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Characterising DNA T-motifs by simulation and experiment

Behnam Najafi, Katherine G. Young, Jonathan Bath, Ard A. Louis, Jonathan P. K. Doye and Andrew J. Turberfield


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.

The full paper is available from arXiv.org.