DNA encodes the information for all the proteins inside the cell, their amino acid sequence, when and where to turn them on, and a whole lot of other things that we probably dont fully understand yet. With the ability to write DNA, to synthesize our own arbitrary stretches of As, Ts, Cs, and Gs, we can create our own instructions for cellular proteins or we can encode sequences that would be junk to a cell but that we could read as a message. This week, George Church, Yuan Gao, and Sri Kosuri published a short paper demonstrating that not only could we encode a few phrases here and there, but write a whole book in DNA. The book, Churchs Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves, which will be published using more traditional means this fall, includes 53,426 words, 11 jpgs, and one JavaScript program. The text and images were converted to html format and then read as bits, 1s and 0s that can be easily encoded into DNA: A or C for 0 and T or G for 1. Having two possible letters for each bit means that the sequence wont end up with long stretches of any single letter, a challenge for chemical DNA synthesis. The perl code they used to covert bits to DNA is available in the papers supplementary information (PDF).

This is by far the largest amount of non-biological information synthesized and stored in DNAa total of 5.27 megabits, way beyond the 7,920 bit record previously held by the Venter Institutes watermarks in their chemically synthesized genome (written using an undisclosed code for each letter and punctuation mark).

The sequence of Watermark 4 in the Venter Institute's synthetic genome

While news reports about the DNA book often acknowledge this previous DNA message, as well as a 1999 paper encoding the World War II spy message JUNE 6 INVASION: NORMANDY in DNA (PDF), they dont mention the very first synthetic DNA message cited in the paper. In 1988, Joe Davis, an artist collaborating with molecular biologist Dana Boyd in Jon Beckwiths lab at Harvard Medical School (and currently a research affiliate in George Churchs lab), designed and synthesized an 18 base-pair message encoding the image of the ancient Germanic rune representing life and the female earth. The Microvenus message was then pasted into a vector and transformed into E. coli, creating a living work of art.

Microvenus--The first non-biological message encoded in DNA, by Joe Davis

The Arecibo Message

The coding scheme for Microvenus was inspired by the binary message sent by Carl Sagan and Frank Drake from the Arecibo radio telescope in 1974, an attempt to open up communication with extraterrestrial intelligence (as well as demonstrate the capabilities of the newly remodeled telescope). The image is a 2373 rectangle (having the dimensions be two prime numbers makes it easier to decode the single stream of binary digits) showing pictures of the telescope, a person, and information about our solar system and our DNA. Microvenus is coded with a similar principle, the lines of the image translated to ones and zeros in a 57 grid, converted to DNA with phase-change values rather than numerical values. The DNA bases are arranged by size C= 1, T=2, A =3, G=4 and represent the number of bits needed before you switch to the opposite bit. For example, 10101 translates to CCCCC because each digit occurs once before it switches, and 00011 would be AG because there are three 0 before it switches to two ones.

Despite its tendency to mutate and evolve as cells divide, DNA is a remarkably inert and stable chemical on its own, lasting long enough for archeologists to be able to sequence strands of DNA many thousands of years old. In a microbial spore hurtling through space, DNA could theoretically last long enough to be found by an extraterrestrial civilization that could sequence it and decode the message inside. In the late 1970s, some scientists even hypothesized the inverse possibilitythat viruses on Earth could have been sent as messages from extraterrestrials. Attempts to decode the X174 viral genome sequence into two dimensional images of course didnt yield any striking alien messages, but did open up the possibility of sending out different kinds of messages of our own.

For Davis, the messages that we send to aliens arent just about sending out a friendly description of life, art, and science on Earth, but of better understanding those things ourselves. He writes in his paper describing the Microvenus project:

By sending messages to extraterrestrial intelligence, human beings are importantly engaged in a search for themselves. They must first reveal themselves to themselves before they can reveal themselves to anyone else. This has not only been a central dilemmain the search for extraterrestrial intelligence, but it has also been an essential element of art, history, psychology, and classical philosophy.

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Communicating with Aliens through DNA

The data storage project represents the largest piece of non-biological data ever stored in this manner

By Monya Baker and Nature magazine

Image: dna, synthetic biology

Showcasing more than fifty of the most provocative, original, and significant online essays from 2011, The Best Science Writing Online 2012 will change the way...

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From Nature magazine

A trio of researchers has encoded a draft of a whole book into DNA. The 5.27-megabit tome contains 53,246 words, 11 JPG image files and a JavaScript program, making it the largest piece of non-biological data ever stored in this way.

