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Author: Thamarasee Jeewandara, Phys.org
Because of its density, ease of reproduction, long lifespan, and sustainability, geneticists can store data in synthetic DNA as a medium for long-term storage. Research in this field has recently made progress in new coding algorithms, automation, preservation, and sequencing. However, the most challenging obstacle in DNA storage deployment is still write throughput, which limits data storage capacity. In a new report, Bichlien H. Nguyen and a group of scientists from the Microsoft Research Institute and Computer Science and Engineering at the University of Washington in Seattle, USA, developed the first nano-scale DNA storage writer. The team intends to expand the DNA write density to 25 x 106 sequences per square centimeter, which will increase the storage capacity compared with existing DNA synthesis arrays. Scientists successfully wrote and decoded a piece of information in DNA to build a practical DNA data storage system. The results are now published in "Science Progress".
The current data generation speed exceeds the existing storage capacity, DNA is a promising solution to this problem, and the actual density is expected to exceed 60 PB/cm3. The material is durable under various conditions, is relevant and easy to replicate, and is expected to be more sustainable or more environmentally friendly than commercial media. In this process, digital data in the form of a bit sequence can be encoded in the sequence of four natural DNA bases-guanine, adenine, thiamine, and cytosine, although additional bases are also possible. The team can then write sequences into molecular form through de novo DNA oligonucleotide synthesis to create specific molecules based on a set of repeated chemical steps. After synthesis, the resulting oligonucleotides can be preserved and stored. In order to access the data, polymerase chain reaction can be used to amplify the DNA storage and sequence, return the DNA base sequence to the digital domain, and then decode the DNA base sequence to restore the original bit sequence.
Overview of a 650 nm array with a spacing of 2 μm. (A) The finite element analysis of anodic acid generation and diffusion of a 650 nm diameter electrode with 200 nm pores is described by a cross-sectional view along the y = x plane and a top-down view on (B) the z = 0 plane . Blue and yellow represent areas with relatively low and high acid concentrations, respectively. (C) An overview of the nanoscale DNA synthesis array, including a scanning electron microscope image of a 650 nm electrode array and a magnified view of one electrode. (D) Fluorescence image, where each hole around the activated anode is patterned with AAA fluorescein. The cartoons depict which electrodes in the layout are activated. (E) Illustration of a well patterned with AAA-Fluorescein and AAA-AquaPhluor, and (F) Overlay of corresponding images of two fluorophores at the end of DNA synthesized on the same 650 nm electrode array. Image source: Science Advances, 10.1126/sciadv.abi6714 A new method for data storage of synthetic DNA
In this study, Nguyen et al. An electrode array was produced that demonstrated independent electrode-specific control of DNA synthesis, with electrode size and spacing to establish a synthesis density of 25 million oligonucleotides per square centimeter. This value is estimated as the electrode density required to achieve the minimum goal of kilobytes per second of data storage in DNA. The team promoted the latest technology of electrochemical control and provided experimental evidence for the write bandwidth required for DNA data storage.
The team introduced a proof-of-concept molecular controller in the form of a tiny DNA storage and writing mechanism on a chip. The chip can tightly synthesize DNA in a way that is 3 orders of magnitude higher than before to achieve higher DNA write throughput. To store information in DNA at the scale required for commercial use, two key processes are required. First, the team must use coding software and a DNA synthesizer to convert the digital bits (1 and 0) into synthetic DNA strands that represent the bits. Then they must be able to read the information and decode it back into place to restore the information to digital form again using a DNA sequencer and decoding software.
Development of electrochemical arrays for nanoscale features
In the traditional DNA strand synthesis process, scientists use a multi-step method called phosphoramidite chemistry, in which DNA strands can grow sequentially by adding DNA bases. Each DNA base contains a blocking group to prevent multiple additions of the DNA base to the growing chain. When connecting to the DNA strand, an acid can be passed in the setting to cut the blocking group and trigger the DNA strand to add the next base. In the process of electrochemical DNA synthesis, each point in the array contains an electrode. When a voltage is applied, acid is generated at the working electrode (anode) to release the blocking of the growing DNA chain, and at the counter electrode (cathode) The equivalent alkali is produced at the place. The team designed an electrode array to prevent acid from spreading in the device. Each working electrode that formed acid during DNA synthesis sinks into a well and is reacted by four common electrodes. The electrode surrounds, that is, the cathode formed by the driving bases, to limit the acid in a specific area. Ruan et al. Finite element analysis is used to verify the effectiveness of the design. During the experiment, when the acid is present at a sufficient concentration, the acid will unblock the surface-bound nucleotide to allow the next nucleotide to couple. Using a chip setup containing feature points to limit acid, they developed an electrochemical array with four independent electrodes to regulate DNA synthesis. Then, the team conducted experiments with two fluorescently labeled bases, green and red. As a proof of concept, they demonstrated the ability of the device to write data by synthesizing four unique DNA strands. Each DNA strand is 100 bases long and contains encoded information without errors.
Outlook: Synthesize short oligonucleotides on electrode arrays for data storage
Nguyen et al. used this setting. The spatially controlled synthesis of short oligonucleotides on the electrode array is also shown to assess the maximum DNA length that can be formed. The scientists created a 180-nucleotide DNA sequence and PCR amplified products of different lengths from the full length of the oligonucleotide. As the amplicon gets longer, the expected PCR product appears dimmer and undefined, while shorter amplicons show stronger and more defined bands, indicating higher synthesis errors. According to the results, the researchers chose a sequence length of 100 bases for purification to provide a practical demonstration of DNA data storage without further optimization. In this way, the proof-of-concept method demonstrated by Bichlien H. Nguyen and colleagues in this work paves the way for the parallel generation of large-scale and unique DNA sequences for data storage. This work surpasses previous reports on densely synthesized DNA sequences and provides the first experimental instructions to achieve the write bandwidth required for nanometer-scale feature size data storage. Scientists look forward to the direct application of these devices in information technology, and foresee their practical applications in materials science, synthetic biology, and large-scale molecular biology analysis. Further exploration of the dawn of enzymatic DNA synthesis More information: Bichlien H. Nguyen et al. Using nanoelectrodes to scale DNA data storage, scientific progress (2021). DOI: 10.1126/sciadv.abi6714
Goldman et al., Realizing practical, high-capacity, low-maintenance information storage in synthetic DNA, Nature (2013). DOI: 10.1038/nature11875 Journal information: Science Advances, Nature
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