New Coding Strategy Maximizes Data-Storage Capacity of DNA Molecules
Humanity may soon generate more data than hard drives or magnetic tape can handle, a problem that has scientists turning to nature’s age-old solution for information-storage—DNA.
In a new study in Science, a pair of researchers at Columbia University and the New York Genome Center (NYGC) show that an algorithm designed for streaming video on a cellphone can unlock DNA’s nearly full storage potential by squeezing more information into its four base nucleotides. They demonstrate that this technology is also extremely reliable.
DNA is an ideal storage medium because it’s ultra-compact and can last hundreds of thousands of years if kept in a cool, dry place, as demonstrated by the recent recovery of DNA from the bones of a 430,000-year-old human ancestor found in a cave in Spain.
“DNA won’t degrade over time like cassette tapes and CDs, and it won’t become obsolete—if it does, we have bigger problems,” said study coauthor Yaniv Erlich, a computer science professor at Columbia Engineering, a member of Columbia’s Data Science Institute, and a core member of the NYGC.
Erlich and his colleague Dina Zielinski, an associate scientist at NYGC, chose six files to encode, or write, into DNA: a full computer operating system, an 1895 French film, “Arrival of a train at La Ciotat,” a $50 Amazon gift card, a computer virus, a Pioneer plaque and a 1948 study by information theorist Claude Shannon.
They compressed the files into a master file, and then split the data into short strings of binary code made up of ones and zeros. Using an erasure-correcting algorithm called fountain codes, they randomly packaged the strings into so-called droplets, and mapped the ones and zeros in each droplet to the four nucleotide bases in DNA: A, G, C and T. The algorithm deleted letter combinations known to create errors, and added a barcode to each droplet to help reassemble the files later.
In all, they generated a digital list of 72,000 DNA strands, each 200 bases long, and sent it in a text file to a San Francisco DNA-synthesis startup, Twist Bioscience, that specializes in turning digital data into biological data. Two weeks later, they received a vial holding a speck of DNA molecules.
To retrieve their files, they used modern sequencing technology to read the DNA strands, followed by software to translate the genetic code back into binary. They recovered their files with zero errors, the study reports. (In this short demo, Erlich opens his archived operating system on a virtual machine and plays a game of Minesweeper to celebrate.)
They also demonstrated that a virtually unlimited number of copies of the files could be created with their coding technique by multiplying their DNA sample through polymerase chain reaction (PCR), and that those copies, and even copies of their copies, and so on, could be recovered error-free.
Finally, the researchers show that their coding strategy packs 215 petabytes of data on a single gram of DNA—100 times more than methods published by pioneering researchers George Church at Harvard, and Nick Goldman and Ewan Birney at the European Bioinformatics Institute. “We believe this is the highest-density data-storage device ever created,” said Erlich.
The capacity of DNA data-storage is theoretically limited to two binary digits for each nucleotide, but the biological constraints of DNA itself and the need to include redundant information to reassemble and read the fragments later reduces its capacity to 1.8 binary digits per nucleotide base.
The team’s insight was to apply fountain codes, a technique Erlich remembered from graduate school, to make the reading and writing process more efficient. With their DNA Fountain technique, Erlich and Zielinski pack an average of 1.6bits into each base nucleotide. That’s at least 60 percent more data than previously published methods, and close to the 1.8-bit limit.
Cost still remains a barrier. The researchers spent $7,000 to synthesize the DNA they used to archive their 2 megabytes of data, and another $2,000 to read it. Though the price of DNA sequencing has fallen exponentially, there may not be the same demand for DNA synthesis, says Sri Kosuri, a biochemistry professor at UCLA who was not involved in the study. “Investors may not be willing to risk tons of money to bring costs down,” he said.
But the price of DNA synthesis can be vastly reduced if lower-quality molecules are produced, and coding strategies like DNA Fountain are used to fix molecular errors, says Erlich. “We can do more of the heavy lifting on the computer to take the burden off time-intensive molecular coding,” he said.
Receive an email update when we add a new DNA DATA STORAGE article.
The Latest on: DNA data storage
via Google News
The Latest on: DNA data storage
- Inovio Pharmaceuticals Inc (INO) Q1 2020 Earnings Call Transcripton May 11, 2020 at 10:55 pm
Investor Relations Thank you operator and thank you everyone for joining the INOVIO first quarter 2020 earnings call. With me today are Dr. J. Joseph Kim, President and CEO; Peter Kies, our Chief ...
- INOVIO Reports First Quarter 2020 Financial Results; Provides Business Updateon May 11, 2020 at 1:05 pm
PRNewswire/ -- INOVIO (NASDAQ: INO), a biotechnology company focused on rapidly bringing to market precisely designed DNA medicines to protect and ...
- Is DNA the next generation of data backup?on May 11, 2020 at 2:08 am
As more of our work and personal lives have become digital, we've seen a staggering growth in the amount of data we're generating, storing and accessing. Source: According to various studies, Google ...
- DNA the next backup?on May 8, 2020 at 3:04 pm
Being ultra-compact and easy to replicate – thanks to its primary role in creating life – gives DNA two big advantages. One gram of DNA could potentially hold as much as 455 exabytes of data, ...
- Diary of our DNA: How my mother's photo albums evolved into a family history bookon May 8, 2020 at 3:05 am
I’m a rookie at the genealogy game, but with lots of sharing and screen time and a little luck, I created a compilation of anecdotes, photographs, family trees and historical documents that go back ...
- Twist Bioscience Reports Second Quarter Fiscal 2020 Financial Resultson May 7, 2020 at 1:05 pm
Twist Bioscience Corporation (NASDAQ: TWST), a company enabling customers to succeed through its offering of high-quality synthetic DNA using its sili ...
- Hong Kong Tests Travelers’ Saliva to Thwart Spread of Coronaviruson May 6, 2020 at 5:19 am
Layla Keith had just gotten off a flight from Singapore when she and her fellow passengers were met at the gate by Hong Kong government officials and ushered onto buses that shuttled them to a nearby ...
- DNA Digital Data Whets Its Appetiteon May 4, 2020 at 8:01 am
Conventional data storage systems risk becoming overstuffed. What else might belly up to the table? DNA-based systems! Better read/write technologies may replace 0s and 1s with As, Ts, Cs, and Gs.
- DNA damage and faulty repair jointly cause mutationson May 1, 2020 at 7:40 am
By analysing genomic data from worms, scientists detailed how mutations are caused by a combination of DNA damage and inaccurate repair. This shows that a single DNA-damaging agent can generate a ...
via Bing News