Creating our DNA Library

When we embarked on the mission of creating our modular DNA typewriter, our aim was to develop an efficient and robust method of producing information coding units that would make DNA a more approachable data storage platform. We have created a library of BabbleBricks that can be assembled in any order depending on the end user's desire. Therefore, we have designed a customisable system that is sustainable as well as affordable.

 

In fact, once the BabbleBricks' library is generated, the only end user cost will be to join the units into constructs or BabbleBlocks. Because of this, our method vastly reduces the cost of DNA data storage. 

 

To demonstrate our concept we chose to encode text and create a molecular library of plasmids (circular DNA), each of which has a different word fragment inserted into it. Once accommodated in the plasmid, the words can be easily reproduced and extracted for sentence assembly. During assembly, alternating ends of the words ensure unidirectional addition: 

 

Every word comes in two forms (AB and BA) that are not compatible with themselves and cannot join together.

The way we initially approached producing our DNA library, was to order pairs of words hosted together in one DNA fragment known as a gBlock. In order to separate each word and insert them into individual plasmids, each gBlock would need to be digested, or cut. The words have to be divided by a "spacer" region to ensure fidelity of the cut. 

 

Gblock of our first 2 encoded words "good" and "day"

Digestion and insertion would occur in one pot, meaning each plasmid needs to be verified for their unique information units. This is done by screening and sequencing (reading) individual plasmids; a very time-consuming and costly process. Our team tackled this hurdle by exploring an alternative idea - generating the library using pairs of annealed primers:

 

Primers are single stranded DNA fragments that can anneal to each other based on complementary base pairing.

 

A set of primers (Forward and Reverse) are designed to anneal in such a way that a BabbleBrick is produced directly with its alternating AB/BA hangs

Annealing pairs of primers produces BabbleBricks with overhangs (or "sticky ends") that can be directly inserted into plasmids, without additional cutting. In addition, at the same time they can be used straight away for BabbleBlock assembly. This makes creating our DNA library and constructing BabbleBlocks, or sentences, much more efficient and qualified. Furthermore, another advantage is that the annealed sets could be inserted into the library individually, without the need for separation by sequencing. This reduces the cost of DNA text encoding significantly:

 

Cost evaluation of DNA text encoding using gBlocks vs. sets of primers. Once the BabbleBricks library is generated the assembly is fairly low-cost.

Driven by the applications of text archival in DNA, we have been in touch with the National Library of Scotland and are working jointly on storing a copy of the last letter of Mary Queen of Scots, addressed to Henri III of France into a DNA molecule. 

The last statement could be encoded in both its original French as well as English, due to the programable property of our DNA library. Moreover, because of its modular design, BabblED reduces the cost of DNA data storage compared to de novo DNA synthesis companies:

 

The modular nature of BabblED exceeds de novo DNA synthesis by proposing a low-cost word assembly opposed to solid state nucleotide synthesis. Both IDT and Gen9 have similiar costs of DNA encoding which is almost 3 times more expensive than the one proposed by our DNA typewriter.

@EdiGEM2016