Induction and Monitoring of DNA Phase Separation in Living Cells by a Light-Switching Ruthenium Complex

Phase
separation of DNA is involved in chromatin packing for the
regulation of gene transcription. Visualization and manipulation of
DNA phase separation in living cells present great challenges. Herein,
we present a Ru­(II) complex (Ru1) with high DNA binding
affinity and DNA “light-switch” behavior that can induce
and monitor DNA phase separation both in vitro and
in living cells. Molecular dynamics simulations indicate that the
two phen-PPh3 ligands with positively
charged lipophilic triphenylphosphine substituents and flexible long
alkyl chains in Ru1 play essential roles in the formation
of multivalent binding forces between DNA molecules to induce DNA
phase separation. Importantly, the unique environmental sensitive
emission property of Ru1 enables direct visualization
of the dynamic process of DNA phase separation in living cells by
two-photon phosphorescent lifetime imaging. Moreover, Ru1 can change the gene expression pattern by modulating chromatin accessibility
as demonstrated by integrating RNA-sequencing and transposase-accessible
chromatin with high-throughput sequencing. In all, we present here
the first small-molecule-based tracer and modulator of DNA phase separation
in living cells and elucidate its impact on the chromatin state and
transcriptome.