Digital images stored in metabolite molecules
Metabolomes are arrays of liquid mixtures containing sugars, amino acids and other types of small molecules.
In the paper published in the journal PLOS ONE, the researchers showed that they could encode kilobyte-scale image files into metabolite solutions and read the information back out again.
DNA molecules can carry huge amounts of biological information, and there has been interest in using DNA in engineered data storage devices that can hold more data than current hard drives. This new research shows that other biological substances can also be used for molecular data storage.
“This is a proof-of-concept that we hope makes people think about using wider ranges of molecules to store information,” said Jacob Rosenstein, a professor in Brown’s School of Engineering and senior author of the study. “In some situations, small molecules like the ones we used here can have even greater information density than DNA.”
The research could also have other advantages over DNA storage. According to Rosenstein, many metabolites can react with each other to form new compounds. This reaction creates the potential for molecular systems to manipulate data — performing computations within metabolite mixtures.
The research was funded by a contract with the Defense Advanced Research Projects Administration (DARPA). Engineers and chemists at Brown has been working on a variety of techniques for using small molecules to create new information systems.
The researchers assembled their own artificial metabolomes — small liquid mixtures with different combinations of molecules. The presence or absence of a particular metabolite in a mixture encodes one bit of digital data, a zero or a one. The number of molecule types in the artificial metabolome determines the number of bits each mixture can hold. For this study, the researchers created libraries of six and 12 metabolites, meaning each mixture could encode either six or 12 bits. Thousands of mixtures are then arrayed on small metal plates in the form of nanoliter-sized droplets. The contents and arrangement of the droplets, precisely placed by a liquid-handling robot, encodes the desired data.The plates are then dried, leaving tiny spots of metabolite molecules, each holding digital information. The data can then be read out using a mass spectrometer, which can identify the metabolites present at each spot on the plate and decode the data.
The researchers used the technique to encode and retrieve a variety of image files of sizes up to 2 kilobytes. There is plenty of potential for scaling up. The number of bits in a mixture increases with the number of metabolites in an artificial metabolome, and there are thousands of known metabolites available for use.
There are some limitations, the researchers point out. For example, many metabolites chemically interact with each other when placed in the same solution, and that could result in errors or loss of data. But that’s a bug that could ultimately become a feature. It may be possible to harness those reactions to manipulate data — performing in-solution computations.
“Using molecules for computation is a tremendous opportunity, and we are only starting to figure out how to take advantage of it,” said Brenda Rubenstein, a Brown assistant professor of chemistry and co-author of the study.
Other authors on the paper are Christopher Arcadia, Joseph Geiser, Peter Weber and Christopher Rose. The research was supported by DARPA (W911NF-18-2-0031).