Composite DNA Fragments for Error-Resilient Data Storage
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Solution Overview
Problem
Current DNA data storage methods face high error rates due to insertion and deletion errors, which are difficult to correct using traditional error correction codes, leading to inefficiencies in writing and reading DNA-encoded files.
Innovation Solution
The use of composite fragments with different nucleotide sequences and ratios allows for more efficient encoding and decoding of information, increasing the number of states and improving error correction by employing a mixture ratio representation in DNA sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional error correction codes are used for DNA data storage, then the system is simple to implement, but the error correction capability is insufficient due to insertion and deletion errors
Solution Approach 1:
The patent segments the DNA encoding into multiple composite fragments, where each fragment represents a portion of the original data. This segmentation allows for localized error correction and reduces the impact of insertion/deletion errors on the entire data set, thereby improving reliability without requiring overly complex global error correction codes.
Solution Approach 2:
The patent employs composite coding that combines multiple error detection and correction mechanisms within a unified framework. By integrating checksums, redundancy bits, and fragment-based encoding into a composite structure, the system achieves robust error correction capability while maintaining manageable complexity through modular design.
2Productivity
If DNA synthesis is performed at current rates, then the process is straightforward, but the writing time for archive files would take decades
Solution Approach 1:
The patent divides the DNA synthesis process into multiple parallel operations by segmenting the data into composite fragments. Each fragment can be synthesized independently and simultaneously, dramatically increasing the effective writing speed. This parallelization approach reduces the total synthesis time from decades to a manageable timeframe while maintaining process simplicity.
Solution Approach 2:
The patent performs preliminary encoding and fragmentation of the data before synthesis begins. By pre-processing the data into optimized composite fragments with embedded error correction codes, the actual synthesis process can proceed efficiently without requiring complex real-time adjustments, thereby reducing overall synthesis time.
3Loss of information
If more nucleotide fragments are used in composite fragments, then the information density increases, but the synthesis cost and complexity increase
Solution Approach 1:
The patent optimizes the number and length of nucleotide fragments in each composite fragment to achieve the desired information density. By carefully selecting fragment parameters (length, composition, and arrangement), the system maximizes information storage capacity while keeping synthesis and assembly processes within manageable complexity bounds.
Solution Approach 2:
The patent uses a moderate number of nucleotide fragments per composite fragment rather than maximizing the number indefinitely. This partial action approach achieves sufficient information density for practical applications while avoiding the exponential increase in synthesis cost and complexity that would result from using excessive numbers of fragments.
4Ease of manufacture
If traditional binary encoding is used for DNA, then the encoding process is simple, but the error rates from insertion and deletion errors are difficult to correct
Solution Approach 1:
The patent creates a composite encoding structure that integrates traditional binary encoding with additional error correction mechanisms. Each composite fragment contains the original binary data along with redundancy information and checksums, allowing simple initial encoding while enabling effective correction of insertion and deletion errors through the composite structure.
Solution Approach 2:
The patent introduces intermediary elements within the composite fragments, such as spacer sequences and checkpoint markers, that facilitate error detection and correction without complicating the fundamental binary encoding process. These intermediaries act as mediators that bridge the simple encoding approach with robust error correction capabilities.
Data Source
AI summary
A computer-implemented method for storing information into a polynucleotide is provided including using multiple types of nucleotide fragments, wherein each of the nucleotide fragments has an individually different sequence of bases, configuring multiple composite fragments, wherein each of the composite fragments has a set of the nucleotide fragments with different ratios of the nucleotide fragments, and encoding, via an encoder, the information into the composite fragments.