The development of sensitive specific devices (e.g., molecular sensors) for the detection, diagnosis and monitoring of diseases, drug discovery, environmental detection of pollutants and/or biological agents has been an active area of research. A molecular sensor is a biomolecule or biomimetic molecule that performs two distinct functions in detecting target molecules. The sensor molecule recognizes a target molecule and specifically binds to it. This specific binding generates a signal in response to the event of target binding that can be then detected. The long term vision of this thesis research work is to develop a specific recognition ligand for detecting proteins in living cell. The purpose of this research is to develop method for designing and engineering nucleic acid molecules, aptamer molecules that are capable of functioning like molecular beacons, except that they respond to non-nucleic acid molecules. The aptamer beacon concept can be generalized to the detection of different types of molecules/proteins such as small molecules (e.g. glucose) or large molecules.