Decoding the role of DNA sequence on protein-DNA co-condensation.

ABSTRACT: The compaction of DNA by phase-separating, DNA-binding proteins has emerged as a key mechanism for organizing chromatin and shaping genome architecture. Although experimental studies have provided insights into the governing principles of such protein-DNA co-condensation, how DNA sequence affects this process remains unclear. Guided by experimental observations, we develop a simple polymer-based model of protein-DNA co-condensation that explicitly accounts for sequence-dependent protein binding. Using coarse-grained Brownian dynamics simulations, we demonstrate that, in the case of a homogeneous DNA, only one condensate forms in equilibrium. In sharp contrast, DNA sequence heterogeneity can result in the coexistence of multiple condensates. Interestingly, we find that interfacial DNA bindi

SUBMITTER: Singh RK 

PROVIDER: S-EPMC12725741 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature