Effects of stacking on the configurations and elasticity of single-stranded nucleic acids.

Stacking interactions in single-stranded nucleic acids give rise to configurations of an annealed rod-coil multiblock copolymer. Theoretical analysis identifies the following resulting signatures for long homopolynucleotides: a nonmonotonic dependence of size on temperature, the corresponding effects on cyclization and a plateau in the extension force law. Explicit numerical results for polydeoxyadenylate [poly(dA)] and polyriboadenylate [poly(rU)] are presented.