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 Tm 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.
ASJC Scopus subject areas
- Colloid and Surface Chemistry