"Punch Card" DNA May Mean Cheaper Mass Data Storage

(source: network sorting)

If everyone on earth has to rely on flash memory, a data storage system for memory cards and USB flash drives, the amount of information expected to be generated worldwide will be 100 times higher than the expected supply of microchip grade silicon by 2040. In order to prevent such a crisis, researchers have been exploring a storage material on which life itself depends: DNA.

In theory, this material can store a lot of information - 1eb (1 billion gigabytes) of information per cubic millimeter of DNA - for thousands of years. The longest life of tape, the basis of most digital archives, is about 30 years, but the DNA of fossils 700000 years ago can still be sequenced. However, one obstacle to making DNA data storage a reality is that the process of creating or synthesizing new DNA sequences that meet the required code is slow, expensive and error prone.

"Synthetic DNA is a major bottleneck in terms of recording cost, accuracy and writing speed," said olgica milenkovic, a coding theorist at the University of Illinois at Urbana Champaign. She and her colleagues proposed a new solution: using "nicks" Patterns mark existing DNA molecules to encode data, rather than customizing synthetic DNA from scratch. This method was inspired by punch cards, a kind of cardboard that punched holes in specific locations to store information from many early computers, including ENIAC during World War II. The researchers detailed their technology in the journal Nature communications on Wednesday.

Previous DNA storage methods deal with four key DNA components, namely bases - adenine, thymine, cytosine and guanine electronic bits, that is, 1 and 0 encoding digital data. For example, each base may be assigned 00, 01, 10, or 11. However, this new method does not convert a series of bits into DNA code, nor synthesize the corresponding base string, but uses the existing genetic material as paper similar to early punched cards. S. Kasra tabatabaei, the lead author of the study, said that enzymes are "drilling devices". In this case, these "holes" are broken bonds between the molecules that make up the DNA skeleton. If this flag appears, it means 1. If not, it means 0.

Brenda Rubenstein, a theoretical chemist at Brown University, said the most interesting aspect of the study is how it depends on nature. She was not involved in the study. "Researchers let these enzymes do their most natural things, leaving traces to store information," she said

To pinpoint these "holes" (traces left by enzymes), the team heated double stranded DNA molecules until they unfolded a little in the middle. This process forms bubbles that expose the bases. Next, the scientists used single stranded DNA molecules, each only 16 bases long, to attach them to the corresponding base sequence in these bubbles. The ends of these single chain molecules act as guides, telling the enzyme where to go. In DNA, each base connects a sugar molecule and a phosphate group to form a compound called nucleotide. The enzyme used in the new technology cuts off the connection between one nucleotide and another, thus forming a gap in the sugar phosphate orbit.

Because this method does not require the synthesis of accurate DNA sequences, the researchers say an important advantage is that they can process almost any DNA molecule like punch cards. For example, they experimented with genetic material cheaply obtained from ready-made strains of E. coli, and the researchers knew the very precise sequences of these strains. Using 450 base pairs of bacterial DNA strands, each containing 5 to 10 holes, scientists encoded 272 words of Abraham Lincoln's Gettysburg speech and a 14 kilobyte image of the Lincoln Memorial. After they put this information on DNA, they used sequencing technology to read the documents with high accuracy.

"For many years, people have thought that molecular computing is mapping what we do on silicon to molecules, resulting in a lot of fussy devices. On the contrary, this new study shows that the efficiency of enzymes over millions of years of evolution is incredible," Rubinstein said

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