Dense in the genome

Prof. Roy Bar-Ziv, from the Department of Materials and Surfaces at the Faculty of Chemistry, wanted to create an artificial system that would combine the convenience of test tube experiments with the real density conditions of the cell

Anyone who has watched a busy train station must have noticed that the crowd is not evenly distributed inside it - the density is concentrated around the ticket counter, the kiosks and the platforms. Although these complexes are not defined by walls, yet the various operations take place within defined sections - a kind of open, separate cells. Scientists at the Weizmann Institute of Science use a similar principle to cram genes into small sections on a chip. In this way, they can also discover how this type of "crowd management" strategies may contribute to the development of approaches to control the activities of genes in cells. The new method they developed gives them a new tool for activating genes in laboratory experiments in a more realistic way. In addition, it may be an important step in efforts to create artificial cells. Gene activity in living things takes place in the dense spaces of the cell, or in the cell nucleus. Recent findings indicate that certain types of activity are delimited in different areas within the compressed nuclear space.

In contrast, in laboratory experiments that mimic cellular activity, DNA strands and other molecules usually float freely in solution. Prof. Roy Bar-Ziv, from the Department of Materials and Surfaces in the Faculty of Chemistry, wanted to create an artificial system that would combine the convenience of test-tube experiments with the real density conditions of the cell. Together with the research student at the time, Amnon Boxbaum, Prof. Bar-Ziv developed a method for attaching relatively long DNA strands to a surface, to create a kind of thick and dense DNA brush. Using the photolithography technique, which is used in the field of microelectronics, they managed to create detailed printed "photographs", so that the distance between the DNA bristles in the brush does not exceed about 30 nanometers.

After completing the development of the brush, members of the research team - including research student Dan Bracha and Dr. Shirley Dauba, director of the Nanosciences Laboratory in the Department of Chemical Research Infrastructures at the Weizmann Institute of Science - turned to check what the DNA brushes could teach them about gene activity under the conditions dense. For this purpose, they started with the simplest scenario: they created DNA brushes whose bristles are made of a single gene, and examined the first stage of genetic activity - the creation of RNA strands according to the genetic code, compared to the same process in DNA strands Islands that float freely in solution. The garden brushes the team created did act as tiny separate compartments. The researchers discovered that in these sections different conditions exist than in the rest of the environment, despite the lack of physical separation. The scientists also tested the activity of their gene brushes under changing environmental conditions - for example, by changing the concentration of salts in the solution, or adding chemical substances that affect DNA activity - and found that the activity of the dense genes in the brush corresponds much more to reality (of the activity of the genes in the cell) compared to the degree of appropriateness of the activity of the genes floating in the solution. Later on, the scientists widened, or narrowed, the spaces between the strands; Added varying amounts of "junk" DNA (non-protein-coding genetic material) between the genes; And they reversed the direction of the genes, so that in some cases the genetic information instructing to "start copying here" was near the free side of the bristles of the brush, and in other times it was near the end attached to the surface.

The researchers discovered that all these changes have an effect on the speed at which the genes work - including those that do not code for a protein. An increase in the density of the bristles slowed the process, as did placing the "start" code closer to the base of the brush. It seems that the dense array limits the DNA's accessibility to the transcription machines (the enzymes that create the RNA molecule), and also keeps the machines and the RNA created inside the separated section for a longer period of time. In addition, the scientists found that the arrangement of the brush allows them to control the direction of the copying of the genetic information (and therefore the output of the proteins created on it) - control that is not possible in experiments performed in solutions, but is normally possible in real cells. Although in living cells the genes are not arranged in orderly and parallel rows, the scientists believe that the model they developed allows for important insights into how the physical arrangement of the DNA strands affects its activity. Thus, for example, they hypothesize that the junk DNA, which makes up about 90% of all the genetic material in our cells, may function as a "packaging material" that maintains the necessary level of density.

In addition, their findings imply that the separation into sections is used as a common strategy, which saves space and maintains order in the crowded and busy cell. "It is possible that such open sections even preceded the closed cell," says Prof. Bar-Ziv. "It is possible that the primary cells were not surrounded by a membrane, but were a structure in which complex molecules crowded together, and it is possible that this structure was preserved as a basic organizational principle."

Prof. Bar-Ziv emphasizes the fact that the members of the research team brought different skills and fields of training to the laboratory. Among them were physicists, biochemists and specialists in bioengineering. "It is the combination of these fields that made this research possible," he says. In the future, Prof. Bar-Ziv and his team plan to continue to improve the capabilities of the gene brushes, and to perform various operations in more complex situations - including arrays involving several types of genes, or changes in the composition of the genetic material. In the future, the scientists aim to create an artificial chromosome, and perhaps even an artificial cell. Prof. Bar-Ziv: "Compared to today's gene chips, which are a passive diagnostic tool, the genes in our brushes are active, and we want to learn how to control their activity."