Etymology
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un- (2)
prefix of reversal, deprivation, or removal (as in unhand, undo, unbutton), Old English on-, un-, from Proto-Germanic *andi- (source also of Old Saxon ant-, Old Norse and-, Dutch ont-, Old High German ant-, German ent-, Gothic and- "against"), from PIE *anti "facing opposite, near, in front of, before, against" (from PIE root *ant- "front, forehead," with derivatives meaning "in front of, before").

More or less confused with un- (1) through similarity in the notions of "negation" and "reversal;" an adjective such as unlocked might represent "not locked" (un- (1)) or the past tense of unlock (un- (2)).
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un- (1)

prefix of negation, Old English un-, from Proto-Germanic *un- (source also of Old Saxon, Old Frisian, Old High German, German un-, Gothic un-, Dutch on-), from PIE *n- (source of Sanskrit a-, an- "not," Greek a-, an-, Old Irish an-, Latin in-), combining form of PIE root *ne- "not." Often euphemistic (such as untruth for "lie").

The most prolific of English prefixes, freely and widely used in Old English, where it forms more than 1,000 compounds. It underwent a mass extinction in early Middle English, but emerged with renewed vigor 16c. to form compounds with native and imported words. It disputes with Latin-derived cognate in- (1) the right to form the negation of certain words (indigestable/undigestable, etc.), and though both might be deployed in cooperation to indicate shades of meaning (unfamous/infamous), typically they are not.

It also makes words from phrases (such as uncalled-for, c. 1600; undreamed-of, 1630s; uncome-at-able, 1690s; unputdownable, 1947, of a book; un-in-one-breath-utterable, Ben Jonson; etc., but the habit is not restricted to un-; such as put-up-able-with, 1812). As a prefix in telegramese to replace not and save the cost of a word, it is attested by 1936.

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a- (3)
prefix meaning "not, without," from Greek a-, an- "not" (the "alpha privative"), from PIE root *ne- "not" (source also of English un-).

In words from Greek, such as abysmal, adamant, amethyst; also partly nativized as a prefix of negation (asexual, amoral, agnostic). The ancient alpha privatum, denoting want or absence.

Greek also had an alpha copulativum, a- or ha-, expressing union or likeness, which is the a- expressing "together" in acolyte, acoustic, Adelphi, etc. It is from PIE root *sem- (1) "one; as one, together with."
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non- 

a prefix used freely in English and meaning "not, lack of," or "sham," giving a negative sense to any word, 14c., from Anglo-French noun-, from Old French non-, from Latin non "not, by no means, not at all, not a," from Old Latin noenum "not one" (*ne oinom, from PIE root *ne- "not" + PIE root *oi-no- "one, unique"). In some cases perhaps from Middle English non "not" (adj.), from Old English nan (see not). "It differs from un- in that it denotes mere negation or absence of the thing or quality, while un- often denotes the opposite of the thing or quality" [Century Dictionary].

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in- (1)
Origin and meaning of in-
word-forming element meaning "not, opposite of, without" (also im-, il-, ir- by assimilation of -n- with following consonant, a tendency which began in later Latin), from Latin in- "not," cognate with Greek an-, Old English un-, all from PIE root *ne- "not."

In Old French and Middle English often en-, but most of these forms have not survived in Modern English, and the few that do (enemy, for instance) no longer are felt as negative. The rule of thumb in English has been to use in- with obviously Latin elements, un- with native or nativized ones.
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dys- 

word-forming element meaning "bad, ill; hard, difficult; abnormal, imperfect," from Greek dys-, inseparable prefix "destroying the good sense of a word or increasing its bad sense" [Liddell & Scott], hence "bad, hard, unlucky," from PIE root (and prefix) *dus- "bad, ill, evil" (source also of Sanskrit dus-, Old Persian duš- "ill," Old English to-, Old High German zur-, Gothic tuz- "un-"), a derivative of the root *deu- (1) "to lack, be wanting" (source of Greek dein "to lack, want").

Very productive in ancient Greek, where it could attach even to proper names (such as dysparis "unhappy Paris"); its entries take up nine columns in Liddell & Scott. Among the words formed from it were some English might covet: dysouristos "fatally favorable, driven by a too-favorable wind;" dysadelphos "unhappy in one's brothers;" dysagres "unlucky in fishing;" dysantiblepos "hard to look in the face."

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dis- 
Origin and meaning of dis-

word-forming element of Latin origin meaning 1. "lack of, not" (as in dishonest); 2. "opposite of, do the opposite of" (as in disallow); 3. "apart, away" (as in discard), from Old French des- or directly from Latin dis- "apart, asunder, in a different direction, between," figuratively "not, un-," also "exceedingly, utterly." Assimilated as dif- before -f- and to di- before most voiced consonants.

The Latin prefix is from PIE *dis- "apart, asunder" (source also of Old English te-, Old Saxon ti-, Old High German ze-, German zer-). The PIE root is a secondary form of *dwis- and thus is related to Latin bis "twice" (originally *dvis) and to duo, on notion of "two ways, in twain" (hence "apart, asunder").

In classical Latin, dis- paralleled de- and had much the same meaning, but in Late Latin dis- came to be the favored form and this passed into Old French as des-, the form used for compound words formed in Old French, where it increasingly had a privative sense ("not"). In English, many of these words eventually were altered back to dis-, while in French many have been altered back to de-. The usual confusion prevails.

As a living prefix in English, it reverses or negatives what it is affixed to. Sometimes, as in Italian, it is reduced to s- (as in spend, splay, sport, sdain for disdain, and the surnames Spencer and Spence).

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