DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double‐helix stability

The thermodynamic parameters for the double‐strand formation of the molecules rCA m G + rCU n G, m , n = 5–7, and dCA m G + dCT n G, m , n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n . The deoxyoligomers are more stable than the ribo‐oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n . Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA 7 G·rCU 7 G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double‐strand formation are discussed.