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We apply continuum solvent models to investigate the relative stability of A- and B-form helices for three DNA sequences, d(CCAACGTTGG)₂, d(ACCCGCGGGT)₂, and d(CGCGAATTCGCG)₂, a phosphoramidate-modified DNA duplex, p(CGCGAATTCGCG)₂, in which the O3‘ atom in deoxyribose is replaced with NH, and an RNA duplex, r(CCAACGUUGG)₂. Structures were taken as snapshots from multi-nanosecond molecular dynamics simulations computed in a consistent fashion using explicit solvent and with long-range electrostatics accounted for using the particle−mesh Ewald procedure. The electrostatic contribution to solvation energies were computed using both a finite-difference Poisson−Boltzmann (PB) model and a pairwise generalized Born model; nonelectrostatic contributions were estimated with a surface-area-dependent term. To these solvation free energies were added the mean solute internal …