Biologists from Harvard University in the United States encoded the world's first GIF, created in the 19th century, in E. coli DNA. The researchers used CRISPR / Cas9 technology to insert nucleotides into the bacterial genome that match the pixels that make up the image. Reading the DNA sequence made it possible to reproduce the video with 90 percent accuracy. The article of scientists was published in the journal Nature.
Edward Muybridge can be considered the creator of
How did the researchers achieve this? The relatively recently discovered CRISPR / Cas9 system has played an important role. This is the name of the molecular mechanism that operates inside bacteria and allows them to fight viruses. CRISPRs are “cassettes” inside the DNA of a microorganism, which are made up of repeating sections and unique sequences - spacers - that are fragments of viral DNA. That is, CRISPR is a kind of databank with information about the genes of pathogenic agents. The Cas9 protein uses this information to correctly identify foreign DNA and render it harmless by cutting at a specific location.
The protospacer matches the sequence that was once "stolen" from the virus and became a spacer. Scientists are using this molecular mechanism. The spacer encodes crRNA, to which the Cas9 protein is then attached. Instead of crRNA, you can use a synthetic RNA with a specific sequence - guide RNA (sgRNA) - and tell the scissors where to make the cut scientists want.
The bacterium obtains spacers naturally by borrowing protospacers from pathogenic viruses. Once the fragment has been inserted into CRISPR, the protospacer becomes a sign that allows the microorganism to recognize the infection.
However, CRISPR is not limited to this. Biotechnologists have found that these "cassettes" can record information using pre-synthesized protospacers. Like any DNA, a protospacer is composed of nucleotides. There are only four nucleotides - A, T, C and G, but their various combinations can encode anything. Such data are read by sequencing - by determining the nucleotide sequences in the genome of the organism.
E. coli Photo: Manfred Rohde / HZI / DPA / Globallookpress.com
Scientists first coded a four-color and 21-color image of a human hand. In the first case, each color corresponded to one of four nucleotides, in the second, to a group of three nucleotides (triplet). Each protospacer was a string of 28 nucleotides, which contained information about a set of pixels (pixel). To distinguish protospacers, they were labeled with four nucleotide barcodes. Inside the barcode, the nucleotide encoded two digits (C - 00, T - 01, A - 10, G - 11). So, CCCT corresponded to 00000001. This designation makes it possible to understand in which part of the image a particular pixel of a given pixel is located.
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The four-color image of the hand consisted of 56x56 pixels. All this information (784 bytes) fit into 112 protospacers. The 21-color image was smaller (30x30 pixels), so 100 protospacers (494 bytes) were enough for it.
However, it is not so easy to insert any nucleotide sequence into a bacterium, hoping that it will insert it into its own DNA with 100% probability. Therefore, combinations of nucleotides in triplets were not chosen randomly, but so that the total content of G and C in a row was at least 50 percent. This increased the chances of the bacteria acquiring the spacer.
Photo: Harry Ransom Center
Protospacers were introduced into the population of Escherichia coli by electroporation - the creation of pores in the lipid membrane of bacterial cells under the action of an electric field. The bacteria possessed functional CRISPR and the Cas1-Cas2 enzyme complex, which made it possible to create new spacers based on protospacers.
The microorganisms were left overnight, and the next day, specialists analyzed the nucleotide sequences in CRISPR and read the pixel value. Reading accuracy reached 88 and 96 percent for four-color and 21-color hands, respectively. Additional studies showed that almost complete acquisition of spacers occurred two hours and 40 minutes after electroporation. Although some bacteria died after the procedure, this did not affect the result.
The scientists noted that some spacers were much more common in bacteria than others. It turned out that this was influenced by nucleotides located at the very end of the protospacer and forming a motif (weakly variable sequence). Such a motif, called AAM (acquisition affecting motif), ended with a TGA triplet. This was used by biologists to encode animation in bacteria. Five 21-color shots of a running horse were captured by American photographer Edward Muybridge. Their size is 36 by 26 pixels.
Each frame was encoded with a set of 104 unique protospacers, and the amount of information reached 2.6 kilobytes. Special nucleotide labels allowing to distinguish the sequence of one frame from the sequence of another were not provided. Instead, different populations of bacteria were used. Thus, a single organism has not yet been used as a carrier of information.
Scientists intend to improve this approach. However, so far living beings are far behind the usual information storage devices. Such studies are primarily aimed at elucidating the computational capabilities of DNA molecules, which can be useful for creating DNA computers capable of simultaneously solving a huge number of problems. Living organisms are a convenient platform for scientific research, since they already contain enzymes and other substances necessary for the modification of nucleotide chains.
Alexander Enikeev