Highly reliable and efficient encoding systems for hexadecimal polypeptide-based data storage

Yubin Ren; Yi Zhang; Yawei Liu; Qinglin Wu; Hong-Gang Hu; Jingjing Li; Chunhai Fan; Dong Chen; Kai Liu; Hongjie Zhang

Fundamental Research (Mar 2023)

Highly reliable and efficient encoding systems for hexadecimal polypeptide-based data storage

Yubin Ren,
Yi Zhang,
Yawei Liu,
Qinglin Wu,
Hong-Gang Hu,
Jingjing Li,
Chunhai Fan,
Dong Chen,
Kai Liu,
Hongjie Zhang

Affiliations

Yubin Ren: Department of Chemistry, Tsinghua University, Beijing 100084, China
Yi Zhang: State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
Yawei Liu: State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
Qinglin Wu: Institute of Process Equipment, College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
Hong-Gang Hu: Institute of Translational Medicine, Shanghai University, Shanghai 200444, China; Corresponding authors.
Jingjing Li: State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Corresponding authors.
Chunhai Fan: Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
Dong Chen: Institute of Process Equipment, College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310027, China; Corresponding authors.
Kai Liu: Department of Chemistry, Tsinghua University, Beijing 100084, China; Corresponding authors.
Hongjie Zhang: Department of Chemistry, Tsinghua University, Beijing 100084, China

Journal volume & issue: Vol. 3, no. 2
pp. 298 – 304

Abstract

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Polypeptides consisting of amino acid (AA) sequences are suitable for high-density information storage. However, the lack of suitable encoding systems, which accommodate the characteristics of polypeptide synthesis, storage and sequencing, impedes the application of polypeptides for large-scale digital data storage. To address this, two reliable and highly efficient encoding systems, i.e. RaptorQ-Arithmetic-Base64-Shuffle-RS (RABSR) and RaptorQ-Arithmetic-Huffman-Rotary-Shuffle-RS (RAHRSR) systems, are developed for polypeptide data storage. The two encoding systems realized the advantages of compressing data, correcting errors of AA chain loss, correcting errors within AA chains, eliminating homopolymers, and pseudo-randomized encrypting. The coding efficiency without arithmetic compression and error correction of audios, pictures and texts by the RABSR system was 3.20, 3.12 and 3.53 Bits/AA, respectively. While that using the RAHRSR system reached 4.89, 4.80 and 6.84 Bits/AA, respectively. When implemented with redundancy for error correction and arithmetic compression to reduce redundancy, the coding efficiency of audios, pictures and texts by the RABSR system was 4.43, 4.36 and 5.22 Bits/AA, respectively. This efficiency further increased to 7.24, 7.11 and 9.82 Bits/AA by the RAHRSR system, respectively. Therefore, the developed hexadecimal polypeptide-based systems may provide a new scenario for highly reliable and highly efficient data storage.

Published in Fundamental Research

ISSN: 2667-3258 (Online)
Publisher: KeAi Communications Co. Ltd.
Country of publisher: China
LCC subjects: Science: Science (General)
Website: https://www.keaipublishing.com/en/journals/fundamental-research/

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