Apparatus and methods are disclosed for single molecule field effect sensors having conductive channels functionalized with a single active moiety. A region of a nanostructure (e.g., such as a silicon nanowire or a carbon nanotube) provide the conductive channel. Trapped state density of the nanostructure is modified for a portion of the nanostructure in proximity with a location where the active moiety is linked to the nanostructure. In one example, the semiconductor device includes a source, a drain, a channel including a nanostructure having a modified portion with an increased trap state density, the modified portion being further functionalized with an active moiety. A gate terminal is in electrical communication with the nanostructure. As a varying electrical signal is applied to an ionic solution in contact with the nanostructure channel, changes in current observed from the semiconductor device can be used to identify composition of the analyte.