"uuid","repository link","title","author","contributor","publication year","abstract","subject topic","language","publication type","publisher","isbn","issn","patent","patent status","bibliographic note","access restriction","embargo date","faculty","department","research group","programme","project","coordinates" "uuid:6844c52e-f388-4110-a385-8bc99b9c7422","http://resolver.tudelft.nl/uuid:6844c52e-f388-4110-a385-8bc99b9c7422","DNA sequence encodes the position of DNA supercoils","Kim, S.H. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); Ganji, M. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft; Ludwig Maximilians University; Max Planck Institute of Biochemistry); Kim, E. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft); van der Torre, J. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft); Abbondanzieri, E. (TU Delft BN/Bionanoscience; Kavli institute of nanoscience Delft; University of Rochester); Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)","","2018","The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes (extended intertwined DNA structures formed upon supercoiling) on individual DNA molecules. Remarkably, our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts that sequence-dependent intrinsic curvature is the key determinant of pinning strength and demonstrate this simple model provides very good agreement with the data. Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters, which we experimentally confirm for selected promotor sequences. Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.","C. elegans; chromosome organization; chromosomes; D. melanogaster; DNA structure; DNA Supercoil; E. coli; fluorescence; gene expression; physics of living systems; plectoneme; S. cerevisiae; single molecule","en","journal article","","","","","","","","","","BN/Bionanoscience","BN/Cees Dekker Lab","","",""