Long term conservation of DNA at ambient temperature. Implications for DNA data storage

Abstract

DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and for DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25°C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.

Emerging Approaches to DNA Data Storage: Challenges and Prospects

“…The interface between these natural systems and DNA nanotechnology is an active area of research, which generates other possibilities for DNA data storage that leverage nature's evolved machinery. We foresee that DNA nanostructures made for information storage will find audiences in cryptography, steganography, and other fields 4,58,116 and that combining DNA data storage with data analysis techniques such as neural networks will afford opportunities in a growing number of sectors. 127 Because of the long-term stability of DNA under appropriate storage conditions, we predict that archival storage will be the most valuable application for DNA data storage.…”

“…Without appropriate protection, DNA (and thus the data encoded within) is degraded by multiple mechanisms, including strand breaks, nucleotide mutations, strand cross-linking by UV, oxidation, hydrolysis, alkylation, or mechanical stress, all of which are due to environmental factors. Among those, hydrolysis is the dominating decay pathway in a data storage context. , Thus, all applicable DNA storage approaches focus on protecting the DNA from moisture and oxygen with either microscopic (i.e., on the level of individual molecules) or macroscopic (i.e., on the level of individual pools) containers. Examples of microscopic containers include encapsulation within silica particles; ,− embedding in alkaline salt, polymer, sugar, or silk protein matrices; and coprecipitation with calcium phosphates imitating bone.…”

“…Examples of microscopic containers include encapsulation within silica particles; ,− embedding in alkaline salt, polymer, sugar, or silk protein matrices; and coprecipitation with calcium phosphates imitating bone. In the latter category, dried or lyophilized DNA is stored on filter paper within hermetically sealed capsules with inert atmosphere ,,, or, as is common in biological practice, simply frozen in aqueous solutions and stored at −20 or −80 °C …”

“…Temperature corrections were performed using Arrhenius Law using 155 kJ/mol as the activation energy of DNA strand breaks. , b Typical concentration for synthetic DNA is 500 ng/μL. c Assumed pool size per DNA shell = 5.5 TB . Weight of the DNA shell is at least 1.3 g d Polymer density was assumed as similar to that of polyethylene glycol at 1.12 g/cm 3 . e Density of filter paper is around 85 kg/m 2 . …”

“…Among those, hydrolysis is the dominating decay pathway in a data storage context. 57 , 58 Thus, all applicable DNA storage approaches focus on protecting the DNA from moisture and oxygen with either microscopic (i.e., on the level of individual molecules) or macroscopic (i.e., on the level of individual pools) containers. Examples of microscopic containers include encapsulation within silica particles; 56 , 59 − 61 embedding in alkaline salt, 62 polymer, 63 sugar, 64 or silk protein 65 matrices; and coprecipitation with calcium phosphates 66 imitating bone.…”