Structure and Energetics of a Hexanucleotide Duplex with Stacked Trinucleotide Ends Formed by the Sequence d(GAATTCGCG)

Nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSC) have been used to investigate structural and energetic features of the helix-to-coil transition of the duplex formed by the partially self-complementary sequence d(GAATTCGCG) (henceforth called 9-mer). These results are compared with those obtained from a corresponding study on the helix-to-coil transition of the duplex formed by the fully self-complementary sequence d(GGAATTCC) (henceforth called 8-mer). The two sequences contain a common GAATTC hexanucleotide duplex with this core flanked by d(GCG) trinucleotide ends in the 9-mer and by dG·dC base pairs in the 8-mer duplex. The NMR parameters for the 9-mer reveal formation of the hexanucleotide core duplex and stacking of the unpaired bases at the trinucleotide ends. The imino proton line widths suggest that under the conditions of the NMR experiment and at low temperature the 9-mer duplexes aggregate through pairing of the complementary ends. DSC on both the 8-mer and 9-mer duplex in 1 M NaCl reveals that the calorimetric transition enthalpies are essentially equal [−60 kcal (mol of double strand)⁻¹] despite a 6.2 °C higher melting temperature, T_m, for the 8-mer relative to the 9-mer duplex. From a comparison of the model-dependent van't Hoff and model-independent calorimetric enthalpies we conclude that the helix-to-coil transition of the 8-mer approaches two-state behavior while the corresponding 9-mer transition involves intermediate states. We assign the cooperative component of the 9-mer transition to disruption of the hexanucleotide duplex core with the remaining noncooperative component being associated with the disruption of the stacked ends.