command to pursue its own nuclear defence programme. All non-French NATO troops are forced to leave France. This precipitates the relocation of the NATO Headquarters from Paris, France to Brussels, Belgium by October 16, 1967. While the political headquarters are located in Brussels the military headquarters, the Supreme Headquarters Allied Powers Europe (SHAPE), are located just south of Brussels, in the town of Mons.
- July 1, 1968: The Nuclear Non-Proliferation Treaty opened for signature. NATO argued its nuclear weapons sharing arrangements did not breach the treaty as U.S. forces controlled the weapons until a decision is made to go to war, at which point the treaty would no longer be controlling. Few states knew of the NATO nuclear sharing arrangements at that time, and they were not challenged.
- May 30, 1978 NATO countries define two complementary aims of the Alliance, to maintain security and pursue détente. This is supposed to mean matching defences at the level rendered necessary by the Warsaw Pact's offensive capabilities without spurring a further arms race.
- December 12, 1979 In light of a build-up of Warsaw Pact nuclear capabilities in Europe, ministers approved the deployment of US Cruise and Pershing II theatre nuclear weapons in Europe. The new warheads are also meant to strengthen the western negotiating position in regard to nuclear disarmament.
- May 30, 1982: Spain joins the alliance.
- 1983-84: Responding to the stationing of Warsaw Pact SS-20 medium-range missiles in Europe, NATO deploys modern Pershing II missiles able to reach Moscow within minutes. This action leads to bitter peace movement protests throughout Western Europe.
- May 1984: A NATO manoeuvre codenamed Able Archer, which simulates a NATO response to a Soviet nuclear attack, causes panic in the Kremlin. Soviet leader Yuri Andropov becomes concerned that U.S. President Ronald Reagan intends to launch a real first strike, and places Soviet nuclear forces at full readiness. Only after the collapse of the Soviet Union does it become clear that US intelligence had mistaken real Soviet nervousness for propaganda efforts.
- October 3, 1990: With the reunification of Germany, the former East Germany becomes part of the Federal Republic of Germany and the alliance. This had been agreed in the Two Plus Four Treaty earlier in the year. To secure Soviet approval of united Germany remaining in NATO, it is agreed that there will be no new foreign military bases in the east, and that nuclear weapons will not be permanently stationed there.
- March 31, 1991: The Warsaw Pact comes to an end. It is officially dissolved on July 1, 1991. The Soviet Union collapses in December of the same year.
- February 8, 1994: NATO takes its first military action, shooting down two Bosnian Serb aircraft violating a UN no-fly zone over central Bosnia and Herzegovina. NATO airstrikes the following year help bring the war in Bosnia to an end, resulting in the Dayton Agreement.
- July 8, 1997: Three former communist countries, Hungary, the Czech Republic, and Poland, are invited to join NATO. They join in 1999.
- March 24, 1999: NATO sees its first broad-scale military engagement in the Kosovo War, where it wages an 11-week bombing campaign against what was then the Federal Republic of Yugoslavia, aimed at preventing the alleged ethnic cleansing of Albanians. It ends on June 11, 1999, when Yugoslavian leader Slobodan Milošević agrees to NATO's demands.
- April 1999: At the Washington summit, Germany proposes that NATO adopt a no-first-use nuclear strategy; the proposal is rejected.
- September 12, 2001: NATO provisionally invokes, for the first time in its history, the collective security clause of its charter. Article 5 states that any attack on a member state is considered an attack against the entire alliance. This comes in response to the September 11, 2001 Terrorist Attack against the United States.
- October 5, 2001: NATO confirms the invocation of Article 5, having determined that the attacks of 11 September were eligible under the terms of the North Atlantic Treaty. [http://www.nato.int/docu/update/2001/1001/e1002a.htm]
- November 21, 2002: During the Prague summit, seven countries are invited to start talks in order to join the Alliance: Estonia, Latvia, Lithuania, Slovenia, Slovakia, Bulgaria, and Romania. The invited countries join NATO on March 29, 2004. Further countries express the wish to join the alliance, including Albania, the Republic of Macedonia, and Croatia. The summit also launches the NATO Response Force (NRF).
- February 10, 2003: NATO faces a crisis when France and Belgium veto the procedure of silent approval concerning the timing of protective measures for Turkey in case of a possible war with Iraq. Germany does not use its right to break the procedure but says it supports the veto. Germany
- April 16, 2003: NATO agrees to take command in August of the International Security Assistance Force (ISAF) in Afghanistan. The decision comes at the request of Germany and the Netherlands, the two nations leading ISAF at the time of the agreement. All 19 NATO ambassadors approve it unanimously. The handover of control to NATO takes place on August 11, and marked the first time in NATO's history that it takes charge of a mission outside the north Atlantic area. Canada had originally been slated to take over ISAF by itself on that date.
- June 19, 2003: A major restructuring of the NATO military commands begins as the Headquarters of the Supreme Allied Commander, Atlantic was abolished and a new command, Allied Command Transformation (ACT), was established in Norfolk, Virginia, U.S. and the Supreme Headquarters Allied Powers Europe (SHAPE) became Allied Command Operations (ACO). ACT is responsible for driving transformation (future capabilities) in NATO, whilst ACO is responsible for current operations.
- March 29, 2004: Bulgaria, Estonia, Latvia, Lithuania, Romania, Slovakia, and Slovenia join NATO.
Member states
2004 Greece and Turkey joined the initial 12 members of the organisation in February 1952. Germany joined as West Germany in 1955 and German reunification on October 3, 1990 extended the membership to the areas of the former German Democratic Republic which became part of the Federal Republic of Germany. Spain was admitted on May 30 1982, and the former Warsaw Pact countries of Poland, Hungary and the Czech Republic made history by becoming members on March 12 1999. France is a member of NATO, but it withdrew from the integrated military command in 1966. Following this decision, the NATO headquarters was moved from Paris to Brussels. Iceland, the sole member of NATO which does not have its own military force (the Icelandic Defense Force being the United States Military contingent permanently stationed in Iceland), joined on the condition that they would not be expected to establish one. Greece withdrew its forces from NATO’s military command structure from 1974 to 1980 as a result of Greco-Turkish tensions following the 1974 Cyprus dispute. The former Warsaw Pact countries of Slovakia, Slovenia, Bulgaria, Romania, Estonia, Latvia and Lithuania officially acceded to NATO on March 29 2004. They attended their first NATO meeting in April 2004. Albania, Croatia, and the F.Y.R. of Macedonia are the three countries currently in the NATO MAP (Membership Action Programme); they are likely to join NATO in the future.
Founding members (April 4, 1949)
2004
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States that joined during the Cold War

