16 February 2016

Chromosomes, I can see right through you!

Biologists saw DNA inside chromosomal "plugs"

Alexander Ershov, N+1

A team of biologists and physicists from the University of North Carolina has developed a new method based on atomic force microscopy, which allows you to trace the movement of DNA both outside and inside DNA protein complexes. This method allowed the researchers to examine in detail telomeres – "plugs" at the ends of chromosomes, the work of which is key to controlling molecular aging and preventing cancer degeneration. A study by Kaur et al. Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2 published in the journal Scientific Reports.

The authors called the method allowing to examine DNA and protein separately on microphotographs DREEM (Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy), which can be translated as electrostatic atomic force microscopy enhanced by double resonance. In general terms, its principle of operation differs little from conventional atomic force microscopy: the drug under study is applied to a substrate, and then felt with the help of the thinnest needle-cantilever (about the same way a gramophone needle feels the sound track on a record).

The difference of the new method is that an alternating electric voltage is applied to the substrate. As a result, the needle-cantilever "feels" not only mechanical rises and dips on the surface of the molecules, but also reacts to their charge. Since the charge of DNA (generally negative) differs from the charge of proteins (mostly positive), DREEM allows you to "see" where which molecule is located. Interestingly, in this way it is possible to obtain data not only about the molecules exposed on the surface, but also about what is hidden inside the molecular complex.

DNA folding on nucleosomes: on the left – atomic force microscopy DREEM, on the right – modeling.
You can see how the DREEM images show a light DNA furrow along the dark protein of the nucleosome.

The researchers described the principle of the new method in detail in an article published a couple of weeks ago in Molecular Cell (Wu et al., Visualizing the Path of DNA through Proteins Using DREEM Imaging). In a new article, the same team describes the application of the DREEM method to study telomeres.

Telomeres are a DNA-protein complex that is located at the ends of chromosomes in almost all nuclear organisms. Its existence is explained by the fact that a break at the end of DNA is an "emergency signal" for the cell – it can be evidence of a dangerous double-stranded break inside the chromosome (enzymes "do not see" the difference between the end and the body of the chromosome). To prevent an unnecessary "emergency reaction" in this case, there are special proteins that hide the ends of chromosomes inside the protein complex. DNA is then folded into a loop, the so-called T-loop.

The key protein of the telomere that ensures the existence of the T-loop in humans is TRF2. It has already been well studied in isolated systems thanks to the X-ray method. However, exactly how TRF2 forms T-loop structures inside cells has not been understood until now.

In a new paper, researchers have shown that TRF2 hides DNA inside a "fur coat" of interconnected molecules. At the same time, contrary to the expectations of biologists, not all nucleic acid turns out to be associated with TRF2 – part of it gets out and, as the authors found, attracts other important enzymes to the telomere. For example, it "causes" telomerase, a protein that lengthens telomeres.

The structure of the human T-loop

The need for telomere elongation and the existence of a special enzyme for this process was predicted by Olovnikov theoretically based on an understanding of the features of the DNA replication mechanism. Unlike RNA-synthesizing enzymes, enzymes that synthesize DNA necessarily require a seed (primer) to begin synthesis. It follows from this that without the invention of a special mechanism for maintaining the ends, conventional replication enzymes cannot cope with the task of preserving linear chromosomes.

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