Hydrophobic Effect in Self-Assembly of Metal-Bound Nucleotides: A Structural Study of Iron-Nucleotide Ternary Complexes

Abstract

The influence of hydrophobic microenvironments on the self-assembly and structural dynamics of nucleotides remains fundamentally elusive at the molecular level. Here, we establish a robust biomimetic platform utilizing a Fe(III)-nucleoside monophosphate-TPA ternary complex, where the bulky TPA ligand serves as a tailored “hydrophobic umbrella”. High-resolution crystallographic investigations reveal that this localized confinement drives 5′-coordinated nucleotides to spontaneously assemble into discrete biological architectures, such as A-motifs and i-motifs. Translating these solid-state findings to aqueous solution, circular dichroism (CD) spectroscopy provides experimental validation of the supramolecular mechanism. Solvent-dependent titrations reveal a sharp, nonlinear sigmoidal phase transition, explicitly demonstrating that the TPA scaffold actively overrides the chaotic, isodesmic π–π stacking characteristic of free nucleotides. Instead, the rigid chiral locking of the assembly is cooperatively driven by the massive thermodynamic compressive forces of hydrophobic exclusion. Comprehensive computational modeling, including DFT, NCI, and Hirshfeld surface analyses, unequivocally maps and quantifies this driving force, isolating the explicit energetic stabilization provided by the dispersive hydrophobic shield. Furthermore, we resolve the paradoxical role of solvent within these confined cavities: while bulk water is aggressively repelled, a specifically localized primary hydration shell is strictly preserved. This inner hydration layer acts as a master thermodynamic determinant, mechanically locking the precise biomimetic sugar ring puckering (C3′-endo/C2′-exo) requisite for assembly. Collectively, these integrated structural, spectroscopic, and thermodynamic insights illuminate the physicochemical forces governing nucleic acid organization in restricted spaces, offering a definitive supramolecular model for biological molecular recognition.