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Related Experiment Video

Updated: Nov 8, 2025

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

Cooperative sequence clustering and decoding for DNA storage system with fountain codes.

Jaeho Jeong¹, Seong-Joon Park¹, Jae-Won Kim²

¹Department of Electrical and Computer Engineering, Seoul National University, Institute of New Media and Communications (INMC), Seoul 08826, South Korea.

Bioinformatics (Oxford, England)

|April 27, 2021

Summary

This study enhances DNA data storage by improving decoding performance. New methods utilize more sequence reads, reducing data retrieval costs without increasing writing expenses.

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Area of Science:

Biotechnology
Bioinformatics
Data Storage

Background:

DNA data storage systems face a trade-off between writing and reading costs.
Higher code rates save writing costs but increase sequencing reads for retrieval.
Current research treats clustering, alignment, and decoding as separate stages.

Purpose of the Study:

To improve DNA data storage by reducing reading costs without increasing writing costs.
To develop a unified decoding process integrating information from clustering, alignment, and decoding.
To validate experimental DNA synthesis and sequencing for practical error assessment.

Main Methods:

Developed a decoding process integrating Hamming-distance clustering, abnormal read discarding, Reed-Solomon error correction, and quality score-based ordering.
Synthesized 513.6 KB of data into DNA oligo pools.
Sequenced synthesized DNA using an Illumina MiSeq instrument.

Main Results:

Successfully synthesized and sequenced 513.6 KB of data.
The proposed decoding method incorporated previously discarded reads with minor errors.
Utilized 10.6-11.9% more sequence reads, reducing reading costs by 6.5-8.9% compared to prior research.
Provided channel characteristics including sequence coverage and read-length distributions.

Conclusions:

The integrated decoding approach significantly improves DNA data storage efficiency.
This method offers a practical solution to reduce reading costs in DNA storage systems.
Experimental validation confirms the effectiveness of the proposed techniques.