We perform molecular dynamics simulations to analyze the wrapping process of a single-stranded (ss) DNA around a gapped CNT immersed in a bath of water. We observe the formation of a stable molecular junction with the ssDNA adopting a helical or circular conformation around one CNT electrode and a linear conformation around the opposite electrode. We find that DNA undergoes several conformational changes during equilibration of the self-assembled molecular junction. This process would allow a higher yield of successful CNT-DNA interconnections, which constitutes a novel structure of interest in chemical and biological sensing at the single-molecule level. © Springer-Verlag 2011.