Words related to *ne-
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."
Middle English had a past-participle adjective annichilate "destroyed, annulled, reduced to nothing" (late 14c.), from past participle of Old French anichiler "annihilate, destroy" (14c.) or the Medieval Latin verb.
early 14c., "declare to be untrue or untenable," from Old French denoiir "deny, repudiate, withhold," from Latin denegare "to deny, reject, refuse" (source of Italian dinegarre, Spanish denegar), from de "away" (see de-) + negare "refuse, say 'no,' " from Old Latin nec "not," from Italic base *nek- "not," from PIE root *ne- "not."
From late 14c. as "refuse, refuse to grant or give," also "refuse to acknowledge, disavow, disown." Sense of "refuse access to" is from 1660s. Related: Denied; denying.
I may not understand what you say, but I'll defend to your death my right to deny it. [Albert Alligator, "Pogo," Sept. 26, 1951]
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.