We present a demonstration of molecular rectification in a metal-molecule-metal junction created by self-assembly where endgroup chemistry does not influence the observed conductance asymmetry. Using a protection scheme which allows for stepwise deprotection of aryl thiols, the deposition of (alpha,omega)-dithio-molecules with a preferred polar order can be achieved. Quartz crystal microgravimetry was used to demonstrate the sequential nature of the deprotection and the preferred orientation of absorption of the monodeprotected dithiols. Current-voltage measurements of metal-molecule-metal junctions reveal a bias polarity asymmetry resulting solely from the internal molecular asymmetry and not from the initial protecting group chemistry.