Decoding the role of DNA sequence on protein-DNA co-condensation
Fig 2
DNA sequence dictates the position of the condensates.
A Schematic represents a homogeneous DNA model; each monomer (blue) binds to proteins (green) with an identical binding affinity (2 kBT). B Schematic represents heterogeneous DNA I model; monomers (red) at the center bind proteins with an affinity of 2.25 kBT, whereas monomers (yellow) at the periphery have an interaction strength of 1.75 kBT. Proteins bind to each other with an interaction strength of 2 kBT. C, D Snapshots of DNA configurations for homogeneous and heterogeneous DNA I, in the absence of proteins, are shown. E, F Snapshots of protein-DNA co-condensates in equilibrium for the two models are shown. To generate the plots, we fixed the normalized end-to-end distance () and varied
. G, H Probability distribution of DNA and proteins along the longitudinal axis at
= 0.6, for different bulk protein concentrations (
), shown for homogeneous and heterogeneous DNA I, respectively. For each
value, data from five independent replicates are included in the plots. I, J Representative kymographs for position of condensates along the contour as a function of time for homogeneous DNA (
=0.6,
= 109.9
) and heterogeneous DNA I (
=0.6,
= 93.01
) are shown.