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Advances in DNA nanotechnology have stimulated the search for simple motifsthat can be used to control the properties of DNA nanostructures. One suchmotif, which has been used extensively in structures such as polyhedral cages,two-dimensional arrays, and ribbons, is a bulged duplex, that is two helicalsegments that connect at a bulge loop. We use a coarse-grained model of DNA tocharacterize such bulged duplexes. We find that this motif can adopt structuresbelonging to two main classes: one where the stacking of the helices at thecenter of the system is preserved, the geometry is roughly straight and thebulge is on one side of the duplex, and the other where the stacking at thecenter is broken, thus allowing this junction to act as a hinge and increasingflexibility. Small loops favor states where stacking at the center of theduplex is preserved, with loop bases either flipped out or incorporated intothe duplex. Duplexes with longer loops show more of a tendency to unstack atthe bulge and adopt an open structure. The unstacking probability, however, ishighest for loops of intermediate lengths, when the rigidity of single-strandedDNA is significant and the loop resists compression. The properties of thisbasic structural motif clearly correlate with the structural behavior ofcertain nano-scale objects, where the enhanced flexibility associated withlarger bulges has been used to tune the self-assembly product as well as thedetailed geometry of the resulting nanostructures.

Characterizing the bending and flexibility induced by bulges in DNA duplexes