Thermodynamics of d(GGGGCCCC) Binding to Neomycin-Class Aminoglycosides

DNA adopts a number of conformations that can affect its binding to other macromolecules. The conformations (A, B, Z) can be sequence- and/or solution-dependent. While AT-rich DNA sequences generally adopt a Canonical B-form structure, GC-rich sequences are more promiscuous. Recognition of GC-rich nucleic acids by small molecules has been much more challenging than the recognition of AT-rich duplexes. Spectrophotometric and calorimetric techniques were used to characterize the binding of neomycin-class aminoglycosides to a GC-rich DNA duplex, G₄C₄, in various ionic and pH conditions. Our results reveal that binding enhances the thermal stability of G₄C₄, with thermal enhancement decreasing with increasing pH and/or Na⁺ concentration. Although G₄C₄ bound to aminoglycosides demonstrated a mixed A- and B-form conformation, circular dichroism studies indicate that binding induces a conformational shift toward A-form DNA. Isothermal titration calorimetry studies reveal that aminoglycoside binding to G₄C₄ is linked to the uptake of protons at pH = 7.0 and that this uptake is pH-dependent. Increased pH and/or Na⁺ concentration results in a decrease in G₄C₄ affinity for the aminoglycosides. The binding affinities of the aminoglycosides follow the expected hierarchy: neomycin > paromomycin > ribostamycin. The salt dependence of DNA binding affinities of aminoglycosides is consistent with at least two drug NH₃⁺ groups participating in electrostatic interactions with G₄C₄. These studies further embellish our understanding of the many factors facilitating recognition of GC-rich DNA structures as guided by their optimum charge and shape complementarity for small-molecule amino sugars.