Shuntaro Takahashi and Naoki Sugimoto
Objective: Pressure can influence the folding of nucleic acids, and the effect of pressure depends on the volumetric difference between folded and unfolded states. In this study, we investigated how modification with hexaethylene glycol affected the folding of a guanine-rich DNA oligonucleotide.
Results: The stability of the G-quadruplex formed by the thrombin binding aptamer (TBA), 5’-GGTTGGTGTGGTTGG-3’ (loop regions underlined) modified with hexaethylene glycol (HEG) at the 5’-terminus decreased more significantly as pressure increased than did the G-quadruplex formed by the unmodified TBA. The change of partial molar volume, ΔV, of 5-HEG TBA folding was 101 cm3 mol-1, where as that of TBA was 54.6 cm3 mol-1. The HEG at 5’ terminus of TBA increased volume of the folded structure due to induction of dehydration. In contrast, replacement of the 5’-most loop of the TBA G-quadruplex with HEG resulted in a ΔV value of 62.8 cm3 mol-1, whereas replacement of the second loop resulted in a ΔV value of 82.8 cm3 mol-1. It has been suggested that bases of the nucleotides in the second loop form stacking interaction with G-quartet but those in the first loop do not.
Conclusion: These results indicate that a 5’ covalently linked HEG disrupts the stacked structure of the second loop on the G-quartet; this stacking accompanied dehydration during the quadruplex formation. Thus, modification with poly(ethylene glycol) units enhances the effect of pressure on the folding of G-quadruplex DNA.
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