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We use a recently developed coarse-grained model for DNA to study kissingcomplexes formed by hybridization of complementary hairpin loops. The bindingof the loops is topologically constrained because their linking number mustremain constant. By studying systems with linking numbers -1, 0 or 1 we showthat the average number of interstrand base pairs is larger when the topologyis more favourable for the right-handed wrapping of strands around each other.The thermodynamic stability of the kissing complex also decreases when thelinking number changes from -1 to 0 to 1. The structures of the kissingcomplexes typically involve two intermolecular helices that coaxially stackwith the hairpin stems at a parallel four-way junction.

The effect of topology on the structure and free energy landscape of DNA kissing complexes