Polynucleotides. XIII. Stoichiometric and Thermodynamic Studies of Polynucleotide Helices with Non‐Complementary Residues

Stoichiometry and thermodynamic properties of polyadenylate–polyuridylate helices containing varying proportions of near‐randomly distributed non‐complementary uridine residues were charactrized from an analysis of their mixing curves and melting profiles measured at 259 nm and at appropriate longer wavelength isochromic points. The noncomplementary residues in this homopolymer–copolymer system (in which the homopolymer has the capacity to readjust with respect to the residues with which it is in opposition) show absolute preference for an extrahelical conformation even when situated in … AAUAA … sequences and must occur therefore as single loops. As the frequency of extrahelical residues in creases, the electrostatic energy of these complexes becomes greater, and is particularly severe for the three‐stranded helices. Thus, an adenyl‐ate‐uridylate copolymer containing 35.2 mole percent uridine residues does not form a three‐stranded complex with polyuridylate even in 0.7M Na + at O°C. The imperfections introduced into the helix lattice by extrahelical residues decrease the cooperativity of thermal denaturation as well as T m . However, for the helices with extrahelical residues in low frequency (∼1 per helix turn) only small increases in concentration of charge‐neutralizing ions are required to bring T m to the level of their perfect analogs. Two‐stranded helices with a higher density of extra helical residues (∼5 per helix turn) show [Na + ] dependence of T m characteristic of perfect three‐stranded helices. These findings together with the absence of an effect of these imperfections on the hypochromicity per base‐pair suggest only minimal disruption of helix continuity or distortion of stacking interactions that normally in volve the base pairs or triplets.