DNA Origami Data Files for Reversible Random Access Storage
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current molecular data archival systems face challenges in achieving selective access to specific data sets (random access) and repeated information access without loss in information fidelity, often requiring complex and irreversible processes like PCR-based amplification and physical separation.
Innovation Solution
The use of DNA Origami techniques to package data into indexed DNA oligonucleotides (DNAFiles) that are reversibly folded into 2D/3D structures, allowing for single-step random access through PCR amplification and reconstitution, with unique barcodes for identification and stabilization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If PCR-based amplification is used for random access, then selective access to specific data sets is improved, but the system requires rigorous primer design and hierarchical addressing, and oligonucleotides are irreversibly removed from the pool
Solution Approach 1:
The patent segments the storage pool into discrete, addressable DNA origami nanostructures (DNAFiles), each containing specific data. This segmentation enables selective access to individual files or groups of files without requiring complex primer design across the entire pool, as each nanostructure can be independently targeted and retrieved.
Solution Approach 2:
The patent introduces DNA origami nanostructures as intermediary carriers that package and organize data-containing oligonucleotides. These nanostructures serve as addressable units that simplify random access operations, allowing selective retrieval without the need for complex hierarchical addressing systems or rigorous primer design, thereby reducing system complexity while maintaining ease of operation.
2Ease of operation
If PCR-based amplification is used for random access, then selective access to specific data sets is improved, but oligonucleotides are irreversibly removed from the pool requiring removal and re-embedding
Solution Approach 1:
The patent enables recovery and reuse of data-containing oligonucleotides by packaging them within DNA origami nanostructures. After selective access and data retrieval, the nanostructures can be reopened and the oligonucleotides recovered and re-embedded into the storage pool, eliminating irreversible removal and loss of substance.
Solution Approach 2:
The DNA origami nanostructures act as reversible intermediaries that temporarily hold data-containing oligonucleotides during access operations. This intermediary approach allows for the recovery and return of oligonucleotides to the storage pool after data retrieval, preventing permanent loss and enabling repeated access cycles.
3Ease of operation
If physical separation through magnetic beads or fluorescent sorting is used, then selective access is achieved, but the process introduces additional complexity and steps
Solution Approach 1:
The patent extracts the addressing and selection functionality directly into the DNA origami nanostructure design itself, through incorporated barcodes or address sequences. This eliminates the need for external physical separation devices like magnetic beads or fluorescent sorting systems, reducing device complexity while maintaining selective access capability.
Solution Approach 2:
The DNA origami nanostructures serve as self-contained intermediaries that integrate both data storage and addressing functions. By embedding address information directly in the nanostructure sequence, the system eliminates the need for complex external separation apparatus, thereby reducing device complexity while preserving random access capability.
4Reliability
If data is stored in DNA sequence, then high data density and durability are achieved, but selective access and repeated information retrieval are challenging
Solution Approach 1:
The patent segments the high-density DNA storage into discrete DNA origami nanostructures, each representing an addressable data file. This segmentation maintains the high data density and durability of DNA storage while enabling selective access to individual nanostructures, thereby improving ease of operation without sacrificing reliability.
Solution Approach 2:
The DNA origami nanostructures serve as intermediary organizational units that preserve the high data density and durability benefits of DNA storage while introducing addressable structures for selective access. These nanostructures act as mediators between the raw DNA data and the access mechanisms, enabling repeated information retrieval without compromising the underlying DNA storage reliability.
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
Enables straightforward, high-fidelity, and efficient retrieval of data with minimal loss, providing stable and organized data storage with enhanced accessibility and flexibility.
Implementation Method 1
a plurality of single stranded DNA staple oligonucleotides that bind through complementary base pairing with two non-contiguous segments of the DNA scaffold, wherein said staple oligonucleotides cause the DNA scaffold to reversibly fold into a two or three dimensional shape
Implementation Method 2
polymerase chain reaction (PCR) based amplification to selectively enrich a sub-pool over the background by added address-specific primers
Implementation Method 3
physical separation of the desired sub-pool through the use of magnetic beads or fluorescent based sorting (FACS)
Implementation Method 4
physical separation of the desired sub-pool through the use of magnetic beads or fluorescent based sorting (FACS)
Data Source
AI summary
The present disclosure is directed to compositions and methods that use the principles of DNA origami to package and archive data stored in multiple indexed DNA oligonucleotides. These structures allow for selective physical data access and retrieval from a molecular pool of DNA origami (DNAO) nanostructures comprising the data bearing oligonucleotides.