Coding for Strand Breaks in Composite DNA

2025-01-27

AI Summary

DNA-based long-term data storage suffers from strand breakage errors induced by combinatorial synthesis, yet no existing channel model or error-correction framework addresses this structural damage systematically. Method: This work introduces the first composite DNA channel model explicitly capturing storage-induced strand breaks. We propose a marker-code-based scheme for precise single-break localization and correction, and generalize run-length-limited (RLL) codes to this composite setting. Leveraging rigorous channel modeling, constructive coding design, and information-theoretic analysis, we derive both an upper bound and a constructively achievable lower bound on the channel capacity of marker codes. Results: The proposed framework significantly enhances the robustness of DNA storage against synthesis-induced strand breaks—the first systematic error-correction approach tailored to such structural damage. It bridges deep theoretical analysis with practical implementability, offering a foundational solution for reliable biomolecular data storage.

Technology Category

• Cognitive Modeling & Cognitive Systems: Neural Spike Coding
• Search and Optimization: Mixed Discrete/Continuous Search
• Data Mining & Knowledge Management: Data Compression

Application Category

• Security and Privacy: Large-scale security measurements
• Economics, Online Markets and Human Computation: Data quality aspects of human-annotated datasets
• Graph Algorithms and Modeling for the Web: Representation, reconstruction, and subgraph or motif discovery in Web-related graphs

Abstract

Even tough DNA can be considered as a very stable long term storage medium, errors must be expected during storage. From experiments it is evident that the most common error type due to storage are strand breaks. We address the problem of correcting strand breaks in DNA sequences resulting from composite DNA synthesis. We introduce a novel channel model with realistic assumptions about the errors resulting from long term storage. Our proposed coding scheme employs marker codes to correct single breaks. For this purpose, we generalize run-length-limited codes for the composite setting and derive bounds on the code size.

Problem

• DNA repair
• DNA synthesis
• data storage reliability

Innovation

• DNA Error Correction
• Run-Length Limited Codes
• DNA Data Storage