DNA has the potential to store huge amounts of information. In theory, two bits of data can be incorporated per nucleotide the single base unit of a DNA string so each gram of the double-stranded molecule could store 455 exabytes of data (1 exabyte is 1018 bytes). Such dense packing outstrips inorganic data-storage devices such as flash memory, hard disks or even storage based on quantum-computing methods.

The book, which is fittingly a treatise on synthetic biology, was encoded by geneticists George Church and Sriram Kosuri at the Wyss Institute for Biologically Inspired Engineering in Boston, Massachusetts, and Yuan Gao, a biomedical engineer at Johns Hopkins University in Baltimore, Maryland. They report their work in Science1 this week.

It marks a significant gain on previous projects the largest of which encoded less than one-six-hundredth of the data but organic flash drives are still many years away. There are a number of reasons why the method is not practical for everyday use. For example, both storing and retrieving information currently require several days of lab work, spent either synthesizing DNA from scratch or sequencing it to read the data.

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Synthetic Biology Book Published in DNA

Lawrence LeBlond for redOrbit.com Your Universe Online

DNA, the building block of life, is now home to more than just the worlds living creatures. Scientists from Harvard University report that they have written an entire novel in DNA, a feat that could revolutionize our ability to save data.

Our genetic code packs billions of gigabytes into a single gram. That is significantly more information that a single microchip could even think about storing. In fact, a single milligram of genetic code could encode the entire Library of Congress and still have room to spare.

Long held as only a theory, the storage of data in DNA has now tipped the genetic scale and has become a reality. George Church of Harvard Medical School and his colleagues stored an entire genetics handbook in less than a picogram trillionth of a gram of DNA.

The experiment, reported in Thursdays edition of the journal Science, could pave the way for eventual data-storage systems that can handle vast amounts of data, perhaps millions of times more data than a single hard drive can handle. Using next-generation sequencing technology, the Harvard team, were not only able to encode the book in DNA, but also were able to accurately copy and read it.

A few other teams have tried to write data into the DNA of living cells. But because the approach carries some disadvantages, it may not prove feasible. Because cells die, writing data into genetic code could mean that you are going to ultimately lose your work. And because cells also replicate, there would be the possibility that new mutations could change the data.

To work around these possible scenarios, Church and his colleagues created a DNA information-archiving system using no cells at all. Instead, they utilized an inkjet printer to embed short fragments of chemically synthesized DNA onto the surface of a tiny glass chip. To encode the file, the team divided it into tiny blocks of data and converted it not into typical digital storage 1s and 0s, but rather DNAs four-letter alphabet of As (adenine), Cs (cytosine), Gs (guanine) and Ts (thymine).

The team explained that each DNA fragment also contains a digital barcode that records its location in the original file. Reading the data requires a DNA sequencer and a computer to put back together the DNA puzzle of fragments in order to convert them into digital format. The computer also corrects for errors; each block of data is replicated thousands of times so that any chance glitch can be identified and fixed by comparing it to the other copies.

To demonstrate the technology, the team used the DNA chips to encode a genetics book co-authored by Church Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves in DNA. After converting the book into DNA and translating it back into digital form, the teams system only produced a rate of two errors per million bits of information, and only amounted to a few single-letter typos, which is on par with DVDs and far better than magnetic hard drives.

However, the impracticability of such a system is not there right now. Sequencing DNA is a costly procedure and is not feasible for general use, according to Daniel Gibson, a synthetic biologist at the J. Craig Venter Institute in Rockville, Maryland. However, he noted, the field is moving fast and the technology will soon be cheaper, faster, and smaller.

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Harvard Scientists Write Book In DNA And Accurately Copy, Read It Back

By John Bohannon, ScienceNOW

When it comes to storing information, hard drives dont hold a candle to DNA. Our genetic code packs billions of gigabytes into a single gram. A mere milligram of the molecule could encode the complete text of every book in the Library of Congress and have plenty of room to spare. All of this has been mostly theoretical until now. In a new study, researchers stored an entire genetics textbook in less than a picogram of DNA one trillionth of a gram an advance that could revolutionize our ability to save data.

A few teams have tried to write data into the genomes of living cells. But the approach has a couple of disadvantages. First, cells die not a good way to lose your term paper. They also replicate, introducing new mutations over time that can change the data.

