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How and where do you use negative prefixes like un-, non-, dis-, etc?

There is no hard and fast rule. Words with these prefixes have come about through accidents of history. The most common is "un-", but always consult a dictionary. The following is an explanation of certain negative prefix patterns found in English, but be warned: there are always exceptions.

a- is a Greek prefix meaning "not" or "without". It is found almost exclusively with words formed
from Greek roots. You can usually spot these by the spellings: "ph", "th", "y", "rh", "chr", "pn", "mn", final "sis" or "ic". Some examples:
theist / atheist chromatic / achromatic rhythmic / arhythmic symmetry / asymmetry

non- has almost exactly the same meaning as "un-", but is less frequent, and here again the
best approach is to learn these separately. It occurs more freely with nouns than many of the other prefixes do. Here are a few common ones:
partisan nonpartisan sectarian / nonsectarian violence / nonviolence standard / nonstandard compliance / noncompliance proliferation / nonproliferation sense / nonsense (here the stress shifts to the prefix: nonsense)

in- is a prefix from Latin, so it is usually seen when the root is from Latin.
Spelling change note: "in-"changes to "im-" before "m", "p", and "b". It changes to "il-" before "l" and to "ir-" before "r". This pattern is quite common with adjectives (derived from Latin):
articulate / inarticulate polite / impolite possible / impossible modest / immodest legal / illegal reverent / irreverent regular / irregular sanity / insanity

Latin also uses the prefix "in-" in other ways, not necessarily for negation, so caution is advised! For example, "improve" is not the negation of "prove, and "inflammable" means the same thing as "flammable, not the opposite, which is nonflammable!

dis- is also a Latinate prefix, but it often means more than the simple negation of "un-". With
verbs it may imply some action (often of removal) employed to create a negative state or the absence of something. The difference is usually more obvious in the past participle. Usually the form with "un-" cannot even be used as a verb.
arm / disarm (remove weapons from) unarmed - not carrying a weapon (adj.) disarmed - having had one's weapon(s) taken away (noun) infect / disinfect (remove possible sources of infection) uninfected - not having an infection (adj.) disinfected - having had possible sources of infection removed (noun) qualify / disqualify (remove from competition or consideration) unqualified - not having the proper qualities or qualifications (adj.) disqualified - judged to be unqualified; having been removed from consideration (noun)

Note: the prefix de- is also sometimes used in the sense of removal, forming verbs from nouns: defrost, dethrone, defrock, declaw, dehumanize, deactivate, decode, dehydrate

anti- is a prefix whose basic meaning is "against." It is used to form adjectives that mean
"counteracting" (such as antiseptic, preventing infection), and nouns referring to substances that counteract other substances (such as antihistamine, a substance counteracting histamine), and nouns meaning "something that displays opposite, reverse, or inverse characteristics of something else" (such as anticyclone, a storm that circulates in the opposite direction from a cyclone). Before a vowel it becomes ant-, as in antacid.

un- is the native English prefix for negation, but it combines freely with nonnative roots as well.
It is the most used prefix of its kind. It is used with verbs, adjectives, and adverbs, but also sometimes with abstract nouns -- not with concrete nouns ("*an unchair", "*an unbowl"). It can indicate simple negation (adjective) ("happy / unhappy") or it can indicate reversal of a process (verb) ("lock / unlock"). In this latter role, the prefix "de-" is sometimes used instead.
able / unable || tidy / untidy || cooperative / uncooperative || safe / unsafe || helpful / unhelpful || grateful / ungrateful || likeable / unlikeable || suitable / unsuitable || kind, unkind

Whenever there is already common word which is the opposite, the "un-" form does not exist: high
/ low (*unhigh, *unlow), fast / slow (*unfast, *unslow), freeze / thaw, (*unfreeze / *unthaw), tighten / loosen, (*untighten, *unloosen). *these are all incorrect forms!

pack / unpack || dress / undress || screw / unscrew || wind / unwind || tie / untie || roll / unroll || veil / unveil || cover / uncover ----- notice none of these words have common opposites.


One more thing

Oftentimes more than one prefix is possible for a word, resulting in different meanings. With some dictionary work you should be able to discover the difference between the words in these groups as well:
interested / disinterested / uninterested prove / disprove / improve integrate / disintegrate / segregate / aggregate assemble / disassemble / dissemble distinguish / distinguishable / indistinguishable distinguished / undistinguished claim / disclaim / unclaimed able / unable / disabled trust / distrust / trustworthy / untrustworthy cover / uncover / discover