- (February 18, 1952)
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Former Eastern Bloc states that joined after the Cold War
1999:
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- (May 27, 1999) 2004:
- (March 29, 2004)
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- (March 29, 2004)
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- (March 29, 2004)
- (March 29, 2004)
- (March 29, 2004)
Non-member states

Partner countries
Main article: Euro-Atlantic Partnership Council The Euro-Atlantic Partnership Council consists of 46 member countries: the 26 NATO members and 20 partner countries:
- 4 non-NATO EU members: :
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NATO-Russia Council

Main article: NATO-Russia Council NATO and Russia made a reciprocal commitment in 1997 "to work together to build a stable, secure and undivided continent on the basis of partnership and common interest." In May 2002, this commitment was strengthened with the establishment of the NATO-Russia Council, which brings together the NATO members and Russia. The purpose of this council is to identify and pursue opportunities for joint action with the 27 (26+1) participants as equal partners.

Structures

Political structure

Organisational structure

Like any alliance, NATO is ultimately governed by its 26 member states. However, the North Atlantic Treaty, and other agreements, outline how decisions are to be made within NATO. Each of the 26 members sends a delegation or mission to NATO's headquarters in Brussels, Belgium. The senior permanent member of each delegation is known as the Permanent Representative and is generally a senior civil servant or an experienced ambassador (and holding that diplomatic rank). Together the Permanent Members form the North Atlantic Council (NAC), a body which meets together at least once a week and has effective political authority and powers of decision in NATO. From time to time the Council also meets at higher levels involving Foreign Ministers, Defence Ministers or Heads of Government and it is at these meetings that major decisions regarding NATO's policies are generally taken. However, it is worth noting that the Council has the same authority and powers of decision-making, and its decisions have the same status and validity, at whatever level it meets. The meetings of the North Atlantic Council are chaired by the Secretary General of NATO and, when decisions have to be made, action is agreed upon on the basis of unanimity and common accord. There is no voting or decision by majority. Each nation represented at the Council table or on any of its subordinate committees retains complete sovereignty and responsibility for its own decisions.
- The second pivotal member of each country's delegation is the Military Representative, a senior officer from each country's armed forces. Together the Military Representatives form the Military Committee, a body responsible for recommending to NATO's political authorities those measures considered necessary for the common defence of the NATO area. Its principal role is to provide direction and advice on military policy and strategy. It provides guidance on military matters to the NATO Strategic Commanders, whose representatives attend its meetings, and is responsible for the overall conduct of the military affairs of the Alliance under the authority of the Council. Like the council, from time to time the Military Committee also meets at a higher level, namely at the level of Chiefs of Defence, the most senior military officer in each nations armed forces.
- In addition to this strictly internal structure, there is a number of institutionalised cooperations and consultations in a spirit of partnership.
- Since 1994, the Mediterranean Dialogue is a forum with pro-western Arab countries (Egypt, Algeria, Jordan, Morocco, Mauritania and Tunisia) and Israel.
- Partnership for Peace The NATO Parliamentary Assembly is made up of legislators from the member countries of the North Atlantic Alliance as well as 13 associate members[http://www.nato-pa.int/Default.asp?SHORTCUT=1].

