Significance of Knotted Structures for Function of Proteins and Nucleic Acids
Poster Session I
28A – POS Board 28
Effect of Knots on Binding of Intercalators to DNA
Shlomi Medalion
and Yitzhak Rabin
Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan
University, Ramat-Gan 52900, Israel
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.
* S. Medalion and Y. Rabin, "Effect of Knots on Binding of Intercalators to DNA", J. Chem.
Phys. (2014), 140, 205101; DOI:10.1063/1.4875804.
- 75 -
