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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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Leverage sequencing capacity for synthesizing raw genetic materials.Accelerating sequencing throughput by contrast to technologies related to writing DNA. (A) Degenerate oligonucleotide provides diverse clonal library (N can be A, T, C or G). The current high-density microarray platform covers around a million scale oligonucleotides in one chip (shaded region represents the range of number of spots in current microarray platforms). Colored triangle in library diversity corresponds to the throughput in terms of number of clusters (reads). (B) Sequencing of degenerate oligonucleotides in the sequencing plate provides a rich source of DNA materials. The sequencing throughput far exceeds the current state-of-the art writing technologies and may become a potential source of making standard genetic materials. (C) After sequencing, mapping the physical location of the clonal sequence information with actual pixel image enables the retrieval of sequence-verified clonal information that will be used as subsequent building blocks for making genetic materials.
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f1: Leverage sequencing capacity for synthesizing raw genetic materials.Accelerating sequencing throughput by contrast to technologies related to writing DNA. (A) Degenerate oligonucleotide provides diverse clonal library (N can be A, T, C or G). The current high-density microarray platform covers around a million scale oligonucleotides in one chip (shaded region represents the range of number of spots in current microarray platforms). Colored triangle in library diversity corresponds to the throughput in terms of number of clusters (reads). (B) Sequencing of degenerate oligonucleotides in the sequencing plate provides a rich source of DNA materials. The sequencing throughput far exceeds the current state-of-the art writing technologies and may become a potential source of making standard genetic materials. (C) After sequencing, mapping the physical location of the clonal sequence information with actual pixel image enables the retrieval of sequence-verified clonal information that will be used as subsequent building blocks for making genetic materials.

Mentions: To address the gap, we present a method for a scalable generation of desired DNA molecules using only one oligonucleotide and next-generation sequencing (NGS), without the need for a microarray synthesis. We hypothesize that the sequencing plate itself can be a rich source of clonal sequences that circumvents the need for a multiple array synthesis (Fig. 1. The throughput in terms of number of clusters in sequencing corresponds to the number of spots on the array).


Toward a new paradigm of DNA writing using a massively parallel sequencing platform and degenerate oligonucleotide
Leverage sequencing capacity for synthesizing raw genetic materials.Accelerating sequencing throughput by contrast to technologies related to writing DNA. (A) Degenerate oligonucleotide provides diverse clonal library (N can be A, T, C or G). The current high-density microarray platform covers around a million scale oligonucleotides in one chip (shaded region represents the range of number of spots in current microarray platforms). Colored triangle in library diversity corresponds to the throughput in terms of number of clusters (reads). (B) Sequencing of degenerate oligonucleotides in the sequencing plate provides a rich source of DNA materials. The sequencing throughput far exceeds the current state-of-the art writing technologies and may become a potential source of making standard genetic materials. (C) After sequencing, mapping the physical location of the clonal sequence information with actual pixel image enables the retrieval of sequence-verified clonal information that will be used as subsequent building blocks for making genetic materials.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Leverage sequencing capacity for synthesizing raw genetic materials.Accelerating sequencing throughput by contrast to technologies related to writing DNA. (A) Degenerate oligonucleotide provides diverse clonal library (N can be A, T, C or G). The current high-density microarray platform covers around a million scale oligonucleotides in one chip (shaded region represents the range of number of spots in current microarray platforms). Colored triangle in library diversity corresponds to the throughput in terms of number of clusters (reads). (B) Sequencing of degenerate oligonucleotides in the sequencing plate provides a rich source of DNA materials. The sequencing throughput far exceeds the current state-of-the art writing technologies and may become a potential source of making standard genetic materials. (C) After sequencing, mapping the physical location of the clonal sequence information with actual pixel image enables the retrieval of sequence-verified clonal information that will be used as subsequent building blocks for making genetic materials.
Mentions: To address the gap, we present a method for a scalable generation of desired DNA molecules using only one oligonucleotide and next-generation sequencing (NGS), without the need for a microarray synthesis. We hypothesize that the sequencing plate itself can be a rich source of clonal sequences that circumvents the need for a multiple array synthesis (Fig. 1. The throughput in terms of number of clusters in sequencing corresponds to the number of spots on the array).

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