Secretaries General

# Lord Ismay (United Kingdom): April 4, 1952, to May 16, 1957 # Paul-Henri Spaak (Belgium): May 16, 1957, to April 21, 1961 # Dirk Stikker (Netherlands): April 21, 1961, to August 1, 1964 # Manlio Brosio (Italy): August 1, 1964, to October 1, 1971 # Joseph Luns (Netherlands): October 1, 1971, to June 25, 1984 # Lord Carrington (United Kingdom): June 25, 1984, to July 1, 1988 # Manfred Wörner (Germany): July 1, 1988, to August 13, 1994 # Sergio Balanzino (Italy, acting): August 13, 1994, to October 17, 1994 # Willy Claes (Belgium): October 17, 1994, to October 20, 1995 # Sergio Balanzino (Italy, acting): October 20, 1995, to December 5, 1995 # Javier Solana (Spain): December 5, 1995, to October 6, 1999 # Lord Robertson of Port Ellen (United Kingdom): October 14, 1999, to January 1, 2004 # Jaap de Hoop Scheffer (Netherlands): January 1, 2004, to present

Military structure

NATO's military operations are directed by two Strategic Commanders, both senior American Officers assisted by a staff drawn from across NATO. The Strategic Commanders are responsible to the Military Committee for the overall direction and conduct of all Alliance military matters within their areas of command. Before 2003 the Strategic Commanders were the Supreme Allied Commander Europe (SACEUR) and the Supreme Allied Commander Atlantic (SACLANT) but the current arrangement is to separate command responsibility between Allied Command Transformation (ACT), responsible for transformation and training of NATO forces, and Allied Command Operations, responsible for NATO operations world wide. The commander of Allied Command Operations retained the title "Supreme Allied Commander Europe (SACEUR)", and is based in the Supreme Headquarters Allied Powers Europe located at Casteau, north of the Belgian city of Mons. This is about 80 km (50 miles) south of NATO's political headquarters in Brussels. Allied Command Transformation (ACT) is based in the former Allied Command Atlantic headquarters in Norfolk, Virginia, USA. NATO operates a fleet of E-3 Sentry AWACS airborne radar aircraft based out of Geilenkirchen Air Base in Germany.

Debate about its future

The future of NATO is currently under debate. The main issues are:
- The necessity. The crumbling of the main "enemy of the west" in Eastern Europe removed for many observers the necessity of a collective defence organisation. The debate about the necessity of NATO has increased due to dissension between members about the American led invasion of Iraq, makes some wonder (largely in North America) whether NATO has not become obsolete. The presumed threat of terrorism could give the institution a new life, but some think also that fighting terrorists needs a completely different political and military organisation, as well as completely different weapon systems to those on which NATO was built.
- The benefits for the US. In the US, some voices emphasis the discrepancy in military spending between the USA and European members. While the USA has the highest military spending in the world, European nations have decreased their budgets significantly after the end of the Cold War. The gap in military capabilities is thus increasing, which raises questions about what the USA gains from membership. The lack of European capabilities was highlighted during the Kosovo crisis. Former NATO-secretary Lord Robertson criticized the European members in 1999, pointing out European nations must commit substantially more funds to defence just to meet their existing commitments to NATO. [http://news.bbc.co.uk/1/hi/uk_politics/546307.stm] However, this commitment has not been fulfilled in the following years, and it is expected that this will remain to be the case for the forseeable future. That the US wants to continue to benefit from military ties with Europe (though not necessarily through NATO) can be seen by the fact that the US has had talks with Poland and other European countries over the possibility of setting up a European base to intercept long-range missiles, as part of the American NMD program. This program is designed to shoot down long-range missiles fired at North America. A European base would also protect some European nations (as well as the US). [http://news.bbc.co.uk/1/hi/world/europe/4445284.stm]
- An obstacle to European integration. Many argue that NATO is in conflict with the prospects of deeper European integration in the fields of foreign policy and security within the framework of the EU institutions. Some advocates for a strong EU Common Foreign and Security Policy (CFSP) would like to see NATO dismantled and a common defence and foreign policy created within the existing EU institutions. In November 2004, after the re-election of United States President George W. Bush, the Norwegian Prime Minister Kjell Magne Bondevik publicly discussed whether Norway would benefit from strengthening her defence relations with the EU. Many Norwegian political analysts consider NATO to be a "politically dead organisation". So do several pundits and political leaders in other member nations. These attitudes will of necessity be reflected in future discussions of NATO expansion.

