Sequence‐Encoded Frustration Directs the Formation of Abridged G‐Quadruplex Architectures

Abstract

ABSTRACT Frustration—competing interactions that cannot be simultaneously optimized—shapes energy landscapes in proteins and soft matter, but has rarely been exploited as a programmable design principle in nucleic acids. Here we demonstrate that sequence‐encoded frustration programmes DNA G‐quadruplex folding, yielding stable “abridged” architectures with fewer guanine tetrads than the sequence would nominally permit. Using an integrated structural, spectroscopic, thermodynamic, and computational approach, we map a frustration‐biased folding landscape featuring a thermodynamically stabilized G‐triplex intermediate, whose identity we assign via TD‐DFT computed electronic circular dichroism spectra, and resolve the dominant unfolding pathway at atomic resolution. These results demonstrate programmable frustration as a predictive design principle for controlling nucleic acid topology and dynamics, offering new strategies for engineering functional DNA‐based systems and for interpreting genomic G‐quadruplex plasticity.