title: Effect of knots on binding of intercalators to DNA.
abstract: We study the effect of knots in circular dsDNA molecules on the binding of intercalating ligands. Using Monte Carlo simulations we show that depending on their handedness, the presence of knots can either suppress or enhance intercalation in supercoiled DNA. When the occupancy of intercalators on DNA is low, the effect of knots on intercalation can be captured by introducing a shift in the mean writhe of the chain that accounts for the writhe of the corresponding ideal knot. In the limit of high intercalator occupancy, the writhe distribution of different knots is strongly affected by excluded volume effects and therefore by salt concentration. Based on the finding that different knots yield well-separated probability distributions of bound intercalators, we propose a new experimental approach to determine DNA topology by monitoring the intensity of fluorescence emitted by dye molecules intercalated into knotted DNA molecules.
authors.affiliation: Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
authors.forename: Shlomi
authors.initials: S
authors.lastname: Medalion
authors.affiliation: Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Rabin
mesh_terms: D055592:Biophysical Phenomena; D004247:DNA / Q000737:chemistry*; D004270:DNA, Circular / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation
chemical_list: D004270:DNA, Circular; D007364:Intercalating Agents; D004247:DNA