Category Archives: DNA

Scientists have stored some Shakespearean sonnets and part of Martin Luther King, Jr.'s "I Have a Dream" speech by encoding them in DNA -- a process that could preserve those famous words for millennia. The team at the European Bioinformatics Institute isn't the first to try this new approach to data storage. A Harvard team stored around 700 terabytes of digital data in a single gram of DNA last year.

Researchers at the European Bioinformatics Institute (EMBL-EBI) on Wednesday announced their success at storing data by encoding it to DNA. The system could stand the test of time -- tens of thousands of years, perhaps.

This method for archiving data could make it possible to store 100 million hours of high-definition video in about a cup of DNA, according to the scientists, and given the trend toward Big Data, that could be a big breakthrough. One gram of DNA could hold as much as information as more than a million CDs.

Nick Goldman of EMBL-EBI looking at synthesised DNA. (Credit: EMBL Photolab)

Unlike existing methods of data storage -- all of which have relatively limited life spans -- DNA has proven it can endure, literally, for ages. Like any physical carbon-based object, DNA can be destroyed, but it happens to be far more sturdy than paper or tape, and it can't easily be damaged by electromagnetic fields.

"We already know that DNA is a robust way to store information, because we can extract it from wooly mammoth bones -- which date back tens of thousands of years -- and make sense of it," said Nick Goldman of EMBL-EBI. "It's also incredibly small, dense, and does not need any power for storage, so shipping and keeping it is easy."

DNA could have an advantage over many current methods of storage.

Although tape is the cheapest storage medium, it's performance is lacking, explained Fang Zhang, storage analyst at IHS iSuppli. Analyzing Big Data using tape would take much longer, compared to SSD and HDD. Depending on how frequently it's used, tape could wear out.

+ While it's highly unlikely that the words of William Shakespeare would ever be lost, 154 of the Bard's sonnets have been spelled out using DNA. An audio file containing part of Martin Luther King, Jr.'s 1963 "I Have a Dream" speech has also been encoded.

Being stored in DNA could allow those famous words to live on for eons.

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DNA Could Become the Next Big Data Warehouse

DNA and Protein syntesis

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City of York - England - Glide Gear DNA 5050
Me and a friend having a first go at using the glide gear equipment. We just walked around York city center. Please don #39;t judge to harshly.. Was lots of fun and hope to make more video #39;s soon. Still working out how to balance the glide gear as it sways abit as you can see in the video. The equipment used was Canon 5D mark iii Canon 17-40mm Glide Gear DNA 50/50

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City of York - England - Glide Gear DNA 5050 - Video

By Robert F. Service, ScienceNOW

Paleontologists routinely resurrect and sequence DNA from woolly mammoths and other long-extinct species. Future paleontologists, or librarians, may do much the same to pull up Shakespeares sonnets, listen to Martin Luther King Jr.s I have a dream speech, or view photos. Researchers in the United Kingdom report today that theyve encoded these works and others in DNA and later sequenced the genetic material to reconstruct the written, audio, and visual information.

The new work isnt the first example of large-scale storage of digital information in DNA. Last year, researchers led by bioengineers Sriram Kosuri and George Church of Harvard Medical School reported that they stored a copy of one of Churchs books in DNA, among other things, at a density of about 700 terabits per gram, more than six orders of magnitude more dense than conventional data storage on a computer hard disk. Now, researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, U.K., report online today in Nature that theyve improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.

To do so, the team first translated written words or other data into a standard binary code of 0s and 1s, and then converted this to a trinary code of 0s, 1s, and 2sa step needed to help prevent the introduction of errors. The researchers then rewrote that data as strings of DNAs chemical bases: As, Gs, Cs, and Ts. At the storage density achieved, a single gram of DNA would hold 2.2 million gigabits of information, or about what you can store in 468,000 DVDs. Whats more, the researchers also added an error correction scheme, encoding the information multiple times, among other tricks, to ensure that it could be read back with 100% accuracy.

Beyond demonstrating DNAs superlative information storage abilities, Goldman, Birney, and their colleagues also asked when such a technology might be worth implementing. Institutions such as the Large Hadron Collider, a particle accelerator in Geneva, Switzerland, produce on the order of 15 petabytes of data each year. So the need for vast archival storage is growing rapidly. Now, such institutions commonly archive data by storing it on magnetic tape. Keeping that data safe over many decades requires rewriting it at regular intervals, adding to the cost of preservation. DNA, on the other hand, can be stable for thousands of years if kept in a cool, dry place. Goldman also notes that the costs of synthesizing DNA, which corresponds to writing the code, as well as sequencing, or reading out the code, are dropping fast. According to the EBI researchers, at current rates, DNA data storage is now cost-effective for only data that need to be archived for 600 years or more. But if the costs of DNA synthesiscurrently the most expensive part of the enterprisedrop 100-fold, that break-even number would drop to about 50 years.

