Homopolymer-Unique Primers for Random Access in Enzymatic Data Storage
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Solution Overview
Problem
Conventional data storage systems struggle to keep pace with the increasing data production rates, and polynucleotides like DNA or RNA offer a high data storage capacity but lack efficient methods for random access, especially as systems scale up.
Innovation Solution
Utilizing a combination of homopolymer and unique primers in PCR to selectively amplify specific polynucleotides, enabling random access by ensuring only desired polynucleotides are amplified and sequenced, thereby reducing the need to sequence the entire pool.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If selective amplification is used to enable random access to specific polynucleotides, then data retrieval efficiency is improved, but the complexity of the amplification process increases due to the need for specific primer design and selective amplification conditions
Solution Approach 1:
The primer is divided into two functional segments: a homopolymer region that provides universal binding capability and a unique sequence region that provides specificity. This segmentation allows the primer to simultaneously achieve selective amplification of target polynucleotides while maintaining a relatively simple amplification process using standard PCR conditions.
Solution Approach 2:
Different regions of the primer have different functional properties: the homopolymer region enables broad binding to complementary sequences, while the unique sequence region provides local specificity for selective amplification. This local differentiation of primer properties enables random access without requiring complex amplification protocols.
2Adaptability or versatility
If homopolymer primers are used for selective amplification, then the ability to perform random access is improved, but the specificity of amplification may be reduced due to the non-specific binding nature of homopolymer sequences
Solution Approach 1:
The primer is segmented into a homopolymer region for universal binding and a unique sequence region for specific recognition. This segmentation resolves the contradiction by allowing the homopolymer portion to provide random access capability while the unique sequence portion ensures amplification specificity, preventing non-specific amplification of non-target polynucleotides.
Solution Approach 2:
The primer functions as a composite structure combining two different sequence types: a homopolymer segment and a unique sequence segment. This composite design integrates the advantages of both homopolymer primers (versatility for random access) and specific primers (amplification precision), thereby resolving the contradiction between adaptability and manufacturing precision.
3Reliability
If the entire pool of polynucleotides is sequenced to retrieve specific data, then data retrieval completeness is ensured, but the time and computational resources required increase significantly
Solution Approach 1:
The method extracts only the specific polynucleotides containing the desired data from the entire pool through selective amplification using the homopolymer primer with unique sequence. By taking out only the relevant polynucleotides for amplification and sequencing, the approach ensures data retrieval completeness while dramatically reducing the time and computational resources needed compared to sequencing the entire pool.
Solution Approach 2:
Selective amplification is performed as a preliminary action before sequencing. The homopolymer primer with unique sequence specifically amplifies only the target polynucleotides containing the desired data, preparing a concentrated sample that ensures retrieval completeness. This preliminary selective amplification step reduces the subsequent sequencing workload and time requirements.
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 efficient retrieval of specific digital data by amplifying and sequencing only the relevant polynucleotides, improving data access efficiency and reducing the computational burden as storage systems grow in size.
Implementation Method 1
Enzymatic synthesis uses an enzyme, a template independent polymerase, rather than chemical reactions to synthesize polynucleotides
Implementation Method 2
polymerase chain reaction (PCR) can be used to amplify the polynucleotides that encode digital data
Implementation Method 3
A pair of primers is used to specify which polynucleotides are amplified. The primers hybridize to only those polynucleotides with complementary primer binding sites
Data Source
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AI summary
This disclosure describes a technique for performing random access in a pool of polynucleotides by using one unique primer and one homopolymer primer to selectively amplify some but not all of the polynucleotides in the pool. The polynucleotides are synthesized by a template independent polymerase such as terminal deoxynucleotide transferase (TdT) rather than by phosphoramidite synthesis. Enzymatic synthesis efficiently creates homopolymer sequences through unregulated synthesis. Use of one homopolymer primer instead of two unique primers decreases the complexity, time, and cost of synthesizing the polynucleotides. Use of a unique primer provides a sequence that can be varied to uniquely identify multiple different groups of polynucleotides. This enables random access by polymerase chain reaction (PCR) amplification while still benefitting from the efficiency of homopolymer synthesis. The polynucleotides may include payload regions that use a sequence of nucleotides to encode digital data.