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Toward a new paradigm of DNA writing using a massively parallel sequencing platform and degenerate oligonucleotide

View Article: PubMed Central - PubMed

ABSTRACT

All synthetic DNA materials require prior programming of the building blocks of the oligonucleotide sequences. The development of a programmable microarray platform provides cost-effective and time-efficient solutions in the field of data storage using DNA. However, the scalability of the synthesis is not on par with the accelerating sequencing capacity. Here, we report on a new paradigm of generating genetic material (writing) using a degenerate oligonucleotide and optomechanical retrieval method that leverages sequencing (reading) throughput to generate the desired number of oligonucleotides. As a proof of concept, we demonstrate the feasibility of our concept in digital information storage in DNA. In simulation, the ability to store data is expected to exponentially increase with increase in degenerate space. The present study highlights the major framework change in conventional DNA writing paradigm as a sequencer itself can become a potential source of making genetic materials.

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Related in: MedlinePlus

Schematic flow of high-throughput data storage in DNA.From a single degenerate oligonucleotide, diverse sequence information can be extracted using high-throughput sequencing (reading DNA). Information is encoded with the Huffman code in DNA using the base-4 scheme. The sequencing of a degenerate oligonucleotide generates diverse clonal sequences. Clonal sequences are then retrieved in a tube using an automated laser pulse. Additional tubes can be used to separately collect duplicate information for correcting errors (see Fig. 3). The pool consisting of the targeted sequence is sequenced to recover the original information. The decoding process is exactly the reverse of the encoding process. After sequencing, an in silico assembly is performed to recover the original data.
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f2: Schematic flow of high-throughput data storage in DNA.From a single degenerate oligonucleotide, diverse sequence information can be extracted using high-throughput sequencing (reading DNA). Information is encoded with the Huffman code in DNA using the base-4 scheme. The sequencing of a degenerate oligonucleotide generates diverse clonal sequences. Clonal sequences are then retrieved in a tube using an automated laser pulse. Additional tubes can be used to separately collect duplicate information for correcting errors (see Fig. 3). The pool consisting of the targeted sequence is sequenced to recover the original information. The decoding process is exactly the reverse of the encoding process. After sequencing, an in silico assembly is performed to recover the original data.

Mentions: The proposed DNA writing was composed of the following steps (Fig. 2); synthesis of a short oligonucleotide with degenerate nucleotides, running NGS of the oligonucleotide to generate maximum possible clonal DNA materials, mapping sequence information along with positional coordinates on the surface of the NGS flow-cell, and subsequent target DNA retrieval from the flow cell onto a collection tube. Finally, the DNA retrieved from the NGS plate can be decoded via the NGS platform. In this experimental setting, the capacity of DNA synthesis can be equalized with the sequencing capacity.


Toward a new paradigm of DNA writing using a massively parallel sequencing platform and degenerate oligonucleotide
Schematic flow of high-throughput data storage in DNA.From a single degenerate oligonucleotide, diverse sequence information can be extracted using high-throughput sequencing (reading DNA). Information is encoded with the Huffman code in DNA using the base-4 scheme. The sequencing of a degenerate oligonucleotide generates diverse clonal sequences. Clonal sequences are then retrieved in a tube using an automated laser pulse. Additional tubes can be used to separately collect duplicate information for correcting errors (see Fig. 3). The pool consisting of the targeted sequence is sequenced to recover the original information. The decoding process is exactly the reverse of the encoding process. After sequencing, an in silico assembly is performed to recover the original data.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120280&req=5

f2: Schematic flow of high-throughput data storage in DNA.From a single degenerate oligonucleotide, diverse sequence information can be extracted using high-throughput sequencing (reading DNA). Information is encoded with the Huffman code in DNA using the base-4 scheme. The sequencing of a degenerate oligonucleotide generates diverse clonal sequences. Clonal sequences are then retrieved in a tube using an automated laser pulse. Additional tubes can be used to separately collect duplicate information for correcting errors (see Fig. 3). The pool consisting of the targeted sequence is sequenced to recover the original information. The decoding process is exactly the reverse of the encoding process. After sequencing, an in silico assembly is performed to recover the original data.
Mentions: The proposed DNA writing was composed of the following steps (Fig. 2); synthesis of a short oligonucleotide with degenerate nucleotides, running NGS of the oligonucleotide to generate maximum possible clonal DNA materials, mapping sequence information along with positional coordinates on the surface of the NGS flow-cell, and subsequent target DNA retrieval from the flow cell onto a collection tube. Finally, the DNA retrieved from the NGS plate can be decoded via the NGS platform. In this experimental setting, the capacity of DNA synthesis can be equalized with the sequencing capacity.

View Article: PubMed Central - PubMed

ABSTRACT

All synthetic DNA materials require prior programming of the building blocks of the oligonucleotide sequences. The development of a programmable microarray platform provides cost-effective and time-efficient solutions in the field of data storage using DNA. However, the scalability of the synthesis is not on par with the accelerating sequencing capacity. Here, we report on a new paradigm of generating genetic material (writing) using a degenerate oligonucleotide and optomechanical retrieval method that leverages sequencing (reading) throughput to generate the desired number of oligonucleotides. As a proof of concept, we demonstrate the feasibility of our concept in digital information storage in DNA. In simulation, the ability to store data is expected to exponentially increase with increase in degenerate space. The present study highlights the major framework change in conventional DNA writing paradigm as a sequencer itself can become a potential source of making genetic materials.

No MeSH data available.


Related in: MedlinePlus