We compared the structure of fission yeast telomeric DNA, 4G4: d(GGGGTTAC)4, and nontelomeric DNA, 4T4: d(TTTTTTAC)4, and examined their interaction with telomeric DNA binding domain of telomeric DNA binding protein Pot1 (Pot1DBD). 4T4 did not form any higher-order structure, but 4G4 formed intramolecular folded tetraplex structure in the presence of Na+. Although Pot1DBD did not induce any significant structural change of 4T4, the intramolecular folded tetraplex structure of 4G4 was unfolded by the interaction with Pot1DBD. Pot1 may facilitate telomere elongation of telomerase by disrupting the tetraplex structure of the telomeric DNA.