Biological systems contain a multitude of molecules with specific functions and three-dimensional shapes that enable
them to selectively interact with other molecules in a coordinated fashion. Engineering, on the other hand, has produced
devices that operate on the micron-scale and that combine electronic and mechanical systems. Microelectromechanical
Systems (MEMS) offer advantages such as the integration of a variety of functions into a single device (i.e. "lab-on-a-chip"
platforms) and portability for "point-of-care" diagnostics. This study utilizes a microscale electrochemical sensor
for detecting BoNT apatamer hybridization, in which we first used top-down lithographic processing to define the
pattern of the electrodes and then used bottom-up manufacturing to modify the surface molecular properties for reducing
The goal was to systemically examine the effects of the design parameters of an electrochemical DNA sensor. Four key
design parameters were examined: the area of the working electrode, the area of the counter electrode, the separation
distance between the working and counter electrodes, and the overlap length between the working and counter
electrodes. Through a log-log analysis of the current generated, representing the signal or noise, across variations of the
different parameters, the significance of each parameter in sensor performance was determined. We found that the area
of the working electrode was important in the performance optimization of the sensor, while the performance seemed to
be independent of the other three parameters. The output signal level increased with the area of the working electrode
and the signal-to-noise ratio was about constant in the tested range.