Hydrophobic dimerization and thermal dissociation of perylenediimide-linked DNA hairpins

The structure and properties of hairpin-forming bis(oligonucleotide) conjugates possessing perylenediimide (PDI) chromophores as hairpin linkers have been investigated using a combination of spectroscopic and computational methods. These conjugates exist predominantly as monomer hairpins at room temperature in the absence of added salt and as head-to-head hairpin dimers in the presence of >50 mM NaCl. The hairpin dimer structure is consistent with the results of small-angle X-ray scattering in aqueous solution and molecular dynamics simulation. The structure of the nonconjugated PDI dimer in water is investigated using potential of mean force calculations. The salt dependence is attributed to increased cation condensation in the hairpin dimer vs monomer. Upon heating at low salt concentrations, the hairpin dimer undergoes sequential dissociation to form the monomer hairpin followed by conversion to a random coil structure; whereas at high salt concentrations both dissociation processes occur over the same temperature range. The monomer and dimer hairpins have distinct spectroscopic properties both in the ground state and excited singlet state. The UV and CD spectra provide evidence for electronic interaction between PDI and the adjacent base pair. Low fluorescence quantum yields are observed for both the monomer and dimer. The transient absorption spectrum of the dimer undergoes time-dependent spectral changes attributed to a change in the PDI-PDI torsional angle from ca. 20 degrees in the Franck-Condon singlet state to ca. 0 degrees in the relaxed singlet state, a process which occurs within ca. 40 ps.