DNA-DNA Interactions Could Influence Chromosome Structure

To carry out their roles, do DNA molecules interact with proteins—the prevailing hypothesis—or with each other? A study now provides direct evidence for the latter.

AsianScientist (Apr. 15, 2016) – It is widely believed that the functions of DNA, such as the way the DNA is organized, largely depend on its interactions with protein molecules. However, a new study, affiliated with the Ulsan National Institute of Science and Technology (UNIST), reveals that DNA molecules interact directly with one another in a way that’s dependent on the sequence of the DNA and epigenetic factors.

In their study, published in Nature Communications, the team presented direct evidence for sequence-dependent attractive interactions between double-stranded DNA molecules that neither involve intermolecular strand exchange, nor are mediated by DNA-binding proteins.

Professor Kim Hajin, the lead author of the study, noted, “DNA molecules tend to repel each other in water, but in the presence of special types of cations, they can attract each other just like nuclei pulling each other by sharing electrons in between.

“Our study suggests that the attractive force strongly depends on the nucleic acid sequence, and also the epigenetic modifications.”

Kim and his colleagues used atomic-level simulations to measure the forces between a pair of double-stranded DNA helices. They proposed that the distribution of methyl groups on the DNA are the key to regulating this sequence-dependent attraction. Then, by observing a single pair of DNAs within nanoscale bubbles, they experimentally verified the model.

From further simulations, researchers theorize that such direct DNA-DNA interactions could play a central role in how chromosomes are organized in the cell and which ones are expanded or folded up compactly, ultimately determining functions of different cell types or regulating the cell cycle.

“Biophysics is a fascinating subject that explores the fundamental principles behind a variety of biological processes and life phenomena,” mused Kim.

Kim added that in the long run, his team is seeking for ways to prevent chronic illnesses and diseases associated with aging.

The article can be found at: Yoo et al. (2016) Direct Evidence for Sequence-Dependent Attraction between Double-Stranded DNA Controlled by Methylation.


Source: Ulsan National Institute of Science and Technology.
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