Harvards Kosuri calls the latest study good work. But he says that cost wont be the hitch. For starters, he notes, once you write a batch of data in DNA, you cant change it or rewrite over it, as is often done with other data storage technologies. And you cant access any particular piece of information, but rather must sequence large swaths of DNA to find what youve archived.

So even though DNAs data storage densities are off the charts, it may still be worth putting those family photos on a DVD for now.

This story provided by ScienceNOW, the daily online news service of the journal Science.

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Half a Million DVDs of Data Stored in Gram of DNA

It can store the information from a million CDs in a space no bigger than your little finger, and could keep it safe for centuries.

Is this some new electronic gadget? Nope. It's DNA.

The genetic material has long held all the information needed to make plants and animals, and now some scientists are saying it could help handle the growing storage needs of today's information society.

Researchers reported Wednesday that they had stored all 154 Shakespeare sonnets, a photo, a scientific paper, and a 26-second sound clip from Martin Luther King Jr.'s "I Have a Dream" speech. That all fit in a barely visible bit of DNA in a test tube.

The process involved converting the ones and zeroes of digital information into the four-letter alphabet of DNA code. That code was used to create strands of synthetic DNA. Then machines "read" the DNA molecules and recovered the encoded information. That reading process took two weeks, but technological advances are driving that time down, said Ewan Birney of the European Bioinformatics Institute in Hinxton, England. He's an author of a report published online by the journal Nature.

DNA could be useful for keeping huge amounts of information that must be kept for a long time but not retrieved very often, the researchers said. Storing the DNA would be relatively simple, they said: Just put it in a cold, dry and dark place and leave it alone.

The technology might work in the near term for large archives that have to be kept safe for centuries, like national historical records or huge library holdings, said study co-author Nick Goldman of the institute. Maybe in a decade it could become feasible for consumers to store information they want to have around in 50 years, like wedding photos or videos for future grandchildren, Goldman said in an email.

The researchers said they have no intention of putting storage DNA into a living thing, and that it couldn't accidentally become part of the genetic machinery of a living thing because of its coding scheme.

Sriram Kosuri, a Harvard researcher who co-authored a similar report last September, said both papers show advantages of DNA for long-term storage. But because of its technical limitations, "it's not going to replace your hard drive," he said.

Kosuri's co-author, Harvard DNA expert George Church, said the technology could let a person store all of Wikipedia on a fingertip, and all the world's information now stored on disk drives could fit in the palm of the hand.

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DNA could store all the world's digital data, says study

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One night a few years ago, two biologists sat in a bar in Hamburg, discussing DNA. Ewan Birney, the associate director of the European Bioinformatics Institute, and Nick Goldman, a research scientist there, were wondering how to handle the tsunami of data flooding the institute, whose job it is to maintain databases of DNA sequences, protein structures, and other biological information that scientists turn up in their researchdatabases that are growing exponentially, thanks mostly to dropping costs and increased automation. The maintenance of all this data on hard drives was pressing their budget to the breaking point.

Being genomicists, they joked that DNA, which is incredibly compact, sturdy, and of course has a rather lengthy history of storing data, would be a better way to go. Joking, however, gave way to fevered napkin-scribbling, and soon, recalls Goldman, We had to order another beer, and call for more napkins to write on.

Three years later, the results of that bar stool inspiration have been published in Nature, in a paper in which Birney, Goldman and their collaborators report using DNA to store a complete set of Shakespeares sonnets, a PDF of the first paper to describe DNAs double helix structure, a 26-second mp3 clip from Martin Luther King, Jr.s I Have a Dream speech, a text file of a compression algorithm, and a JPEG photograph of the institute. You may not be storing your personal data on DNA anytime soonthe process is time-consuming and expensive, and theres the small matter of needing a DNA sequencer to open the filesbut as the costs of making and sequencing DNA continue to plunge and as computer engineering approaches the limits of just how densely information can be encoded on silicon, such biological data storage be just whats needed for institutes and other organizations with massive archival needs.

