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

Abstract

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 Bform 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 GCrich DNA duplex, G 4 C 4 , in various ionic and pH conditions. Our results reveal that binding enhances the thermal stability of G 4 C 4 , with thermal enhancement decreasing with increasing pH and/or Na + concentration. Although G 4 C 4 bound to aminoglycosides demonstrated a mixed A-and B-form conformation, circular dichroism studies indicate that binding induces a conformational shift toward Aform DNA. Isothermal titration calorimetry studies reveal that aminoglycoside binding to G 4 C 4 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 G 4 C 4 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 NH 3 + groups participating in electrostatic interactions with G 4 C 4 . 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.

Parallel G-quadruplex recognition by neomycin

“…In the DNA-binding studies including some of the hybrid duplexes, neomycin emerged as the strongest binder among other related aminoglycosides ( Figure 1 ) containing the 2-deoxystreptamine core. 20 Biophysical experiments with a diverse nucleic acid structural landscape revealed shape-dependent nucleic acid recognition by neomycin with a general preference toward A-form nucleic acid structures ( Arya et al, 2003b ; Xi et al, 2011 ; Watkins et al, 2017 ; Conner et al, 2023 ).…”