DNA Overview

red blood cell This section presents an introductory and therefore incomplete overview of DNA.
- Genes can be loosely viewed as the organism's "cookbook" or "blueprint";
- A strand of DNA contains genes, areas that regulate genes, and areas that either have no function, or a function we do not (yet) know (also see last bullet point in this section for the difference between DNA and RNA);
- DNA is organized as two complementary strands, head-to-toe, with bonds between them that can be "unzipped" like a zipper, separating the strands;
- DNA is a chain of chemical "building blocks", called "bases", of which there are four types: these can be abbreviated A, T, C, and G. Each base can only "pair up" with one single predetermined other base: A+T, T+A, C+G and G+C are the only possible combinations; that is, an "A" on one strand of double-stranded DNA will "mate" properly only with a "T" on the other, complementary strand;
- N.B.: U occasionally replaces T, notably in PBS1 phage DNA; you can thus substitute "U" for "T" throughout this section.
- Because each strand of DNA has a directionality, the sequence order does matter: A+T is not the same as T+A, just as C+G is not the same as G+C;
- For each given base, there is just one possible complementary base, so naming the bases on the conventionally chosen side of the strand is enough to describe the entire double-strand sequence;
- The genetic information contained in a strand of DNA is determined by the sequence of bases along its length;
- The cell begins DNA replication by forcibly unzipping the DNA double strand down the middle, and then recreates the "other half" of each new single strand by drowning each half in a "soup" made of the four bases. An enzyme makes a new strand by finding the correct "base" in the soup and pairing it with the original strand. In this way, the base on the old strand dictates which base will be on the new strand, and the cell ends up with an extra copy of its DNA.
- Mutations are simply chemical imperfections in this process: a base is accidentally skipped, inserted, or incorrectly copied, or the chain is trimmed, or added to; many basic mutations can be described as combinations of these accidental "operations". Mutations can also occur through chemical damage (through mutagens), light (UV damage), or through other more complicated gene swapping events.
- DNA (for DeoxyriboNucleic Acid) differs from RNA (for RiboNucleic Acid) by having the sugar 2-deoxyribose instead of ribose in its backbone (ribose contains one extra oxygen atom compared to deoxyribose -- in other words, DNA contains deoxygenated ribose, whereas RNA contains "plain" ribose.) This is the basic chemical distinction between RNA and DNA.

DNA in practice

DNA in crime

Forensic scientists can use DNA located in blood, semen, skin, saliva, or hair left at the scene of a crime to identify a possible suspect, a process called genetic fingerprinting or DNA profiling. In DNA profiling the relative lengths of sections of repetitive DNA, such as short tandem repeats and minisatellites, are compared. DNA profiling was developed in 1984 by English geneticist Alec Jeffreys, and was first used in 1986 in the Enderby murders case in Leicestershire, England. Many jurisdictions require convicts of certain types of crimes to provide a sample of DNA for inclusion in a computerized database. This has helped investigators solve old cases where the perpetrator was unknown and only a DNA sample was obtained from the scene (particularly in rape cases between strangers). This method is one of the most reliable techniques for identifying a criminal, but is not always perfect, for example if no DNA can be retrieved, or if the scene is contaminated with the DNA of several possible suspects.

