The specific detection and precise quantification of protein molecules play an essential role in basic discovery research as well as in clinical practice. In this research work, a novel protein detection mechanism based on nanoscale dielectric sensor functionalized with aptamer probes is developed. This work has been done in collaboration with Rational Affinity Devices LLC. The use of aptamer based detection offers several advantages over the traditional labor intensive antibody based immunosensing. In the initial phase of the work, the binding affinities of rationally designed oligomers towards a specific protein molecule (IgG) was studied and optimized under varying conditions of ionic strength and pH using fluorescence based methods. Also, various immobilization strategies for aptamer probes including agarose gel based biomimetic surfaces and self assembled monolayers were studied. In the second phase of the sensor development, two separate transduction mechanisms to produce a measurable signal from the immobilized aptamer-protein binding events were analyzed. Initially, a piezoelectric sensing mechanism utilizing the mass of the protein molecules was developed. Although found to be sensitive, this mechanism suffered from viscous damping in liquid phase measurements. Therefore, a novel nanoscale dielectric sensor was developed capable of monitoring biomolecular recognition events in liquid phase with high sensitivity. The use of this sensor for attaining highly sensitive label-free detection of alpha thrombin using immobilized aptamer probes is demonstrated in this work.