Molecular states in single‐stranded adenylate chains by relaxation analysis

The single‐strand helix‐coil transition in various oligo‐ and polyadenylates is characterized by means of an improved cable temperature‐jump technique. In all the polymers studied {poly(rA), poly(dA), poly[A(m 2′ )] and poly[A(e 2′ )]} helix‐coil relaxation is observed in the time range from 30 to 1000 nsec. Relaxation‐time constants observed at wavelengths λ<280 nm (τ α ) are different from those found at λ >280 nm (τβ), indicating the presence of more than two conformational states. The time constants τ α increase in the series poly(dA), poly[A(m 2′ )], constants τ β /τ α is approximately 2.5, except in poly(dA) where τ β /τ α ≈ 9. Relaxation measurements with r(A) n ‐ oligomers show a decrease in conformational mobility with increasing chain length. The relaxation curves also demonstrate that “internal” residues have lower reaction rates than residues at the ends of the oligomer chain. Measurement in D 2 O reveal a solvent isotope effect for τ α of +87% for poly(rA), and of +53% for poly(dA), whereas no isotope effect is found in τ β . The absence of “slow” relaxation processes in the model compound 9,9′ ‐trimethylenebisadenine shows that the relatively low rate of the single‐strand helix‐coil transitions is due to the coupling of base stacking with the folding of the sugar–phosphate chain. The absence of a seprate relaxation process (corresponding to τ β ) in 9,9′‐trimethylenebisadenine, as well as in the dinucleotides ApC and CpA, suggests that this relaxation process is dependent upon the presence of both the sugar–phosphate chain and of adjacent adenine bases. The experimental data provide evidence that there is more than one ordered conformation in various single‐stranded oligo‐ and polyadenylates and that the transition between these conformations is influenced by the sugar conformation.