Characterising DNA T-motifs by Simulation and Experiment

TL;DR

This study combines simulation and experimental approaches to characterize DNA T-motifs, revealing how sticky end polarity and coaxial stacking influence their stability and geometry, advancing understanding in DNA nanotechnology.

Contribution

It provides a detailed comparison of experimental data with oxDNA simulations, highlighting the effects of sticky end polarity and stacking interactions on T-motif stability.

Findings

5' sticky ends produce more stable junctions across bulge sizes

Coaxial stacking interactions significantly stabilize the T-motif

Simulation predictions align well with experimental results

Abstract

The success of DNA nanotechnology has been driven by the discovery of novel structural motifs with a wide range of shapes and uses. We present a comprehensive study of the T-motif, a 3-armed, planar, right-angled junction that has been used in the self-assembly of DNA polyhedra and periodic structures. The motif is formed through the interaction of a bulge loop in one duplex and a sticky end of another. The polarity of the sticky end has significant consequences for the thermodynamic and geometrical properties of the T-motif: different polarities create junctions spanning different grooves of the duplex. We compare experimental binding strengths with predictions of oxDNA, a coarse-grained model of DNA, for various loop sizes. We find that, although both sticky-end polarities can create stable junctions, junctions resulting from 5$'$ sticky ends are stable over a wider range of bulge loop sizes. We highlight the importance of possible coaxial stacking interactions within the motif and investigate how each coaxial stacking interaction stabilises the structure and favours a particular geometry.