In order to understand the biosensing mechanism of field-effect based biosensors and optimize their performance, the effect of each of its molecular building block must be understood. In this work the gating effect of self-assembled linker molecules on field-effect transistor was studied in detail. We have combined Kelvin probe force microscopy, current-voltage measurements, capacitance-voltage measurements, equivalent circuit modeling and device simulations in order to trace the mechanism of silicon-on-insulator biological field-effect transistors. The measurements were conducted on the widely used linker molecules (3-aminopropyl)-trimethoxysilane (APTMS) and 11-aminoundecyltriethoxysilane (AUTES), which were self-assembled on ozone activated silicon oxide surface covering the transistor channel. In a dry environment, the work function of the modified silicon oxide decreased by more than 1.5 eV, and the transistor threshold voltage increased by about 30 V following the selfassembly. A detailed analysis indicates that these changes are due to negative induced charges on the top dielectric layer, and an effective dipole due to the polar monolayer. However, the self-assembly did not change the silicon flat-band voltage when in contact with an electrolyte. This is attributed to electrostatic screening by the electrolyte.