Atomistic Stability of Q-DNA: Molecular Dynamics Simulations and Structural Persistence Criteria

Abstract

Theoretical plausibility of a canonical tetra-stranded genome must ultimately be confronted with atomistic stability. Even if topological, thermodynamic, and electrostatic conditions are satisfied in principle, a viable Q-DNA architecture must persist under thermal fluctuations at atomic resolution. In this work, I define a reproducible molecular dynamics (MD) protocol to evaluate candidate tetra-stranded Q-DNA architectures and establish quantitative criteria for structural persistence. I apply this framework to three representative Q-DNA architectures and compare their behavior to canonical B-DNA and well-characterized G-quadruplex motifs. Using standard MD observables—RMSD, hydrogen-bond occupancy, helical twist, and breathing modes—I identify a top three set of Q-DNA architectures that remain structurally coherent over simulation timescales and derive sequence-level design recommendations for future experimental and computational studies.

Keywords: Q-DNA, molecular dynamics, tetra-stranded DNA, atomistic stability, structural persistence, G-quadruplex comparison