For the first time, scientists have studied in detail how DNA strands move inside the nucleus of cells.
Scientists from Moscow State University. Lomonosov discovered several new mechanisms at once that control the readability of genes. In the course of the study, they calculated at the atomic level how the position of the DNA strand inside the cell nucleus changes.
The DNA double helix is like a screw. It is assumed that it can simultaneously slide and scroll along the surface of the proteins of its shell. We were able to show that due to local deformations of DNA and histone proteins, this process occurs in stages. First, one piece of DNA is scrolled, and then the next is a kind of caterpillar-screw mechanism.
Alexey Shaitan, one of the authors of the work, leading researcher at Moscow State University
The total length of all DNA molecules from human chromosomes is about two meters. Our cells compress DNA strands 10,000 times to fit into the nucleus. For example, a cell winds a DNA strand on special molecular “coils” of histone proteins. Thanks to this, the genome can be packaged very compactly, but at the same time, a significant part of the DNA strand is hidden inside these structures.
How exactly DNA moves in the nucleosome remained unclear until recently. To deal with this, scientists have modeled the molecular dynamics of nucleosomes at the atomic level on the Lomonosov-2 supercomputer at a record time long for computer simulations – 15 microseconds. That is, the supercomputer acted as a kind of computational microscope, which made it possible to examine the mechanisms of DNA movement in the genome.
Thanks to this, Shaitan and his colleagues traced how a DNA strand is detached from proteins, how its structure changes, and what factors affect the movement of the nucleotide chain, as well as its re-connection with protein coils.
The study also makes an important contribution to deciphering the mechanisms of genome functioning.