Data stored in live cells

By Kimberly Patch, Technology Research News

Every type of storage media -- from stone to paper to magnetic disks -- is subject to destruction. From the great fire that destroyed Alexandria's world-class library in 48 B.C. to that unfortunate hard drive crash last week, information has had a habit of suddenly disappearing because the media that contains it succumbs to the forces of nature.

Researchers from Pacific Northwest National Laboratory are tapping forces of nature to store information more permanently.

The researchers used artificial DNA sequences to encode portions of the text of the children's song It's a Small World, added the sequences to bacteria DNA, allowed the bacteria to multiply, then extracted the message part of a DNA strand and retrieved the encoded information.

Because DNA is passed down through generations of living organisms, information stored this way should survive for as long as the line of organisms survives, said Pak Wong, a chief scientist at the Pacific Northwest National Laboratory. DNA is made up of four bases attached to a sugar-phosphate backbone. Different sequences of the four bases can represent digital information.

Storing information is DNA's natural function, said Wong. "We [are] taking advantage of a time-tested, natural, nanoscale data storage technology perfected over the last 3 billion years." The encoding method could be used to store any digital information, he said. "Text, pictures, music -- anything you can send or receive over the Web could be saved in this form."

DNA stores a large amount of information in a very small space. Considering that a milliliter of liquid can contain up to 10 billion bacteria, the potential capacity of bacterial-based DNA memory is enormous, assuming that the data can be retrieved in an organized way, according to Wong.

One challenge to storing information in living DNA is is that it naturally mutates, changing the information. Information stored using the researchers' method is subject to mutation, but embedding the information in the DNA of an organism that can survive harsh environments cuts down on potential errors, said Wong.

Wong's lab is also carrying out projects that involve genetically engineering hearty Deinococcus radiodurans bacteria "for bioremediation in a radioactive environment," said Wong. "The bacterium's extreme resistance to environmental insults gave us the idea of selecting it as data storage," he said.

This radiation-resistant bacteria could be used to preserve data in the event of nuclear attack or accident, according to Wong.

Organisms succumb to radiation because the radiation causes so many mutations that the organisms life processes do not work correctly. And organism that is resistant to radiation damage would by definition be resistant to mutation. "By carefully choosing the host organism and the data encoding method, the error rate caused by mutation is very low," Wong said.

In a related development, scientists from the Weizmann Institute of Science in Israel, the National Institutes of Health, and the Uniformed Services University of the Health Sciences have found a clue to the mystery of how this particular bacteria can survive high doses of radiation. The bacteria's DNA forms tightly packed rings so that when radiation slices the DNA, the pieces stay in place and the DNA mends in the correct order.

The data storage method could also produce many copies of the data, and these could be compared in order to correct the errors that do occur, said Wong. "There is very high redundancy in the message since there is a copy in each bacterial cell and there may be millions of cells in a needle-size bacterial colony," he said.

The researchers embedded DNA containing information into a circular DNA molecule capable of self-replicating within a bacterial host. They introduced the circular DNA molecules into the bacteria using high-voltage shocks. The DNA was then incorporated into the genome of the bacteria for long-term information storage.

The researchers let the bacteria propagate for 100 generations, then retrieved the encoded information by extracting the message part of the DNA strand from the youngest generation and reading it via polymerase chain reaction, a laboratory procedure that took about two hours and involved a series of heating and cooling cycles.

The researchers used seven different bacteria to store and retrieve seven DNA fragments that ranged from 57 to 99 base pairs long and encoded text from the children's song, according to Wong. One of the segments was the text "and the oceans are wide."

Showing that it's possible to store and retrieve information using the DNA of a living organism is a step toward a new data storage medium, according to Wong.

The next step is devising a way to retrieve the information quickly enough to make the method useful. "The technical challenge will be to develop high throughput of retrieving the information already stored in the bacteria," said Wong. The researchers are currently working on an idea toward that end, he said.

Although the idea of storing information in DNA is not new, the research has merit, said Lila Kari, an associate professor of computer science at the University of Western Ontario in Canada. "DNA can accomplish astounding information density... in principle it is a worthwhile endeavor," she said.

In an experiment published in 1999, researchers from Mount Sinai School of Medicine encoded information in a strand of DNA, included the DNA in a printed period in a document, then recovered the embedded message after sending the document through the U.S. mail.

The Pacific Northwest National Laboratory researchers' experiments have moved the concept of DNA as a storage medium in a different direction by storing information-containing DNA in a living organism.

There are some potential problems with some of the researchers' projections, however, Kari said. "They say that the memory capacity would be huge because each bacteria in a colony could encode different information; it is very difficult to select a single bacteria from a colony," she said.

It's too early to tell when the method could be used to store data in a practical way, said Wong. "Being able to apply the technology practically involves not only technological advancements but also... social and environmental issues, which have not been addressed," he said.

The ultimate goal of the research "is to use living organisms to store and retrieve significant amounts of data quickly," said Wong. Living organisms, including weeds and cockroaches, that have survived on Earth now the first number is for hundreds of millions of years are good candidates for protecting critical information for future generations, according to Wong.

Other potential applications include DNA watermarking to protect intellectual property rights to organisms like crop seeds, and even allowing people to store personal information within their own DNA, according to Wong.

Wong's research colleagues were Kwong-kwok Wong and Harlan Foote. They published the research in the January, 2003 issue of Communications of the ACM. The research was funded by the Pacific Northwest National Laboratory.

Timeline:   Unknown
Funding:   Government
TRN Categories:  Biotechnology; Biological, Chemical, DNA and Molecular Computing; Data Storage Technology
Story Type:   News
Related Elements:  Technical paper, "Organic Data Memory Using the DNA Approach," Communications of the ACM, January, 2003; technical paper "Ringlike Structure of the Deinococcus radiodurans Genome: A Key to Radioresistance?", Science, January 10, 2003.


January 29/February 5, 2003

Page One

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