DNA in computation

Despite its biological origins, DNA plays an important role in computer science, both as a motivating research problem and as a method of computation in itself, called DNA computing. As a simple example, research on string searching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, was motivated by DNA research, where it is used to find specific sequences of nucleotides in a large sequence. In other applications like text editors, even simple algorithms for this problem usually suffice, but DNA sequences cause these algorithms to exhibit near-worst-case behavior due to their small number of distinct characters. Databases have also been strongly motivated by DNA research, which requires special tools for storing and manipulating DNA sequences. Databases specialized for this purpose are called genomic databases, and have a number of unique technical challenges associated with the operations of approximate matching, sequence comparison, finding repeating patterns, and homology searching. In 1994, Leonard Adleman of the University of Southern California made headlines when he discovered a way of solving the directed Hamiltonian path problem, an NP-complete problem, using tools from molecular biology, in particular DNA. The new approach, dubbed DNA computing, has practical advantages over traditional computers in power use, space use, and efficiency, due to its ability to highly parallelize the computation (see parallel computing)(there is labor worth mention involved in retrieving answers computed these computational DNA techniques.). A number of other problems, including simulation of various abstract machines, the boolean satisfiability problem, and the bounded version of the Post correspondence problem, have since been analyzed using DNA computing. Due to its compactness, DNA also has an important role in cryptography, where in particular it allows unbreakable one-time pads to be efficiently constructed and used.[http://citeseer.ist.psu.edu/gehani99dnabased.html]

Overview of molecular structure

one-time pad Although sometimes called "the molecule of heredity", pieces of DNA as people typically think of them are not single molecules. Rather, they are pairs of molecules, which entwine like vines to form a double helix (see the illustration at the right). Each vine-like molecule is a strand of DNA: a chemically linked chain of nucleotides, each of which consists of a sugar, a phosphate and one of five kinds of nucleobases ("bases"). Because DNA strands are composed of these nucleotide subunits, they are polymers. The diversity of the bases means that there are five kinds of nucleotides, which are commonly referred to by the identity of their bases. These are adenine (A), thymine (T), uracil (U), cytosine (C), and guanine (G). U is rarely found in DNA except as a result of chemical degradation of C, but in some viruses, notably PBS1 phage DNA, U completely replaces the usual T in its DNA. Similarly, RNA usually contains U in place of T, but in certain RNAs such as transfer RNA, T is always found in some positions. Thus, the only true difference between DNA and RNA is the sugar, 2-deoxyribose in DNA and ribose in RNA. In a DNA double helix, two polynucleotide strands can associate through the hydrophobic effect and pi stacking. Specificity of which strands stay associated is determined by complementary pairing. Each base forms hydrogen bonds readily to only one other -- A to T and C to G -- so that the identity of the base on one strand dictates the strength of the association; the more complementary bases exist, the stronger and longer-lasting the association. The cell's machinery is capable of melting or disassociating a DNA double helix, and using each DNA strand as a template for synthesizing a new strand which is nearly identical to the previous strand. Errors that occur in the synthesis are known as mutations. The process known as PCR (polymerase chain reaction) mimics this process in vitro in a nonliving system. Because pairing causes the nucleotide bases to face the helical axis, the sugar and phosphate groups of the nucleotides run along the outside; the two chains they form are sometimes called the "backbones" of the helix. In fact, it is chemical bonds between the phosphates and the sugars that link one nucleotide to the next in the DNA strand.

The role of the sequence

Within a gene, the sequence of nucleotides along a DNA strand defines a messenger RNA sequence which then defines a protein, that an organism is liable to manufacture or "express" at one or several points in its life using the information of the sequence. The relationship between the nucleotide sequence and the amino-acid sequence of the protein is determined by simple cellular rules of translation, known collectively as the genetic code. The genetic code is made up of three-letter 'words' (termed a codon) formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT). These codons can then be translated with messenger RNA and then transfer RNA, with a codon corresponding to a particular amino acid. There are 64 possible codons (4 bases in 3 places

