Hybridization between Oxy-Peptide Nucleic Acids and DNAs:  Dependence of Hybrid Stabilities on the Chain-Lengths, Types of Base Pairs, and the Chain Directions

Oxy-peptide nucleic acids (OPNAs) of [-NH-CH(CH2-CH2-Base)-CH2-O-CH2-CO-]-type main chain with four different types of nucleobases (Base = A, G, C, and U) or with an abasic side group (X) were synthesized. Melting curves of the 1:1 hybrids of o(A n )−d(T n ) pairs with n = 6, 9, 12, and 15 showed very sharp transitions at high T m values, particularly for long chains, indicating that nearly optimum matching is attained in the structure of the o(A n )−d(T n ) hybrids. Effect of different types of base pairs on the hybrid stabilities was examined for the o(A4NA4)−d(T4N‘T4) 1:1 mixtures where N is A, G, C, U, or X and N‘ is A, G, C, or T. In all series of the hybrids the complementary pairs showed the highest T m values. The T m values of the complementary pairs were about 35 °C when purine bases were inserted as the N group in the OPNA, but they were 20−23 °C when pyrimidine bases were inserted. The melting curves of the hybrids with a single mismatch were similar to those with a single X−N‘ pair, suggesting that the mismatch base pairs have been ignored in the hybrids. All complementary OPNA−DNA hybrids showed higher T m values and sharper transitions than the corresponding DNA−DNA hybrids. The OPNA−DNA hybrids favor a parallel direction i.e., the N-terminal of OPNA is directed to the 5‘-terminal of DNA.