Analytical Model for OWL Sensors: A look at the Strain-Mismatch interaction in DNA

Abstract

DNA-hybridisation-based biosensing stands at the forefront of liquid biopsy development and, consequently, the next generation of non-invasive tumour detection. These biosensors are fundamentally limited by the thermodynamic challenge of discriminating trace single-nucleotide variants (SNVs) from the large excess of wild-type DNA background. Recent advances indicate that incorporating structural constraints in the design of molecular beacon-based OWL sensors can significantly enhance their selectivity. However, the underlying mechanism behind these constraints remains speculative. In this work, we test the hypothesis that these constraints induce torsional strain within these probes and seek to optimise their working regime by developing an analytically solvable coarse-grained model. The sensor is modelled as a one-dimensional lattice system in which nodes are coupled via harmonic interactions of exponentially decaying (Kac-Baker-like) strength. Through the Schur complement of the twist coordinate of the cgDNA+ stiffness matrix, the model effectively accounts for the higher-dimensional degrees of freedom in the DNA duplex. In a general framework, we aim to identify the non-additive free-energy interaction term ΔΔF that arises between two perturbations in the system, and then analyse its application to the presence of a single-base mismatch and to global frustration in the system. This approach allows us to analyse regimes in which the mismatch destabilises the duplex. Specifically, we demonstrate that an optimisable destabilising regime exists for any softening mismatch within this framework, consistent with the expected mechanical effect of a mismatch. To validate the hypothesis that these constraints induce torsional frustration in the sensor, we perform coarse-grained molecular dynamics simulations with the oxDNA LAMMPS module. We construct a closed-loop system resembling OWL sensors. This closed loop is expected to impose significant structural strain because the 9-base-pair hybridising region is incompatible with DNA’s natural helical periodicity (∼ 10.4 bp). This structure is subsequently compared with its helically compatible 10-base-pair counterpart and an open-loop variant. Using 3DNA analysis, we can extract physical degrees of freedom from the simulated duplexes and find that bending of the hybridised region, rather than twist, imposes the dominant contribution to strain.