Molecular dynamics studies of temperature-induced DNA–cation interaction: role of valency and size

In many important biological functions like gene storage, transcription, and gene regulation, nucleic acids play a vital role. Cations like Na⁺, K⁺, Ca²⁺ and Mg²⁺ play a crucial role in nullifying the coulombic repulsions between the negatively charged phosphate backbone. Some studies show that monovalent cations are generally less strongly solvated than divalent cations. While the monovalent cations are found to be more localised at preferred sites with low occupancies, the divalent cations strongly and selectively bind to the DNA molecules. Understanding the role of these cations in the modulation of the DNA structure is crucial to understanding the biological function of the molecule. For biotechnological applications, the problem of salt/cation concentration and DNA carries an important weight. We consider these four cations in the present work and investigate their interactions with the negatively charged DNA molecule at different temperatures. Our studies reveal interesting and contrasting behaviour of these cations when they interact with DNA molecules. While the Na⁺ ions tend to stay near the minor grooves and do not change their location with temperature, K⁺ ions tend to bind DNA at the minor grooves at room temperature and change their location to the major grooves at higher temperatures. The Mg²⁺ ions change their location with temperature, while Ca²⁺ ions remain near the phosphate backbone at all temperatures.