Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA

• The binding strength was associated with side chain effects of polyamine.
• Polyamine conjugates could bind to herring sperm DNA by intercalation and groove.
• Compounds 1–7 could cause the B to A-like DNA conformational change.
• The type of interaction force was mainly hydrogen bonding and hydrophobic force.
• The fluorescent quenching mechanism is a static type.

The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1–7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH = 7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1–6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2–6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds–DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine–DNA complexes. The circular dichroism assay about the impact of compounds 1–7 on DNA conformation testified the B to A-like conformational change.

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