DNA Encoding Using Degenerate Bases for High-Capacity Storage
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Solution Overview
Problem
Current DNA chip technologies face challenges in manipulating nanopore size and charge, making them sensitive to environmental conditions, and limiting data storage capacity and efficiency.
Innovation Solution
The integration of semiconductor technology to graft DNA chips with adjustable nanopore diameters and the development of a DNA encoding and decoding method using basic and degenerate base values to enhance data storage and reading capabilities, along with a semiconductor-based DNA chip design for improved data storage and analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If DNA chip technologies use fixed nanopore structures, then manufacturing is simpler, but the ability to manipulate nanopore size and charge is limited
Solution Approach 1:
The patent implements dynamically adjustable nanopores using tunable hydrogels that can change their pore size and charge properties in real-time. The hydrogel material allows the nanopore dimensions and electrostatic characteristics to be modulated by external stimuli such as pH, temperature, or chemical composition changes, enabling adaptive control without redesigning the entire chip structure.
Solution Approach 2:
The invention changes the physical and chemical parameters of the nanopore environment by using hydrogels with variable crosslinking densities, polymer compositions, and charge densities. By adjusting these parameters, the system can optimize nanopore properties for different DNA sequencing applications without increasing structural complexity.
2Quantity of substance
If conventional DNA encoding uses only basic base values (A, T, C, G), then the encoding method is simpler, but data storage capacity is limited
Solution Approach 1:
The patent extends the DNA encoding system to handle multiple data formats simultaneously. By incorporating degenerate base values that can represent multiple binary states, the system achieves multi-functionality where the same DNA structure can encode different types of information (binary, quaternary, or custom data formats) depending on the base composition and sequence interpretation.
Solution Approach 2:
The invention uses degenerate base values to create redundant encoding copies. Each degenerate base represents multiple possible base combinations, allowing the system to store the same information in multiple equivalent forms, thereby increasing storage capacity while maintaining decoding simplicity through consensus algorithms.
3Quantity of substance
If DNA storage systems are designed for high capacity, then more data can be stored, but sensitivity to environmental conditions increases
Solution Approach 1:
The patent applies local quality control by creating spatially varying hydrogel regions with different pore sizes, charge densities, and chemical compositions within the chip. This allows different areas to be optimized for specific functions (e.g., high-capacity storage vs. environmentally stable reference regions), enabling high overall capacity while maintaining reliability through localized stability.
Data Source
AI summary
The present specification discloses a DNA encoding and decoding method capable of converting and storing data more efficiently, wherein the DNA encoding method according to the present specification may convert binary data into sequence information using basic base values and degenerate base values, the degenerate base value may be a combination of at least two basic base values among four basic bases and the DNA decoding method according to the present specification may divide the basic base value and the degenerate base value into binary data according to base types for the same position in a plurality of DNA strands.