2020/05/23 by Behnam Najafi, Najafi, Behnam, Katherine Young +9
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Advanced biosensing and bioanalysis techniques #Bacteriophages and microbial interactions #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #FOS: Physical sciences
paper · pdf · doi:10.48550/arxiv.2005.11545
openalex publication_date 2020/05/23 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.