Sequence-Controlled Polymer Memory Objects for DNA Data Retrieval
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Solution Overview
Problem
Current DNA-based memory systems face limitations in handling large data sets, including inefficiencies in editing, deleting information, and performing computations due to non-specific interactions, off-target amplification, and the need for extensive PCR reactions, which are costly and time-consuming, and lack the ability to perform Boolean logic operations and spatially isolate specific data molecules.
Innovation Solution
The development of sequence-controlled polymer memory objects (SMOs) that encode information using nucleic acids or peptides, allowing for controlled segregation and retrieval of data through barcoded nanoparticles, enabling Boolean logic computations, spatial association, and parallel processing by encapsulating bio-polymers in nanoparticles with programmable tags for multiplexed addressing and purification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If PCR methods are used for random access of DNA-encoded memory, then data retrieval is enabled, but off-target amplification occurs and manufacturing precision deteriorates
Solution Approach 1:
The patent segments the DNA memory into discrete nanoparticle containers, each containing a specific DNA molecule. This physical segmentation allows selective access to individual molecules without affecting others, eliminating off-target amplification while maintaining ease of data retrieval through targeted nanoparticle selection.
Solution Approach 2:
The patent introduces nanoparticle containers as intermediary structures that physically separate and isolate specific DNA molecules. These nanoparticles serve as mediators between the DNA encoding and the retrieval process, enabling precise targeting without the non-specific interactions that occur in bulk PCR methods.
2Ease of operation
If bulk PCR reactions are used to access DNA memory, then data can be retrieved, but the process becomes costly and time-consuming
Solution Approach 1:
By dividing the DNA memory into separate nanoparticle containers, the patent enables parallel processing of multiple data molecules simultaneously. This segmentation allows the retrieval system to access multiple nanoparticles in parallel, dramatically reducing total retrieval time compared to sequential bulk PCR reactions.
Solution Approach 2:
The patent transitions from a single-bulk reaction dimension to a multi-dimensional parallel processing architecture where multiple nanoparticle containers can be processed simultaneously across different spatial locations, enabling concurrent data retrieval operations that reduce overall time loss.
3Quantity of substance
If simple DNA storage is used, then storage density is achieved, but the ability to perform computations and Boolean logic operations is lost
Solution Approach 1:
The nanoparticle container system provides multi-functionality: it serves as both the physical storage medium for high-density DNA encoding and as the computational addressing mechanism. The same nanoparticles that store data also provide the selective binding interfaces needed for Boolean logic operations and data manipulation, eliminating the need for separate computational components.
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 storage, retrieval, and manipulation of large data sets with reduced energy consumption and environmental impact, enabling dynamic addressing, reconfigurability, and long-term stability of memory blocks, overcoming the limitations of existing DNA storage techniques.
Implementation Method 1
The information encoded within the sequence-controlled polymer of each memory block corresponds to one or more labels or 'barcodes' encoded within address tags present at the surface of the block
Implementation Method 2
Random access of direct encoded memory has only been demonstrated by PCR methods using barcoding strategies and spatial segregation of information pools into distinct wells
Implementation Method 3
These coding strategies have been simple direct to base (Church, G M et al., Science. 337, 1628 (2012); Clelland, C T et al., Nature. 399, 533-534 (1999); Wong, P C et al., Communications of the ACM. 46, 95-98 (2003))
Data Source
AI summary
Methods for controlled segregation of blocks of information encoded in the sequence of a biopolymer, such as nucleic acids and polypeptides, with rapid retrieval based on multiply addressing nanostructured data have been developed. In some embodiments, sequence controlled polymer memory objects include data-encoded biopolymers of any length or form encapsulated by natural or synthetic polymers and including one or more address tags. The sequence address labels are used to associate or select memory objects for sequencing read-out, enabling organization and access of distinct memory objects or subsets of memory objects using Boolean logic. In some embodiments, a memory object is a single-stranded nucleic acid scaffold strand encoding bit stream information that is folded into a nucleic acid nanostructure of arbitrary geometry, including one or more sequence address labels. Methods for controlled degradation of biopolymer-encoded blocks of information in the memory objects are also developed.