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 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. (PROSE: First Frontier)

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)

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