Improved Molecular Data Storage

Increasing amounts of data require storage, often for long periods. Synthetic polymers are an alternative to conventional storage media, because they maintain stored information while using less space and energy. However, data retrieval by mass spectrometry limits the length, and thus, the storage capacity of individual polymer chains.

Kyoung Taek Kim, Seoul National University, Korea, and colleagues have developed a method that overcomes this limitation and allows direct access to specific parts without reading the entire chain.

Data Storage in Polymers

Data accumulates constantly, resulting from business transactions, process monitoring, quality assurance, or tracking product batches. Archiving this data for decades requires much space and energy. For the long-term archival storage of large amounts of data that requires infrequent access, macromolecules with a defined sequence, like DNA or synthetic polymers, are an attractive alternative.

Synthetic polymers have advantages over DNA: simple synthesis, higher storage density, and stability under harsh conditions. Their disadvantage is that the information encoded in polymers is decoded by mass spectrometry (MS) or tandem-mass sequencing (MS²).

Reading Whole Polymer Chains

For these mass spectrometry methods, the size of the molecules must be limited, which severely limits the storage capacity of each polymer chain. In addition, the complete chain must be decoded in sequence, building block by building block—the parts of interest cannot be accessed directly. It is like having to read through an entire book instead of just opening it to the relevant page.

In contrast, long chains of DNA can be cut into fragments of random length and sequenced individually. The original sequence can then be reconstructed computationally.

Increasing the Storage Limit by Fragmentation

The team has developed a new method by which very long synthetic polymer chains whose molecular weights greatly exceed the analytical limits of MS and MS² can be efficiently decoded. As a demonstration, the team encoded their university address into ASCII code and translated this—together with an error detection code (CRC, an established method used to ensure data integrity)—into a binary code, a sequence of ones and zeroes.

This 512-bit sequence was stored in a polymer chain made of two different monomers: lactic acid to represent a 1 and phenyllactic acid to represent a 0. At irregular intervals, they also included fragmentation codes containing mandelic acid. When chemically activated, the chains break at those locations. In their demonstration, the team obtained 18 fragments of various sizes that could be individually decoded by MS² sequencing.

Reconstructing the Sequence

Specially developed software initially identified the fragments based on their mass and their end groups, as shown by the MS spectra. During the MS² process, previously measured molecular ions break down further, and these pieces were then also analyzed. The fragments could be sequenced based on the mass difference of the pieces. With the aid of the CRC error detection code, the software reconstructed the sequence of the entire chain, overcoming the length limit for the polymer chains.

The team was also able to decode interesting bits without sequencing the entire polymer chain (random access), such as the word “chemistry” in the code for their address. By taking into account that the parts of their address are all in a specific order (department, institution, city, postal code, country) and separated by commas, they were able to isolate the location where the desired information was stored within the chain and only sequenced the relevant fragments.