DNA Random Access Storage via ID Sequence Ligation
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Solution Overview
Problem
Current DNA storage systems face inefficiencies in accessing specific data without converting all DNA-encoded information into digital format, leading to challenges in bandwidth and access type, as they rely on sequential access methods rather than random access.
Innovation Solution
The use of ID sequences on DNA strands allows for selective hybridization with staples and sequencing adaptors, enabling DNA ligase to form covalent bonds and create longer strands that can be sequenced, thereby isolating specific DNA strands with desired information from a pool, facilitating random access.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If all DNA-encoded information is converted into digital format for access, then complete data retrieval is achieved, but bandwidth efficiency deteriorates and access time increases
Solution Approach 1:
The patent extracts only the necessary DNA strands containing specific information from the entire DNA storage pool by using complementary oligonucleotide probes that hybridize to unique identifier sequences on target DNA strands. This extraction approach avoids converting all DNA-encoded information to digital format, thereby improving access efficiency while maintaining reliable retrieval of the required data.
2Reliability
If sequential access methods are used to read DNA strands, then all strands can be processed, but access time increases and bandwidth is reduced
Solution Approach 1:
The patent segments the DNA storage pool into individually addressable strands, each with a unique identifier sequence. By using complementary oligonucleotide probes that specifically hybridize to these unique identifiers, the system can selectively access and process only the required DNA strands in parallel, rather than sequentially processing all strands. This segmentation enables random access and significantly reduces access time while maintaining complete data access capability.
3Ease of operation
If selective hybridization with staples and sequencing adaptors is implemented, then random access to specific DNA strands is enabled, but system complexity increases
Solution Approach 1:
The patent introduces complementary oligonucleotide probes as intermediary molecules that mediate between the unique identifier sequences on DNA strands and the sequencing adaptors. These probes hybridize to the unique identifiers and facilitate the attachment of sequencing adaptors through this intermediate step, enabling selective random access to specific DNA strands. While this adds a molecular intermediary step, it maintains operational simplicity by using natural hybridization processes rather than complex mechanical or electronic sorting systems.
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 enhances the efficiency of DNA sequencing by allowing arbitrary and random access to specific data within a DNA pool, improving bandwidth and access methods by selectively amplifying and sequencing only relevant DNA strands.
Implementation Method 1
A relatively short DNA strand referred to herein as a 'staple' includes one portion that hybridizes to a particular ID sequence and another portion that hybridizes to part of a sequencing adaptor
Implementation Method 2
DNA ligase forms a covalent bond between the DNA strands and the sequencing adaptors
Data Source
AI summary
Techniques for random access of particular DNA strands from a mixture of DNA strands are described. DNA strands that encode pieces of the same digital file are labeled with the same identification sequence. The identification sequence is used to selectively separate DNA strands that contain portions of the same digital file from other DNA strands. A DNA staple positions DNA strands with the identification sequence adjacent to sequencing adaptors. DNA ligase joins the molecules to create a longer molecule with the region encoding the digital file flanked by sequencing adaptors. DNA strands that include sequencing adaptors are sequenced and the sequence data is available for further analysis. DNA strands without the identification sequence are not joined to sequencing adaptors, and thus, are not sequenced. As a result, the sequencing data produced by the DNA sequencer comes from those DNA strands that included the identification sequence.