Stabilization of Hoogsteen H-bonds in G-quartet sheets by coordinated K⁺ ion for enhanced efficiency in guanine-rich...

G-rich DNA nanomotors function as nanoscale devices and nanoswitches powered by the conversion of chemical energy into mechanical motion through transitions between duplex (DU) and tetraplex (TE) conformations. The stability of the TE conformation, crucial for nanomotor function, relies on G-quadruplex structures formed by guanine quartets. However, the detailed factors influencing TE stability remain unclear.

This study investigated the role of coordinated K⁺ ion and Hoogsteen H-bonds in stabilizing the TE structure of a truncated 15-nucleotide G-rich DNA nanomotor with the sequence GGTTGGTGTGGTTGG using atomic-scale computational analysis. Three systems were simulated: TE1K with a crystal K⁺ ion, TE2K with a manually embedded K⁺ ion, and TE3 lacking a K⁺ ion. All systems underwent molecular dynamics simulations using the Amber force field and TIP3P water model.

The simulations revealed a clear dependence of G-quadruplex rigidity and TE conformation stability on the presence of coordinated K⁺ ion. TE1K and TE2K, containing K⁺ ions, exhibited significantly lower RMSD values compared to TE3, indicating more excellent structural stability and rigidity. K⁺ ion coordination facilitated the formation of all eight Hoogsteen H-bonds within G-quartets, whereas the K⁺ ion-free system (TE3) displayed distorted G-quadruplexes and a reduction in H-bonds, leading to a less stable "wobble TE*" state. The diameter of G-quartets and the radius of gyration (Rg) further supported these observations, with TE1K and TE2K maintaining compact structures compared to the more open and flexible "wobble TE*" conformation in TE3.

These findings demonstrate that coordinated K⁺ ion play a critical role in stabilizing the TE conformation of G-rich DNA nanomotors by promoting G-quadruplex rigidity and facilitating Hoogsteen H-bond formation. This enhanced stability is essential for efficient DNA nanomotor function in the DU-TE nanoswitching process.