The stabilizing contribution of thymine in duplexes of (dA)24 with (dU)24, (dT)24, (dU12-dT12), (dU-dT)12, (dU2-dT2)6, or (dU3-dT3)4: Nearest neighbor and next-nearest neighbor effects

Abstract

Ultraviolet melting curves are used to determine the effect of the pyrimidine 5‐methyl group on the stability of duplexes of (dA)₂₄ with (dU)₂₄, (dT)₂₄, (dU₁₂–dT₁₂), (dU–dT)₁₂, (dU₂–dT₂)₆, and (dU₃–dT₃)₄. Substitution of a T for a U results in an increase in stability, which is attributed to an increase in strength of dipole‐induced dipole and dispersion (van der Waals) interactions. Significant additional enhancement occurs when two T residues are adjacent. A further increase in the number of adjacent T's has a relatively slight effect on T_m. The sequence effect appears to be largely attributable to an increment in dispersion forces. The CD spectra of the duplexes are all closely similar except in the region between 260 and 290 nm. A band near 272 nm associated with the presence of U in the spectrum of (dA)₂₄·(dU)₂₄ decreases in intensity when T's are incorporated in the pyrimidine strand. The band is completely replaced in the spectrum of (dA)₂₄·(dT)₂₄ with a new maximum at 282 nm and a minimum at 268 nm, both of lower magnitude. The emergence of the two new bands is correlated with the presence of adjacent T's once more, and only two adjacent T's appear necessary for a major part of the change to occur. The degree of cation release on thermal dissociation of the oligomer dimers ranges from Δi = 0.14 to 0.16, about the same or slightly less than values reported for polynucleotide duplexes and less than predicted from theoretical calculations. © 2005 Wiley Periodicals, Inc. Biopolymers 78:221–229, 2005