Long-Strand Polynucleotide Encoding via Nanopore Chemical Modification
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing methods for data storage using polynucleotides, such as DNA, are slow, costly, and prone to errors due to the requirement of de novo synthesis and amplification steps, limiting their feasibility for large-scale data storage and retrieval.
Innovation Solution
The method involves moving a polynucleotide strand through a nanoreactor, such as a nanopore, and selectively modifying portions of the strand using controlled reaction conditions to encode data, without altering the overall length of the strand.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If de novo synthesis of DNA sequences is used to encode data, then data can be stored on polynucleotides, but the encoding process becomes very slow and costly
Solution Approach 1:
The patent applies preliminary action by pre-synthesizing long polynucleotide strands without data encoding, then performing selective chemical modifications after the strands are in place. This separates the time-consuming synthesis step from the data encoding step, allowing parallel processing and dramatically increasing encoding throughput while maintaining data storage reliability
Solution Approach 2:
The patent segments the data encoding process into two independent stages: (1) synthesis of polynucleotide strands, and (2) selective chemical modification to encode data. This segmentation allows each stage to be optimized independently and enables parallel processing of multiple strands during the modification stage, resolving the contradiction between reliability and productivity
2Reliability
If de novo synthesis of DNA sequences is used to encode data, then data can be stored on polynucleotides, but the cost increases significantly
Solution Approach 1:
The patent performs preliminary synthesis of polynucleotide strands using cost-effective methods, then applies relatively inexpensive selective chemical modifications for data encoding. This approach avoids the need for expensive de novo synthesis of each encoded sequence, significantly reducing manufacturing costs while maintaining data storage reliability through the use of established polynucleotide synthesis and modification techniques
3Reliability
If amplification of DNA is performed for data retrieval, then data can be read from stored polynucleotides, but errors are introduced and throughput speed is limited
Solution Approach 1:
The patent extracts the need for amplification by designing a system where data is directly readable from the chemically modified polynucleotide strands. The selective chemical modifications create detectable signals that can be read without requiring DNA amplification, thereby eliminating amplification-induced errors and enabling high-throughput data retrieval that matches the high-speed encoding process
4Reliability
If blocks of DNA are synthesized and combined to store large amounts of data, then data capacity increases, but the process becomes more complex and slower
Solution Approach 1:
The patent applies preliminary action by synthesizing long polynucleotide strands in advance with sufficient capacity to store large amounts of data, then using selective chemical modifications to encode information directly onto these pre-positioned strands. This eliminates the need to synthesize and assemble multiple smaller DNA blocks, significantly reducing process complexity and increasing encoding speed while maintaining high data storage capacity
Solution Approach 2:
The patent segments the data storage approach into two independent components: (1) pre-synthesized polynucleotide strands that provide storage capacity, and (2) selective chemical modifications that provide data encoding. This segmentation allows the capacity aspect to be addressed by strand length while the encoding aspect is handled by controlled chemical reactions, reducing overall process complexity compared to block assembly methods
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach allows for high-precision, high-rate encoding of data on long polynucleotide strands, enabling efficient and reliable storage and retrieval of large amounts of data with high accuracy.
Implementation Method 1
confining a portion of a polynucleotide strand in a nanoreactor, such that the polynucleotide strand can be moved with respect to the nanoreactor
Implementation Method 2
the movement of the polynucleotide strand with respect to the nanopore is controlled using a polynucleotide-handling enzyme
Data Source
Figure 1
Figure 2A~2C
Figure 3
AI summary
Provided herein are methods of encoding data on a polymer. Also provided are methods of reading data encoded on a polymer. Also provided are systems for encoding data on a polymer; systems for reading data encoded on a polymer; and data encoding / data reading platforms.