DNA Storage Flow Cell with Fluorescent Read Mechanism
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Solution Overview
Problem
Current data storage technologies face limitations in read-write speed, data retention, power usage, and data density, particularly in DNA storage methods where existing DNA reading techniques are inefficient and prone to errors.
Innovation Solution
A system and method for non-volatile DNA storage that includes a processor, a flow cell with multiple wells for polynucleotide storage, a fluidics device for reagent delivery, and a sequencing device for analyzing polynucleotides, enabling simultaneous read-write capabilities and error correction through encoding schemes and indexing information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional DNA reading techniques (sequencing-by-synthesis) are used, then data can be read from DNA storage, but the read speed is slow and error-prone
Solution Approach 1:
The patent replaces the mechanical/chemical sequencing-by-synthesis process with a fluorescent detection system that uses light emission from nucleotides to directly read DNA sequences. This substitution of the reading mechanism enables parallel detection of multiple nucleotides simultaneously, dramatically increasing read speed while maintaining high accuracy through fluorescent signal detection.
Solution Approach 2:
The patent divides the DNA storage system into separate functional regions: write locations for data encoding and read locations for data retrieval. This segmentation allows simultaneous read and write operations to occur in different spatial zones, improving overall system productivity without interfering with each other's accuracy.
2Quantity of substance
If DNA storage is implemented, then data density is high and data retention is long, but read-write speed is slow
Solution Approach 1:
The patent transitions from linear sequential reading to two-dimensional array-based parallel reading by organizing nucleotides in a grid structure with row and column addresses. This dimensional change enables simultaneous detection of multiple data points across the array, dramatically increasing read-write speed while preserving the high data density of DNA storage.
Solution Approach 2:
The patent segments the DNA storage medium into multiple independently addressable wells or locations within the array, allowing parallel access to different data regions. This segmentation enables simultaneous read-write operations across multiple locations, resolving the speed bottleneck while maintaining overall system density.
3Productivity
If simultaneous read-write capabilities are added to DNA storage, then productivity improves, but device complexity increases
Solution Approach 1:
The patent designs the DNA storage array to serve multiple functions: the same physical structure supports both writing operations (through addressable well access) and reading operations (through fluorescent detection). This multi-functionality enables simultaneous read-write capabilities without requiring entirely separate systems, thereby limiting the increase in device complexity.
Solution Approach 2:
The patent introduces an addressable well array structure as an intermediary between the DNA storage medium and the read-write mechanisms. This intermediary provides organized access points that simplify control of simultaneous operations, reducing the complexity burden that would otherwise arise from direct manipulation of dense DNA arrays.
4Reliability
If error correction through encoding schemes is implemented, then reliability improves, but device complexity increases
Solution Approach 1:
The patent applies error correction encoding schemes during the data writing process, before storage occurs. By pre-encoding data with redundancy and error-detection capabilities at the time of writing, the system ensures reliable retrieval without requiring complex real-time correction mechanisms during reading, thereby limiting the increase in device complexity.
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
The system provides faster read-write speeds, longer data retention, reduced power usage, and higher data density by enabling efficient DNA sequencing and error correction, enhancing the reliability and efficiency of DNA storage.
Implementation Method 1
detect fluorescence of light emitted from a label associated with a nucleotide in each well of the plurality of wells
Data Source
AI summary
A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.