A tool for creating cellular computers

The BLADE framework has been created for laying computational chains in mammalian and human DNA

Anatoly Alizar, Geektimes

Here and below are the drawings from the article by Weinberg et al. Large-scale design of robust genetic
circuits with multiple inputs and outputs for mammalian cells (Nature Biotechnology, 2017)

The fundamental goal of synthetic biology is to predictably and efficiently reprogram cells so that they perform calculations and perform a given biological task. Cells are genetically modified – chains for bio-calculations are introduced there. Such mini-computers demonstrate promising results in therapy, diagnostics and industrial biotechnologies. Synthetic biology is one of the most promising areas of modern science.

When programming cells, scientists have to solve complex applied problems. For example, the implementation of a simple binary Boolean function (with two input operands) in a prokaryotic or eukaryotic cell requires laying many genetic chains, extensive design and tuning of genetic components. As for more complex computational circuits, this is an exceptional rarity in the scientific literature.

The problem is solved by compiling a catalog of genetic components for computational circuits and developing software for automatic design of computational circuits in a cell. Unfortunately, such software is still available for programming bacterial cells, but not for mammalian and human cells. It is currently unknown whether it is possible to transfer various parts of the software from the programming of bacterial cells to the cells of higher organisms.

This problem was solved by a group of scientists from the Department of Bioengineering and the Center for Biological Design at Boston University, the Department of Electrical and Computer Engineering at Boston University, as well as the Department of Biosystems Science and Electrical Engineering at the Swiss Higher Technical School of Zurich. They introduced the BLADE framework. It is a general-purpose framework that helps to build complex genetic computational chains in mammalian cells using site–specific recombinases - enzymes that perform recombination between individual DNA segments. It is the use of site-specific recombinases that is the main innovation of this framework.

Recombinases work like scissors, cutting and binding specific sections of DNA in a cell. The specific enzymes used in this scientific work recognize two patterns in a DNA chain, each between 30 and 50 base pairs long. As soon as the recombinase finds the target fragments, it cuts out all the unnecessary DNA between them and connects the ends of the double helix. This technique of genetic editing BLADE is similar to the well-known CRISPR technique.

To design genetic chains, traditional cellular mechanics is used: the DNA chain is rewritten into RNA, and then the RNA is translated into the corresponding proteins. The beginning and end of the work on the translation of genes into proteins is controlled by the corresponding DNA fragments. One of them, the promoter, signals the beginning of the operation, and it continues until the DNA chain reaches another fragment, which signals the termination of the operation.

The authors of the scientific work say that the BLADE framework, unlike previous developments, requires minimal optimization on the part of the bioprogrammer. He is ready to lay chains with a large number of input and output operands without increasing the number of transcription elements, that is, without increasing the complexity of the chain.

To test the framework in action, the researchers designed and implemented more than 100 different functional computing circuits, including the most complex logical operations that have ever been performed in living cells.

For example, the illustration shows how site-specific recombinations of tyrosine and serine integrases make it possible to construct a Boolean function AND with several input operands.

(a) Recombinations perform simple logical BUF operations by cutting or inversion; (b) Checking the effectiveness of all recombinations for logical BUF operations; (c) Logical AND operation with six input operands

The capabilities of the BLADE framework are not limited to this. It allows you to create much more complex computational circuits. The following illustration shows the programmable logic of a storage device that can be programmed using site-specific recombinases in a mammalian cell.

Scientists constructed 113 different circuits, of which 96.5% functioned successfully. This is significantly more than the usual success rate of 25% for genetic engineering.

The development of the BLADE framework is essential for synthetic biology. Scientists have laid more than 100 different computational circuits in mammalian DNA, most of which have been implemented for the first time. Although this paper does not implement any useful computing systems, but the researchers have proposed a universal programming technique that colleagues can use to implement specific applications. Programmable cells can be used in various fields: from cancer treatment to the creation of biological tissues that, on command, replace worn-out parts of the body.

Until today, experiments with cell programming have mainly been conducted on cells of E.coli and other bacteria, because their genes are relatively easy to manipulate. Now the approach of synthetic biology has been extended to mammalian and human cells.

Portal "Eternal youth" http://vechnayamolodost.ru  30.03.2017