4^3

) that encode 20 amino acids. Most amino acids, therefore, have more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region, namely the UAA, UGA and UAG codons. In many species, only a small fraction of the total sequence of the genome appears to encode protein. For example, only about 1.5% of the human genome consists of protein-coding exons. The function of the rest is a matter of speculation. It is known that certain nucleotide sequences specify affinity for DNA binding proteins, which play a wide variety of vital roles, in particular through control of replication and transcription. These sequences are frequently called regulatory sequences, and researchers assume that so far they have identified only a tiny fraction of the total that exist. "Junk DNA" represents sequences that do not yet appear to contain genes or to have a function. The reasons for the presence of so much non-coding DNA in eukaryotic genomes and the extraordinary differences in genome size ("C-value") among species represent a long-standing puzzle in DNA research known as the "C-value enigma". Some DNA sequences play structural roles in chromosomes. Telomers and centromeres typically contain few (if any) protein-coding genes, but are important for the function and stability of chromosomes. Some genes code for "RNA genes" (see tRNA and rRNA). Some RNA genes code for transcripts that function as regulatory RNAs (see siRNA) that influence the function of other RNA molecules. The intron-exon structure of some genes (such as immunoglobin and protocadeherin genes) is important for allowing alternative splicing of pre-mRNA which allows several different proteins to be made from the same gene. Some non-coding DNA represents pseudogenes that can be used as raw material for the creation of new genes with new functions. Some non-coding DNA provided hot-spots for duplication of short DNA regions; such sequence duplication has been the major form of genetic change in the human lineage (see evidence from the Chimpanzee Genome Project). Exons interspersed with introns allows for "exon shuffling" and the creation of modified genes that might have new adaptive functions. Large amounts of non-coding DNA is probably adaptive in that it provides chromosomal regions where recombination between homologous portions of chromosomes can take place without disrupting the function of genes. Some biologists such as Stuart Kauffman have speculated that there must be mechanisms by which the rate of evolution of a species can be increased or decreased. Non-coding DNA provides mechanisms for gene creation, modification and recombination it is probably important for control of the rate of human evolution. Sequence also determines a DNA segment's susceptibility to cleavage by restriction enzymes, the quintessential tools of genetic engineering. The position of cleavage sites throughout an individual's genome determines one kind of an individual's "DNA fingerprint".

DNA replication

Main article: DNA replication DNA replication DNA replication or DNA synthesis is the process of copying the double-stranded DNA prior to cell division. The two resulting double strands are generally almost perfectly identical, but occasionally errors in replication can result in a less than perfect copy (see mutation), and each of them consists of one original and one newly synthesized strand. This is called semiconservative replication. The process of replication consists of three steps: initiation, replication and termination.

Mechanical properties relevant to biology

Main article: Mechanical properties of DNA.

Strands association and dissociation

The hydrogen bonds between the strands of the double helix are weak enough that they can be easily separated by enzymes. Enzymes known as helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase. The unwinding requires that helicases chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. The strands can also be separated by gentle heating, as used in PCR, provided they have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate.

Circular DNA

When the ends of a piece of double-helical DNA are joined so that it forms a circle, as in plasmid DNA, the strands are topologically knotted. This means they cannot be separated by gentle heating or by any process that does not involve breaking a strand. The task of unknotting topologically linked strands of DNA falls to enzymes known as topoisomerases. Some of these enzymes unknot circular DNA by cleaving two strands so that another double:stranded segment can pass through. Unknotting is required for the replication of circular DNA as well as for various types of recombination in linear DNA.

Great length versus tiny breadth

The narrow breadth of the double helix makes it impossible to detect by conventional electron microscopy, except by heavy staining. At the same time, the DNA found in many cells can be macroscopic in length -- approximately 5 centimetres long for strands in a human chromosome. Consequently, cells must compact or "package" DNA to carry it within them. This is one of the functions of the chromosomes, which contain spool-like proteins known as histones, around which DNA winds.

Entropic stretching behavior

When DNA is in solution, it undergoes conformational fluctuations due to the energy available in the thermal bath. For entropic reasons, more floppy states are thermally accessible than stretched out states; for this reason, a single molecule of DNA stretches similarly to a rubber band. Using optical tweezers, the entropic stretching behavior of DNA has been studied and analyzed from a polymer physics perspective, and it has been found that DNA behaves like the Kratky-Porod worm-like chain model with a persistence length of about 53 nm. Furthermore, DNA undergoes a stretching phase transition at a force of 65 pN; above this force, DNA is thought to take the form that Linus Pauling originally hypothesized, with the phosphates in the middle and bases splayed outward. This proposed structure for overstretched DNA has been called "P-form DNA," in honor of Pauling.

Different helix geometries

The DNA helix can assume one of three slightly different geometries, of which the "B" form described by James D. Watson and Francis Crick is believed to predominate in cells. It is 2 nanometres wide and extends 3.4 nanometres per 10 bp of sequence. This is also the approximate length of sequence in which the double helix makes one complete turn about its axis. This frequency of twist (known as the helical pitch) depends largely on stacking forces that each base exerts on its neighbors in the chain.

