Iterative DNA Editing for Unbounded Binary Data Storage
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Solution Overview
Problem
Current methods for storing binary data within cells are limited by requiring specialized constructs for each bit, restricting maximum storage capacity to only a few bytes and being inefficient in encoding binary data.
Innovation Solution
The method involves using precise gene editing techniques like CRISPR/Cas and TALEN to dynamically record binary data by incrementally editing cellular DNA through homology-directed repair, allowing for the insertion of new DNA sequences that encode binary data, which can be passed to subsequent cellular generations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If specialized orthogonal genetic constructs are used for each bit, then storage precision is improved, but device complexity increases and storage capacity is limited to a few bytes
Solution Approach 1:
The patent applies universality by using a single genetic construct that can store multiple bits of information through different DNA sequence states, rather than requiring separate constructs for each bit. The homology-directed repair mechanism serves multiple functions: it cuts DNA, inserts new sequences, and records binary data, replacing the need for specialized constructs for each storage operation.
Solution Approach 2:
The patent implements nesting by inserting new DNA sequences within existing DNA strands through iterative homology-directed repair. Each new sequence is nested within the parental DNA, creating a hierarchical structure where binary data is encoded through successive insertions at the same locus, allowing unbounded storage capacity within a compact genetic construct.
2Quantity of substance
If iterative DNA editing is used to store unbounded binary data, then storage capacity is improved, but the number of editing operations increases
Solution Approach 1:
The patent applies continuity by designing the homology-directed repair construct to enable continuous iterative editing operations. The same genetic construct remains active across multiple cell divisions and editing cycles, allowing binary data to be accumulated through successive insertions without requiring new constructs for each operation, thereby maintaining productivity while increasing storage capacity.
Solution Approach 2:
The patent implements preliminary action by pre-designing the homology-directed repair construct with all necessary components (guide sequences, homology arms, and insertion sequences) before iterative editing begins. This preliminary preparation allows the system to perform rapid successive editing operations without requiring re-engineering for each bit stored, improving editing efficiency across multiple operations.
3Quantity of substance
If new DNA sequences are inserted repeatedly into existing strands, then information density is improved, but manufacturing complexity increases
Solution Approach 1:
The patent applies self-service by designing the homology-directed repair construct to automatically perform the insertion of new DNA sequences into the parental strand through the cell's own repair machinery. The construct contains all necessary information (homology arms matching the target site, insertion sequences for binary encoding) to guide the cell's natural HDR pathway, eliminating the need for complex external manufacturing intervention for each editing operation.
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 enables the storage of an unbounded amount of binary data within a live cell by repeatedly cutting and inserting new DNA sequences, overcoming the limitations of existing storage methods and allowing for heritable data recording.
Implementation Method 1
DNA in a cell, or in another environment such as a cell free system, may be cut to create a double strand break ("DSB")
Implementation Method 2
New DNA may be inserted into the break using homology directed repair (HDR)
Data Source
AI summary
Information is stored in existing DNA through an iterative process of creating a break in dsDNA and adding new DNA by repairing the break with a homologous repair template. The order and sequence of DNA sequences added to the breaks in the dsDNA can encode binary data. By using a context-dependent encoding scheme, three unique homologous repair templates can encode an unbounded number of bits. When the existing DNA is in a cell, the changes are heritably passed to subsequent generations of the cell. Synthesis of the homologous repair templates may be under the control of a promoter and operator. Intra- or extra-cellular signals may regulate the synthesis of homologous repair templates.