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

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.