(MORE: Whats Holding Energy Tech Back? The Infernal Battery)

To encode files in DNA, Birney and Goldman started by converting text, image, or audio data into binary code. Then, in several steps using software that Goldman wrote, they converted that into A, T, G, or C code, which stand for the four DNA bases. Working from that string of letters, they drew up the blueprints for thousands of pieces of DNA , each containing a snippet of a file, and sent their designs to Agilent Technologies, which manufactures custom DNA for biologists. Agilent sent back the completed DNA fragmentsjust a smidge of white dust in the bottom of a plastic tube, Goldman recalls. To open the files, the team used a standard DNA sequencer, a process that took about 2 weeks. They then used Goldmans software to reassemble the sequenced DNA into coherent, readable files. With the exception of two small gaps in the DNA, the sonnets, photo, speech, PDF, and text file re-emerged from the white dust almost completely unscathed. After the scientists performed a little repair work, all of the informationabout 739 KB worthwas retrieved with 100% accuracy.

The fidelity is impressive, and DNA, when kept in a cold, dry, dark place, can stay intact for thousands of years. But how long would you have to want to store something for this process to be cheaper than using archival magnetic tape, which needs to be replaced every 5 years but is still the current gold standard, thanks to its low power demands compared to hard drives or other storage technologies? Birney and Goldman calculate that if you wanted to put a file in storage today and have it last for at least 600 years, DNA would be cheaper than re-recording the data to fresh magnetic tape every half-decade or so, a process that would have to be repeated 120 times over the six-century span.

(MORE: The Internet of Things: Hardware With a Side of Software)

Goldman speculates that if the price of making and sequencing DNA continues to fall at current rates, commercial services that store data in DNA might spring up around 50 years from now. You would email documents and photographs and stuff that were valuable to you and your family [tothe DNA storage company],and maybe a day later or a week later, they would ship you back a little bit of DNA, says Goldman. You could stick it in the fridge or bury it in the garden or they would store it. And they can guarantee it will be there a hundred thousand years later.

Birney and Goldman are not the only genomicists who have realized the data-storage potential of DNA. In September 2012, genomicists George Church, Yuan Gao, and Sriram Kosuri published a short description of a similar system in Science. The Nature team stored slightly more data, and Goldman avoided one of the sources of error in the Science paperstrings of repeated bases that DNA sequencers have trouble handlingby adjusting the way his software converts the information into A, T, G, and C. But on the whole, the ideas are similar, and represent a big step forward from earlier, smaller studies.

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Is DNA the Future of Data Storage?

Sixty years after scientists described the chemical code of life an interweaving double helix called DNA researchers have found four-stranded DNA is also lurking in human cells.

The odd structures are called G-quadruplexes because they form in regions of deoxyribonucleic acid (DNA) that are full of guanine, one of the DNA molecule's four building blocks, with the others being adenine, cytosine, thymine. The structure comprises four guanines held together by a type of hydrogen bonding to form a sort of squarelike shape. (The DNA molecule is itself a double strand held together by these building blocks and wrapped together like a helix.)

The new visualization of the G-quadruplex is detailed this week in the journal Nature Chemistry.

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"I think this paper is important in showing directly the existence of this structure in vivo in the human genome, but it is not completely unexpected," said Hans-Joachim Lipps, of the University of Witten in Germany, who was not involved in the study. [ See Images of the 4-Stranded DNA ]

Scientists had shown in the past that such quadruplex DNA could form in test tubes and had even been found in the cells of ciliated protozoa, or single-celled organisms with hairlike appendages. Also there were hints of its existence in human cells, though no direct proof, Lipps said.

But scientists still didn't have concrete evidence for its existence in the human genome. In the new study, researchers, including chemist Shankar Balasubramanian, of the University of Cambridge and Cambridge Research Institute, crafted antibody proteins specifically for this type of DNA. The proteins were marked with a fluorescent chemical, so when they hooked up to areas in the human genome packed with G-quadruplexes, they lit up.

Next, they incubated the antibodies with human cells in the lab, finding these structures tended to occur in genes of cells that were rapidly dividing, a telltale feature of cancer cells. They also found a spike in quadruplexes during the s-phase of the cell cycle, or the phase when DNA replicates just before the cell divides.

As such, the researchers think the four-stranded DNA could be a target for personalized medicine in the future. If they could block these odd ducks perhaps they could stop the rapid cell division of cancer cells.

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Four-stranded DNA discovered