DNA storage-from natural biology to synthetic biology

Abstract

Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).

Keywords: DNA; Data storage; Natural processing; RNA; Synthetic biology.

Graphical abstract

Fig. 1

A: Streamlined DNA storage in bacteria allows fast read-out, processing and fast read-out. Left: Plasmid rings as the smallest unit. Larger structures: DNA chromosome with RNA polymerase. Right: mRNA is direct transcribed and translated (“Christmas tree” structures). B: Extravagant, much larger DNA storage in eukaryotes. This spread-out DNA storage contains 1000-fold more storage space, allows for sophisticated access and different levels of information release, incorporation and modification (methylation patterns, miRNAs, RNA editing, mRNA, histones etc. see text). Left: Chromosome, next DNA with histones forms nucleosomes. Middle: Activator/repressor and enhancer/silencer and, towards the middle, transcription factor complexes. Right: chromosomal territories.

Fig. 2

Natural DNA and nucleotide storage media. Lnc RNA, miRNA; viral packing and DNA; DNA proofreading (gate keeper) complex; DNA (plasmid, chromosome); Histone packing (gyrases, helicases); initiation complex (mRNA polymerase); ENCODE regulatory elements; chromosomal territories.

Fig. 3

Simple technical DNA storage. You start from (1) file to be stored (text, image, sound); (2) next there is the conversion into code and a suitable binary file (3). You then synthesize the DNA and have the encoded DNA strings (4); For decoding the DNA oligos are sequenced (5) → From this information, the original data file is regenerated (text, image, sound).

Fig. 4

State-of-the-art DNA storage: Top: The DNA sequence of choice should be encoded with error correcting codes in a PC. Then (follow the work flow, blue arrows) a synthesizer allows to synthesize the DNA sequence (left). Next, the obtained DNA is stored in a DNA storage device (Icon in the middle). Bottom, left: natural DNA sequences from patients such as blood samples can also be easily stored in the DNA storage device. Right: Storage read-out (follow arrows): By Illumina or Nanopore sequencing. Cartoon at bottom right: Modern lab methods include the DNA hard drive. DNA Sequences to be stored are anchored to a stable and large DNA backbone molecule; fast read-out is done by latest nanopore sequencing.