To get around these problems, a team led by George Church, a synthetic biologist at Harvard Medical School in Boston, created a DNA information-archiving system that uses no cells at all. Instead, an inkjet printer embeds short fragments of chemically synthesized DNA onto the surface of a tiny glass chip. To encode a digital file, researchers divide it into tiny blocks of data and convert these data not into the 1s and 0s of typical digital storage media, but rather into DNAs four-letter alphabet of As, Cs, Gs, and Ts. Each DNA fragment also contains a digital barcode that records its location in the original file. Reading the data requires a DNA sequencer and a computer to reassemble all of the fragments in order and convert them back into digital format. The computer also corrects for errors; each block of data is replicated thousands of times so that any chance glitch can be identified and fixed by comparing it to the other copies.

To demonstrate its system in action, the team used the DNA chips to encode a genetics book co-authored by Church. It worked. After converting the book into DNA and translating it back into digital form, the teams system had a raw error rate of only two errors per million bits, amounting to a few single-letter typos. That is on par with DVDs and far better than magnetic hard drives. And because of their tiny size, DNA chips are now the storage medium with the highest known information density, the researchers report online today in Science.

Dont replace your flash drive with genetic material just yet, however. The cost of the DNA sequencer and other instruments currently makes this impractical for general use, says Daniel Gibson, a synthetic biologist at the J. Craig Venter Institute in Rockville, Maryland, but the field is moving fast and the technology will soon be cheaper, faster, and smaller. Gibson led the team that created the first completely synthetic genome, which included a watermark of extra data encoded into the DNA. The researchers used a three-letter coding system that is less efficient than the Church teams but has built-in safeguards to prevent living cells from translating the DNA into proteins. If DNA is going to be used for this purpose, and outside a laboratory setting, then you would want to use DNA sequence that is least likely to be expressed in the environment, he says. Church disagrees. Unless someone deliberately subverts his DNA data-archiving system, he sees little danger.

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

Image: Scientists have found a way to store an entire textbook in the code of DNA. (JohnGoode/Flickr)

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DNA: The Ultimate Hard Drive

(Phys.org) -- A team of researchers in the US has successfully encoded a 5.27 megabit book using DNA microchips, and they then read the book using DNA sequencing. Their experiments show that DNA could be used for long-term storage of digital information.

George Church and Sriram Kosuri of Harvards Wyss Institute for Biologically Inspired Engineering, and colleagues, encoded Churchs book Regenesis of around 53,400 words into DNA sequences, along with 11 images in JPG format and a JavaScript program. This is 1,000 times more data than has been encoded in DNA previously.

DNA is made up of nucleotides, and in theory at least each nucleotide can be used to encode two bits of data. This means that the density is a massive 1 million gigabits per cubic millimeter, and only four grams of DNA could theoretically store all the digital data created annually. This is much denser than digital storage media such as flash drives, and more stable, since the DNA sequences could be read thousands of years after they were encoded.

The experiments success lay in the strategy of encoding the data in short sequences of DNA rather than long ones, and this reduced the difficulty and cost of writing and reading the data. Dr Kosuri said the process was analogous to storing data on a hard drive, where data is written in small blocks called sectors.

They first converted the book, program and images to HTML and then translated this into a sequence of 5.27 million 0s and 1s, and these 5.27 megabits were then sequenced into sections of nucleotides 96 bits long using one DNA nucleotide for one bit. The nucleotide bases A and C encoded for 0, while G and T encoded for 1. Each block also contained a 19 bit address to encode the blocks place in the overall sequence. Multiple copies of each block were synthesized to help in error correction.

After the book and other information was encoded into the DNA, drops of DNA were attached to microarray chips for storage. The chips were kept at 4C for three months and then dissolved and sequenced. Each copy of each block of nucleotides was sequenced up to 3,000 times so that a consensus could be reached. In this way they reduced the bit errors in the 5.27 megabits to just 10.

The procedure, described in a paper in the journal Science, cannot be used for rewritable data but could be used for very long-term storage of data. One advantage of using DNA is that a much greater density of information can be stored, but another major advantage is that DNA is a biological molecule that will always be able to be read biologically without special equipment such as CD or DVD players that can quickly become obsolete.

The main disadvantage of this system is that at the moment the technologies used to synthesize and sequence DNA are far too expensive for it to be a practical system for everyday use. Another problem is that while DNA has been sequenced from sources such as mummies thousands of years old, the DNA tends to be fragmented, and work needs to be done on improving the stability of DNA over centuries and longer.

More information: Next-Generation Digital Information Storage in DNA, Science, DOI: 10.1126/science.1226355

ABSTRACT Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. Here, we develop a strategy to encode arbitrary digital information in DNA, write a 5.27-megabit book using DNA microchips, and read the book using next-generation DNA sequencing.

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DNA used to encode a book and other digital information