DNA 4-way junction, or the Holliday junction, appears as an intermediate structure of the homologous DNA recombination, which is a critical process for gene maintenance and genetic diversity. To completely unravel the mechanism of the recombination process, therefore, it is important to understand how the Holliday junction behaves. Previous single-molecule FRET (fluorescence resonance energy transfer) measurements revealed that the Holliday junction is a dynamics structure switching between well-defined two different FRET states. To build a complete picture of the molecular motion of the Holliday junction with four helical arms, however, the conventional two-color FRET does not give enough information. By developing three-color FRET, which can probe the correlated motion of single biomolecules, we showed that the Holliday junction adopts the two possible stacking conformers. By combining single-molecule FRET and optical tweezers, we could also prove the existence of the meta-stable intermediate state, which has been hypothesized but could not be detected for a long time.