DNA Sequence can Pin the Position of DNA Supercoils

Abstract

While DNA obviously functions as the carrier of genetic information, it may also encode the three-dimensional spatial structure of DNA in cells. Here we study the relationship between structure and sequence in supercoiled DNA, which involves a reorganization of the DNA configuration via the formation of so-called plectonemes - coiled loop structures that locally form to minimize the torsional stress within the DNA. We use a novel high-throughput single-molecule assay called ISD (‘Intercalation-induced Supercoiling of DNA’, see Ganji et al, Nano Lett. 16, 4699, 2016), where we induce supercoiling of surface-attached DNA molecules by adding an intercalating dye. This assay allows us to visualize individual plectonemes and characterize their position-dependent frequency as well as dynamics such as nucleation, termination, and diffusion. From profiles of the average plectoneme density as a function of the position along the DNA molecule, we can study whether plectonemes exhibit any preference for certain DNA sequences. We indeed find that particular local DNA sequences pin plectonemes. Specifically, we identify DNA stretches with exclusively A or T bases (which we name ‘TorA tracts’) that strongly pin plectonemes. Interestingly, TorA tracts pin plectonemes just as well as poly-A tracts. This suggests that it is not a local intrinsic bending of the DNA (such as predicted for polyA tracts) that underlies the plectoneme pinning. Instead, we propose that local melting may lead to the formation of a kink at the tip of a plectoneme that provides a pinning site. Indeed we observed strong pinning at DNA mutation sites where 1 to 10 neighboring nucleotides are mispaired such that a ssDNA bubble is formed. Our data show that the DNA sequence does not merely encode for genetic information but also for structural information that governs the three-dimensional organization of supercoiled DNA.