DNA Random Access via Parallel PCR and Copy Normalization
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing DNA data storage systems face inefficiencies and inconsistencies in random access due to biological processes like PCR and primer pair variations, leading to resource wastage and unreliable data retrieval as the scale increases.
Innovation Solution
Implementing parallel PCR amplification using microdroplets or wells with controlled thermocycling and copy normalization to ensure equal DNA quantities across samples, allowing efficient multiplex sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If selective PCR amplification is used for random access, then specific data can be retrieved from DNA pools, but reagent waste and time consumption increase significantly
Solution Approach 1:
The patent divides the DNA pool into multiple smaller pools, each containing a subset of the total data. This segmentation allows random access requests to be directed to specific smaller pools rather than processing the entire large pool, thereby reducing reagent consumption and processing time while maintaining data retrieval reliability.
2Ease of operation
If PCR amplification is used for random access, then specific DNA sequences can be selectively amplified, but inconsistent behavior and variations lead to unreliable sequence data
Solution Approach 1:
The patent implements a pre-amplification step where DNA is amplified before being divided into multiple pools. This preliminary action ensures sufficient DNA quantity and consistency across all pools before the random access operation, reducing variations and improving sequence data reliability during the selective amplification process.
3Adaptability or versatility
If the entire DNA pool is sequenced for every data request, then random access is possible, but the process becomes unworkable as system scale increases
Solution Approach 1:
The patent segments the DNA pool into multiple smaller pools organized in a hierarchical structure. This allows the system to maintain random access capability by directing queries to specific pools while dramatically improving productivity by avoiding the need to sequence entire large pools for each data request.
4Productivity
If many random-access requests are combined, then processing efficiency may improve, but resource wastage and data loss increase due to PCR variations
Solution Approach 1:
The patent divides random-access requests into batches that are processed on specific smaller DNA pools rather than combining all requests into a single large-scale PCR operation. This segmentation reduces reagent wastage and minimizes the impact of PCR variations while maintaining batch processing efficiency.
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
Enhances the efficiency and accuracy of random-access data retrieval by minimizing variations in DNA quantities, optimizing resource use, and improving sequencing quality.
Implementation Method 1
One technique for performing random access at the molecular level makes use of polymerase chain reaction (PCR) and specific primer pairs to selectively amplify portions of a DNA pool.
Implementation Method 2
The isolated reaction volumes are thermocycled under conditions suitable for PCR.
Data Source
Figure 1
Figure 2
Figure 3
AI summary
This disclosure provides techniques and systems for efficient random access to digital data encoded in oligonucleotides (e.g., DNA). Random access to DNA-encoded data is provided by amplification using polymerase chain reaction (PCR) and primer pairs that selectively amplify only the oligonucleotides encoding a desired set of digital data. Multiple separate random-access requests are prepared for multiplex DNA sequencing by generating copy-normalized amplification products. Copy-normalized amplification products are efficiently created by performing multiple singleplex PCR reactions in parallel and measuring the quantity of oligonucleotides in each reaction. The PCR reactions are performed in parallel through the use of multiple isolated reaction volumes such as water-in-oil microdroplets or individual wells on a plate. Copy normalization may be achieved by performing additional rounds of thermocycling on individual reaction volumes with low quantities of oligonucleotides or by batching samples with similar quantities of oligonucleotides together for multiplex DNA sequencing.