Reading DNA memory

Article By : Ron Neale

The inherent redundancy of the memory means not all oligos are required for the decoding, so those of doubtful value are discarded.

« Previously: Decoding the memory 'write' process
To retrieve the information, the oligo pool is initially amplified by Polymerase Chain Reaction (PCR) and the DNA library sequenced using a propriety one Illumina MiSeq flow cell. PCR is a technique used to create from a single or a few copies of a DNA segment a few thousand or even millions of perfect copies of that sequence.

This is a well-established process for DNA analysis. In brief, the denatured oligos have added to the ends terminators and are allowed to attach themselves to the surface of a lawn also seeded with terminators. What then happens is the single strand of the oligos bended to attach themselves to a matching terminator, as a single strand. Using the single strand as a template a matching strand grows from the lawn finishing the process when the growth ceases at the terminator on the other end of the strand. Now the resulting DNA spiral is denatured (split into single strands). The process is then repeated until large clusters as copies of the original single strand have been created, as illustrated in simplified form in Figure 1, for just two of the many strands within one of the multiple strand clusters.

DNA memory 04 (cr)
Figure 1: Using PCR technique, large clusters of DNA spiral strands are created. (Source: Ron Neale)

Starting at the terminator the complementary DNA strand is allowed to grow by immersion in a mixture of all nucleotide base types each of which has been tagged with a different colour fluorescent dye and a blocker. Once the tagged base is attached the blocker acts to inhibit any further growth of the strand.

After the first base attaches itself to its complementary base on the chain and blocks any further growth laser illumination will cause each column of strands to fluoresce with a colour identifying the particular nucleotide. The dye and the blocker are then then removed and the process repeated slowly building a picture of the nucleotide sequence.

The inherent redundancy of the memory means not all oligos are required for the decoding, so those of doubtful value are discarded reducing the exposure to erroneous oligos. At each step the colour images are scanned and recorded to produce the sequence chart and from it the original data, see the inset in fig 1. This data is then subjected to the reverse transform to obtain the original data. Reading the memory is a destructive process, however the ease with which the PCR step can be used to make an almost unlimited number of perfect copies removes this as a potential problem.

At the moment, the write process must be measured in days because of the need to send the oligos to a specialist fabrication facility. The rest of the processing for both read and write is measured in minutes and hours. The reported cost was $3,500 per Mbyte. All those values must be considered as early days values, with room for improvement.

The real success story is the closeness this latest work came to theoretical packing density 2 bits per molecule. While biochemical constraints limit the efficiency of DNA memory to 1.98bit/nt, which is reduced further by Shannon capacity considerations achieved a value of 1.57bits/nt, just 14% lower.

The future

The complex write/read processes associated with the DNA-data memory might be eliminated as the end-point of some of the work already underway in interfacing biological material with silicon, which might eventually lead to silicon chip loaded with a blob of DNA acting as the memory.

It is interesting to note while the solid state silicon fabrication processes struggles with obtaining 10nm structures, the biochemists are able to grow such structures—might that point the way to the future of lithography?

There are two other possibilities: one good, the other bad. The good is it might one day be possible to carry in the perfect environment of your body a few grams of DNA loaded with a knowledge pool of all the data ever generated. The bad news it might be possible to write a DNA data string that unintentionally gets mixed in the human system and acts like an uncontrollable contagious viral disease endlessly reproducing itself—a data black death for humans.

The career of Ron Neale, as a researcher, process developer, and designer of solid-state memory devices, stretches back over 50 years. More recently he has been involved as a consultant, writer, and keen and critical observer of the latest memory developments. His EE Times Progress Reports on the state of play in memory developments have a large following. He has a number of firsts in memory device development and manufacture in the areas of phase change memory (PCM) and programmable read-only memory (PROM), including anti-fuzes and programmable VIAS. He holds 20 patents in the area of memory and programmable interconnect and is a member of The Institute of Physics and a Chartered Physicist. He is also qualified as both a mechanical and electronic engineer. As well as memory device development and research, Ron has also held senior positions in companies involved in computer development and the manufacture of semiconductor fabrication equipment, as well as serving a stint as editor of Electronic Engineering magazine.

First published by EE Times U.S.

« Previously: Decoding the memory 'write' process

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