Modulation of DNA Nanostructure Morphology by Metal Ions and Temperature: An AFM Study

In biological systems, DNA serves as the primary carrier of genetic information, and the stability of its structure is fundamental to cellular function. Metal ions and temperature are critical environmental factors that modulate DNA conformation and activity. However, the differential morphological effects of alkali, alkaline earth, and transition metal ions, especially when combined with thermal treatment, have not been systematically visualized and quantified. In this work, atomic force microscopy (AFM) was employed to investigate the effects of different metal ions (Na⁺, K⁺, Mg²⁺, Ca²⁺, Cu²⁺) and temperature on DNA structure. The results demonstrated that monovalent ions (Na⁺ and K⁺) neutralized the negative charges on the DNA backbone, thereby reducing intermolecular electrostatic repulsion and promoting DNA aggregation into dendritic structures. Divalent ions (Mg²⁺ and Ca²⁺) not only provided more effective charge screening but also formed ion bridges between DNA strands, leading to more compact and cross-linked networks. In contrast, Cu²⁺ ions directly coordinated with DNA bases, causing local structural distortion and strand scission. Elevated temperatures induced DNA melting, with distinct morphological transitions from extended double strands to condensed single-stranded globules observed at temperatures exceeding the melting point (Tm). These findings elucidate the mechanisms by which environmental factors govern DNA morphology, providing insights relevant to nanotechnology and molecular biology applications.