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

Byungjin Hwang,Duhee Bang

doi:10.1038/srep37176

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.

Highlights

All synthetic DNA materials require prior programming of the building blocks of the oligonucleotide sequences
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
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

Summary

Introduction

All synthetic DNA materials require prior programming of the building blocks of the oligonucleotide sequences. 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. Recent advances in programmable microarray synthesis have expanded the throughput up to the millions of oligonucleotides per chip, performing a large number of testing hypotheses on a given array is still daunting task. Unlike the DNA writing field, the sequencing cost per base has been dropping precipitously in the last few years owing much to innovative technologies and competition among industries. A widening of the throughput capacity gap between the state-of-the art DNA writing and reading is inevitable, which will eventually limit the scalable use of synthetic DNA for making high capacity genetic or memory materials

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Conclusion