@article {211,
	title = {Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation},
	journal = {Nature Communications},
	volume = {7},
	year = {2016},
	month = {03/2016},
	pages = {11045},
	abstract = {<p>Although proteins mediate highly ordered DNA organization\&nbsp;<em>in vivo</em>, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA{\textendash}DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA{\textendash}DNA interactions that we report here may play a role in the chromosome organization and gene regulation.</p>
},
	doi = {10.1038/ncomms11045},
	author = {Jejoong Yoo and Hajin Kim and Aleksei Aksimentiev and Taekjip Ha}
}
