The phenomenon of "blinking" is unique to single-molecule fluorescence measurements. By designing a fluorophore with an appropriate dark state lifetime (τoff), we have devised a kinetic analysis based on the control of fluorescence blinking (KACB) to investigate the dynamics of biomolecules. By controlling the redox reaction based blinking (rKACB), we have previously investigated conformational dynamics of RNA at the single-molecule level. However, there have been little knowledge about suitable fluorescent molecules for rKACB, and the application of rKACB has been limited to the analysis of hairpins and duplex structures of nucleic acids. In this paper, we evaluated various fluorescent molecules, including ATTO 655, ATTO 647N, TAMRA, R6G, and Alexa 488, for rKACB. rKACB was adapted to the discrimination of DNA/DNA and DNA/RNA nucleic acid duplexes and investigation of antigen-antibody interactions. Further, by changing the size of the oxidant, we were able to determine the solvent accessibility of the target domain of the biomolecules analysed.