Base pairing equilibria between polynucleotides and complementary monomers

Abstract Equilibrium dialysis measurements and optical melting curve data have been used to study the formation and stability of a number of complexes between polynucleotides and complementary monomers. The cooperativity parameter, (dθ/d ln c ) θ = 0.5 , where θ is the fraction of U or C residues complexed, and c is the concentration of free monomer has been measured as 1.4 for the 2:1 poly U:d‐adenosine‐complex, and 2.0 5 for the 2:1 poly C:d‐guanosiue complex at pH 7. The variation of T m with c for several complexes has been used to calculate their partial molar enthalpies of formation at the midpoint of the transition: in 1.0 M Na + at pH 7, for the 2:1 complex of poly‐U with 2‐amino‐adenine, this is − 18.7 kcal/mole of 2‐amino‐adenine, for poly‐U with adenosine it is − 18.7 kcal/ mole; for poly‐C with dG, it is − 16.8 kcal/mole. These results do not agree very well with calorimetric integral heats of reaction reported in the literature. 33 Complexes with random copolymers were also studied. The random copolymer, poly‐UC, can form a mixed complex with dG and either dA or 2‐amino‐adenosine; the binding of dG is enhanced by an adenine derivative and vice versa. Similarly, poly AC can form a mixed complex with dG and 3‐methyl‐xanthine. In each case, it appears that the ideal composition is a 2:1 hydrogen‐bonded complex, but the actual stoichiometry is such that each base on the random polynucleotide binds less than one‐half of a molecule of its complementary monomer. Poly UG can bind dG and dA, but in a less cooperative and specific way.