Saccharomyces cerevisiae Stm1 protein (273 amino acids) is a purine motif triplex DNA-binding protein. We have previously found that Stm(1-113) (amino acids 1-113) is the minimal domain to specifically bind with the purine motif triplex. Here, to reveal the triplex recognition mechanism of Stm(1-113), we have examined the interaction between Stm(1-113) and each of the purine motif triplexes with various lengths and base sequences. As the length of the target triplex was increased, the binding affinity of Stm(1-113) to the target triplex was increased. Stm(1-113) had the ability to bind to the purine motif triplexes with various base sequences. We conclude that Stm(1-113) may recognize the shape of the triplex rather than the base sequence of the triplex.