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Nanites were machines designed to manipulate matter on the atomic and molecular level.

The nanites created by Genetec Systems were called nanoforms. They could deconstruct objects on a molecular level and then reconstruct them into a new form. They needed to be kept at sub-zero temperatures to remain inactive. (TV: Prisoner of the Judoon)

The Tremas Master made a deal with the Tzun to help them invade Earth in exchange for a new body. This was done with nanites that broke down the corrupted Trakenite DNA in his cells and restructured it. The Master was restored to being a "full" Time Lord, allowing him a new regenerative cycle. After being shot by Ace, he regenerated into a new body, (PROSE: First Frontier) but this Master was then reduced to ashes by the Daleks, (PROSE: The Novel of the Film, The TV Movie) and by the time his spirit resurfaced using a Deathworm Morphant, the nanites had "failed", leading the Master's default appearance to revert to the decayed form he inhabited before he even possessed the Trakenite Tremas, his original thirteenth incarnation. (AUDIO: Mastermind, Planet of Dust)

Selachian battlesuits were equipped with nanites to repair damage and to counteract the nanites of the Terran Security Forces. (PROSE: The Final Sanction)

The Contagium was a Dalek device. When released into an environment, it transformed its biological host into a factory which produced nanites which burrowed into the brain and placed anyone infected under Dalek control. (COMIC: Fire and Brimstone)

There were nanites in the Pentaquoteque Gallery on Ouloumos. When approached by people, they would form a painting of their faces. (COMIC: The Arts in Space)

The Cyberons' Conversion Engine contained nanites within it. A Cyberon estimated that these nanites would expire approximately two weeks after the engine failed. (PROSE: Flight of the Cyberons)

In an alternate timeline where Rassilon formed an alliance with the Cyberiad, the Cybermen who invaded Earth in the year 2006 created a nanite-based techno-virus that quickly upgraded the population. (COMIC: Supremacy of the Cybermen)