Blue-light labeling uncovers unexpected protein partners of folded DNA structures

This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility: DNA can be more than just a double helix. When four strands are folded into a compact bundle, they form a G-quadruplex (G4).

These bundles form in guanine-rich regions across the genome, including telomeres at the ends of chromosomes and the control regions of genes, where the proteins that dock onto them help decide which genes are switched on. G4 does not act the same way everywhere. What it does depends on where it forms and which proteins bind to it.

This is why understanding the interactions surrounding G4 is so important. Biochemical assays give us more information about the intricacies of these interactions. These assays assess how DNA and proteins interact during processes such as DNA replication, transcription and repair.

However, previous assays haven't been able to capture the full picture. A team led by Kazumitsu Onizuka and Shinichi Sato of Tohoku University, with Takanori Oyoshi of Shizuoka University, has developed a photocatalytic proximity labeling method that overcomes previous pitfalls and captures partners that earlier methods missed. The technique also revealed hexokinase-1 to be an unexpected player in these interactions.

The work is published in the journal Communications Chemistry. "The problem is that identifying the proteins that bind G4 is not at all straightforward," explains Sato. "Conventional bait-and-capture methods miss weak or transient binders.

Newer chemical probes also have downsides, as they bind into the quadruplex themselves and block some of the proteins they are meant to catch." The researchers tested their new method, attaching a photocatalyst (which reacts to light) directly to a human telomere G4 and adding a small tagging reagent. Thirty seconds of blue light generated singlet oxygen, a reactive form of oxygen with a range of only a few nanometers, so only proteins sitting immediately beside the structure received a chemical tag that could later be identified by mass spectrometry. The new method flagged more than 1,000 candidate binders, but the one that ranked first was unexpected.