Many scientists are trying to build nanodevices whose activity can be programmed in advance. But why not use the system we already have at our disposal?
Institute December 33, 2003
Dr. Roy Bar-Ziv. Gardens in a circle
Information processing and retrieval is the name of the game in the advanced industry. Scientists and engineers invest a lot of effort in developing ways and methods to perform these processes more efficiently and quickly, and in smaller facilities. Dr. Roi Bar-Ziv from the Department of Materials and Surface Research at the Weizmann Institute of Science believes that the absolute optimization and miniaturization is already in our hands: this is the genetic material, DNA. Hardware engineers can only dream of devices on the scale of DNA. Software engineers can marvel at the efficiency, reliability and "automatic" repair mechanisms of the genetic material. All of these require the possibility of developing ways to utilize the unique properties of DNA to build artificial systems that can be the basis of various technologies and devices, which will have a variety of promising properties.
Dr. Bar-Ziv, Prof. Albert Liebeschaver and Dr. Vincent Noireau from Rockefeller University in New York, took a significant step towards the realization of this vision. They created and demonstrated an action circuit reminiscent of an electronic circuit, except that their circuit was based on genes that operated outside of living cells. The design process of the circuit, which is, in fact, a kind of imitation of the biological system, was based on the identification of the essential components and the order of operations of a normal electronic circuit. An electronic information system usually includes four main components - input, processing (the change or calculation that is carried out in the input), output (the result), and successive stages of operation where the output of a certain stage is the input of the next advanced stage of operation. The circuit is made up of three genes, and it also contains various enzymes, amino acids, and substances that provide energy.
The DNA-based circuit did not at all resemble the electronic circuits embedded in silicon chips, which are used in existing electronic installations. For its construction, the scientists used a biological system that produces proteins in a test tube, based on an extract of wheat germ, from which the cell nuclei and membranes were removed. What remains is,
In fact, a kind of soup of intracellular substances, including the ribosomes, which translate the information stored in the genes, and create proteins according to it. The celts were plasmids, which are structures of different genes, as well as the enzymes that reproduce the DNA and create messenger RNA molecules from it. The output was the proteins made by the ribosomes. The circuit was designed so that the proteins encoded by one gene connected to the other gene and activated it, and so on. The main circuit breaker was the sugar lactose. When this sugar was added to the system, it prevented one enzyme from blocking the activity of the first gene in the circuit, which enabled the circuit to activate (in contrast, a lack of sugar caused the circuit to stop working).
But the chances that bowls of biological soup will replace calculators and electronic diaries in the near future seem extremely slim at this point.
The protein production process lasts about an hour, and sometimes more. And if that's not enough, it turns out that the whole process is delayed even more because the second stage in the cycle begins only after a sufficiently large amount of the protein that is the output (product) of the first stage is formed in the "soup". When you try to add too many stages to the sequence, everything starts to go wrong, because the available resources run out and the output levels reach saturation. Dr. Bar-Ziv says that understanding the causes of these bottlenecks is the key to the future application of DNA-based circuits. Careful coordination of intermediate steps in the process and improvements in circuit engineering (for example, the creation of feedback processes), may solve some of the problems, but even so, DNA circuits will never compete in speed with electronic circuits, in which the speed of signal transfer is almost instantaneous.
The possible advantages of the DNA circuits derive from the ability of billions of molecules to operate simultaneously, and from the fact that the genes come from the "factory" with the software already included in them. In addition, the DNA can create exact copies of itself, and repair damages and "breakdowns" that harm it. Dr. Bar-Ziv: "It is better that we move away from the electronic model, and that we move towards developing the ability to apply the language of biological systems in artificial systems. The garden is hardware, software and information, mixed together without being able to separate them. Many scientists are trying to build nanodevices whose activity can be programmed in advance. But why not use the system we already have at our disposal?"
Dr. Bar-Ziv received a master's and a master's degree in physics from the Feinberg Seminary of the Weizmann Institute of Science (under the supervision of Prof. Shmuel Shafran and Prof. Elisha Mozes). He then carried out post-doctoral research at the Rockefeller University in the laboratory of Prof. Albert Liebshaber, who was recently awarded an honorary doctorate by the Weizmann Institute of Science. In the research he is currently conducting at the Weizmann Institute, he is trying to find ways to integrate DNA into complex systems. He aims to reach practical applications of DNA-based circuits in various systems in the field of computers, as well as in medical diagnostics, medical treatments, biotechnology and more.