Supercoiled DNA

The B form of the DNA helix twists 360° per 10.6 bp in the absence of strain. But many molecular biological processes can induce strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively "supercoiled". DNA in vivo is typically negatively supercoiled, which facilitates the unwinding of the double-helix required for RNA transcription.

Sugar pucker

There are four conformations that the ribofuranose rings in nucleotides can acquire: # C-2' endo # C-2' exo # C-3' endo # C-3' exo Ribose is usually in C-3'endo, while deoxyribose is usually in the C-2' endo sugar pucker conformation. The A and B forms differ mainly in their sugar pucker. In the A form, the C3' configuration is above the sugar ring, whilst the C2' configuration is below it. Thus, the A form is described as "C3'-endo." Likewise, in the B form, the C2' configuration is above the sugar ring, whilst C3' is below; this is called "C2'-endo." Altered sugar puckering in A-DNA results in shortening the distance between adjacent phosphates by around one angstrom. This gives 11 to 12 base pairs to each helix in the DNA strand, instead of 10.5 in B-DNA. Sugar pucker gives uniform ribbon shape to DNA, a cylindrical open core, and also a deep major groove more narrow and pronounced that grooves found in B-DNA.

Conditions for formation of A and Z helices

The two other known double-helical forms of DNA, called A and Z, differ modestly in their geometry and dimensions. The A form appears likely to occur only in dehydrated samples of DNA, such as those used in crystallographic experiments, and possibly in hybrid pairings of DNA and RNA strands. Segments of DNA that cells have methylated for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis like a mirror image of the B form.

Table of comparison of the properties of different helical forms

Non-helical forms

Other, including non-helical, forms of DNA have been described, for example a side-by-side (SBS) configuration. Indeed, it is far from certain that the B-form double helix is the dominant form in living cells.

Direction of DNA strands

The asymmetric shape and linkage of nucleotides means that a DNA strand always has a discernible orientation or directionality. Because of this directionality, close inspection of a double helix reveals that nucleotides are heading one way along one strand (the "ascending strand"), and the other way along the other strand (the "descending strand"). This arrangement of the strands is called antiparallel.

Chemical nomenclature (5' and 3')

For reasons of chemical nomenclature, people who work with DNA refer to the asymmetric ends of ("five prime" and "three prime"). Biologists and the DNA enzymes they use, predominantly read nucleotide sequences in the "5' to 3' direction". However, because chemically produced DNA is synthesized and manipulated in the opposite or in non-directional manners, the orientation should not be assumed. In a vertically oriented double helix, the 3' strand is said to be ascending while the 5' strand is said to be descending.

Sense and antisense

As a result of their antiparallel arrangement and the sequence-reading preferences of enzymes, even if both strands carried identical instead of complementary sequences, cells could properly translate only one of them. The other strand a cell can only read backwards. Molecular biologists call a sequence "sense" if it is translated or translatable, and they call its complement "antisense". It follows then, somewhat paradoxically, that the template for transcription is the antisense strand. The resulting transcript is an RNA replica of the sense strand and is itself sense.

Distinction between sense and antisense strands

A small proportion of genes in prokaryotes, and more in plasmids and viruses, blur the distinction made above between sense and antisense strands. Certain sequences of their genomes do double duty, encoding one protein when read 5' to 3' along one strand, and a second protein when read in the opposite direction (still 5' to 3') along the other strand. As a result, the genomes of these viruses are unusually compact for the number of genes they contain, which biologists view as an adaptation. This merely confirms that there is no biological distinction between the two strands of the double helix. Indeed, typically each strand of a DNA double helix will act as sense and antisense in different regions.

As viewed by topologists

Topologists like to note that the juxtaposition of the 3′ end of one DNA strand beside the 5′ end of the other at both ends of a double-helical segment makes the arrangement a "crab canon".

Single-stranded DNA (ssDNA) and repair of mutations

In some viruses DNA appears in a non-helical, single-stranded form. Because many of the DNA repair mechanisms of cells work only on paired bases, viruses that carry single-stranded DNA genomes mutate more frequently than they would otherwise. As a result, such species may adapt more rapidly to avoid extinction. The result would not be so favorable in more complicated and more slowly replicating organisms, however, which may explain why only viruses carry single-stranded DNA. These viruses presumably also benefit from the lower cost of replicating one strand versus two.

