Stable triplexes play key roles in many biological processes. Due to the Hoogsteen base pairing, triplexes are, however, thermodynamically less stable than the corresponding duplexes. The poor stabilization of these structures limits their practical applications under physiological conditions. To understand the factors effect on the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the interactions of [RuL2(uip)](2+) {where L = 2,2'-bipyridine (bpy) or 1,10-phenanthroline phen, uip = 2-(5-uracil)-1H-imidazo[4,5-f][1,10]phenanthroline} with the RNA triplex poly(U)center dot poly(A)*poly(U) are examined by spectrophotometry, spectrofluorometry, circular dichroism, and viscosimetry in this work. The main results obtained here suggest that the third-strand stabilization depends on the hydrophobicity effects of ancillary ligands bpy and phen.