Sequence-Dependent DNA Condensation as a Driving Force of DNA Phase Separation

Hyunju Kang, Jejoong Yoo, Hong Soo Lee, Byeong-Kwon Sohn, Seung-Won Lee, Wenjie Ma, Jung-Min Kee, Aleksei Aksimentiev, and Hajin Kim
Nucleic Acids Research 46(18) 9401-9413 (2018)
DOI:10.1093/nar/gky639   BibTex

The physical properties of DNA have been suggested to play a central role in spatio-temporal organization of eukaryotic chromosomes. Experimental correlations have been established between the local nucleotide content of DNA and the frequency of inter- and intra-chromosomal contacts but the underlying physical mechanism remains unknown. Here, we combine fluorescence resonance energy transfer (FRET) measurements, precipitation assays, and molecular dynamics simulations to characterize the effect of DNA nucleotide content, sequence, and methylation on inter-DNA association and its correlation with DNA looping. First, we show that the strength of DNA condensation mediated by poly-lysine peptides as a reduced model of histone tails depends on the DNA’s global nucleotide content but also on the local nucleotide sequence, which turns out to be qualitatively same as the condensation by spermine. Next, we show that the presence and spatial arrangement of C5 methyl groups determines the strength of inter-DNA attraction, partially explaining why RNA resists condensation. Interestingly, multi-color single molecule FRET measurements reveal strong anti-correlation between DNA looping and DNA–DNA association, suggesting that a common biophysical mechanism underlies them. We propose that the differential affinity between DNA regions of varying sequence pattern may drive the phase separation of chromatin into chromosomal subdomains.

Coarse-grained molecular dynamics simulation of a DNA mixture’s phase separation driven by sequence-specific forces. The system contains equal amounts of poly(CpG) and poly(TpA) dsDNA molecules randomly placed in a cubic volume (blue rectangle) 200 nm on edge. Each DNA molecule is 120 basepairs long and is represented using a custom beads-on-a-string model, where 1 bead represents 10 basepairs. The movie illustrates 100 microseconds of the coarse-grained simulation.