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 reverse 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-D1·D2 and ps-D5·D6) or antiparallel-stranded (aps-D1·D3 and aps-D5·D7) 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_m values (by 17 and 34 °C, ±0.7 °C) and lower transition enthalpies (34 and 51 kcal-mol^-1, ±3 kcal mol^-1) 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 dG-dC base pairs. Substitution of four dA·dT base pairs of the ps-D1·D2 duplex for four dG-dC base pairs to create the ps-D5·D6 duplex results in a destabilization of 11.9 °C that is entropically driven. The same substitution in the aps duplexes results in a stabilization of 4.9 °C that is enthalpically driven.