The history of DNA research

mutate at the University of Cambridge]] The discovery that DNA was the carrier of genetic information was a process that required many earlier discoveries. The existence of DNA was discovered in the mid 19th century. However, it was only in the early 20th century that researchers began suggesting that it might store genetic information. This was only accepted after the structure of DNA was elucidated by Watson and Crick in their 1953 Nature publication. Watson and Crick proposed the central dogma of molecular biology in 1957, describing the process whereby proteins are produced from nucleic DNA.

First isolation of DNA

Working in the 19th century, biochemists initially isolated DNA and RNA (mixed together) from cell nuclei. They were relatively quick to appreciate the polymeric nature of their "nucleic acid" isolates, but realized only later that nucleotides were of two types--one containing ribose and the other deoxyribose. It was this subsequent discovery that led to the identification and naming of DNA as a substance distinct from RNA. Friedrich Miescher (1844-1895) discovered a substance he called "nuclein" in 1869. Somewhat later, he isolated a pure sample of the material now known as DNA from the sperm of salmon, and in 1889 his pupil, Richard Altmann, named it "nucleic acid". This substance was found to exist only in the chromosomes. In 1929 Phoebus Levene at the Rockefeller Institute identified the components (the four bases, the sugar and the phosphate chain) and he showed that the components of DNA were linked in the order phosphate-sugar-base. He called each of these units a nucleotide and suggested the DNA molecule consisted of a string of nucleotide units linked together through the phosphate groups, which are the 'backbone' of the molecule. However Levene thought the chain was short and that the bases repeated in the same fixed order. Torbjorn Caspersson and Einar Hammersten showed that DNA was a polymer.

Establishing a link between heritable traits and chromosomes

Max Delbrück, Nikolai V. Timofeeff-Ressovsky, and Karl G. Zimmer published results in 1935 suggesting that chromosomes are very large molecules the structure of which can be changed by treatment with X-rays, and that by so changing their structure it was possible to change the heritable characteristics governed by those chromosomes. In 1937 William Astbury produced the first X-ray diffraction patterns from DNA. He was not able to propose the correct structure but the patterns showed that DNA had a regular structure and therefore it might be possible to deduce what this structure was. In 1943, Oswald Theodore Avery discovered that traits proper to the "smooth" form of the Pneumococcus could be transferred to the "rough" form of the same bacteria merely by making the killed "smooth" (S) form available to the live "rough" (R) form. Quite unexpectedly, the living R Pneumococcus bacteria were transformed into a new strain of the S form, and the transferred S characteristics turned out to be heritable. Avery called the medium of transfer of traits the transforming principle; he identified DNA as the transforming principle, and not protein as previously thought. In 1953, Alfred Hershey and Martha Chase did an experiment (Hershey-Chase experiment) that showed, in T2 phage, that DNA is the genetic material (Hershey shared the Nobel prize with Luria). genetic material double-helix pattern]] In 1944, the renowned physicist, Erwin Schrödinger, published a brief book entitled What is Life?, where he maintained that chromosomes contained what he called the "hereditary code-script" of life. He added: "But the term code-script is, of course, too narrow. The chromosome structures are at the same time instrumental in bringing about the development they foreshadow. They are law-code and executive power -- or, to use another simile, they are architect's plan and builder's craft -- in one." He conceived of these dual functional elements as being woven into the molecular structure of chromosomes. By understanding the exact molecular structure of the chromosomes one could hope to understand both the "architect's plan" and also how that plan was carried out through the "builder's craft." Three groups took up Schrödinger's challenge to work out the structure of the chromosomes and the question of how the segments of the chromosomes that were conceived to relate to specific traits could possibly do their jobs. Just how the presence of specific features in the molecular structure of chromosomes could produce traits and behaviors in living organisms was unimaginable at the time. Because chemical dissection of DNA samples always yielded the same four nucleotides, the chemical composition of DNA appeared simple, perhaps even uniform. Organisms, on the other hand, are fantastically complex individually and widely diverse collectively. Geneticists did not speak of genes as conveyors of "information" in such words, but if they had, they would not have hesitated to quantify the amount of information that genes need to convey as vast. The idea that information might reside in a chemical in the same way that it exists in text--as a finite alphabet of letters arranged in a sequence of unlimited length--had not yet been c

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NATO

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DNA

DNA Overview

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Overview of molecular structure

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Strands association and dissociation

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Sense and antisense

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As viewed by topologists

Single-stranded DNA (ssDNA) and repair of mutations

The history of DNA research

First isolation of DNA

Establishing a link between heritable traits and chromosomes