Abstract: The folding of the thrombin DNA aptamer was studied with single molecule fluorescence imaging. The aptamer was singly labeled with TMR and immobilized on the glass surface. In the presence of K⁺ , the folding of the aptamer resulted in the formation of G-quartets, thus brought TMR close to the guanosines. This led to the fluorescence decrease of TMR through the electron transfer between the dye and guanosines. From the fluorescence intensity of individual TMR, the distribution of aptamer molecules between the folded and random coil conformations was monitored at different concentrations of K⁺. The results show a new approach for the investigation of aptamer conformational change by electron transfer induced fluorescence quenching, which is complementary to the commonly used fluorescence resonance energy transfer in single molecule study.

Key words: Single molecule fluorescence, Electron transfer, G-quartet, Thrombin aptamer, Folding