Electrochemical detection of nucleic acids has been a very important research area in the past several decades. In this research field, the stability of the nucleic acid structure is important and crucial for many aspects of nucleic acid metabolism. Also the binding of small molecule ligands to nucleic acids and resulting increase in stability of the nucleic acids can play a key role in many context including DNA-targeted therapy against various cancers, bacteria or viruses. Melting curve analysis using electrochemical detection, as a new method to characterize nucleic acids' stability and interactions between small molecules, provides high sensitivity and is also well suited for high-throughput formats. This thesis describes efforts to develop melting curve analysis using electrochemical detection method on a temperature-controlled microscale platform.