A search for base analogs to enhance third-strand binding to 'inverted' target base pairs of triplexes in the pyrimidine/parallel motif

Eight base analogs were tested as third strand residues in otherwise homopy rimidine strands opposite each of the 'direct' (A.T and G.C) and 'inverted' (T.A and C.G) Watson-Crick base pairs, using UV melting profiles to assess tripler stability. The target duplexes contained 20 A.T base pairs and a c entral test base pair X.Y, while the third strand contained 20 T residues a nd a central Z test base. Z included 5-bromouracil, 5-propynyluracil, 5-pro pynylcytosine, 5-methylcytosine, 5-bromocytosine, hypoxanthine, 2-aminopuri ne and 2,6-diaminopurine, Some of the base analogs enhanced third strand bi nding to the target duplex with one or other 'inverted' central base pair r elative to the binding afforded by any of the canonical bases, Other analog s did the same for the duplexes with the 'direct' target pairs, The increas ing order of tripler stabilization by these base analogs is: opposite the ' inverted' base pairs, for T.A, A < C < 5-pC < 5-pU < T < 5-BrC < 5-meC < 5- BrU < 2-AP < 2,6-DAP < Hy < G, for C.G, 2-AP < A < Hy < G < 5-pC < 5-BrC < 5-meC < C < 2,6-DAP < T < 5-BrU < 5-pU; opposite the 'direct' base pairs, f or A T, 2-AP < A < 5-meC < C < G < Hy < 2,6-DAP < 5-pU < T = 5-BrU < 5-BrC < 5-pC, for G.C, G < 2,6-DAP < 2-AP < A < Hy < T < 5-BrU < 5-pU < 5-pC < 5- BrC < C < 5-meC.