Calorimetric Characterization of Parallel-Stranded DNA: Stability, Conformational Flexibility, and Ion Binding

Parallel-stranded DNA is a novel double-stranded, helical form of DNA. Its secondary structure is established by reuerse Watson-Crick base pairing between the bases of the complementary strands, forming two equivalent grooves. A combination of differential scanning calorimetry and temperature-dependent UV spectroscopy techniques have been employed to characterize the stability, conformational flexibility, and counterion binding of two sets of 25-mer deoxyoligonucleotide duplexes containing either exclusively dA.dT base pairs or substitutions with four dG.dC base pairs. These form either parallel-stranded (ps-DleD2 and ps-DSsD6) or antiparallel-stranded (aps-DI.D3 and aps-DSsD7) duplexes. All four duplexes show two-state transition behavior with similar values for the thermodynamic release of counterions, indicating that the charge densities are similar. The parallel duplexes melt with both lower T, values (by 17 and 34 OC, f0.7 "C) and lower transition enthalpies (34 and 5 1 kcal-mol-', 13 kcal mol-') than the corresponding antiparallel reference duplexes. These unfavorable differential free energy terms are enthalpically driven, reflecting a reduction in base-stacking interactions and in hydrogen bonding for the case of the duplexes containing dGdC base pairs. Substitution of four dA.dT base pairs of the ps-DIsD2 duplex for four dG.dC base pairs to create the ps-D5.D6 duplex results in a destabilization of 11.9 OC that is entropically driven. The same substitution in the aps duplexes results in a stabilization of 4.9 OC that is enthalpically driven.