DNA Origami Nanostructures for Selective Molecular Data Retrieval
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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, with methods like PCR-based amplification and physical separation introducing complexity and irreversible data loss.
Innovation Solution
The use of DNA Origami techniques to package data encoding DNA strands into indexed DNA origami nanostructures (DNAFiles) allows for a single-step method of random access, enabling high storage density and stability, with PCR retrieval that preserves the data organization and material.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If PCR-based amplification is used for random access, then data retrieval is enabled, but primer design complexity increases and data is irreversibly removed from the pool
Solution Approach 1:
The patent introduces address oligonucleotides as intermediary components that bind to specific data oligonucleotides through complementary base pairing. These address oligonucleotides serve as mediators between the retrieval system and the stored data, enabling selective access without requiring complex primer designs. The address oligonucleotides can be easily synthesized and paired with magnetic beads for simple separation and retrieval operations.
2Ease of operation
If physical separation through magnetic beads or fluorescent sorting is used, then selective data access is achieved, but system complexity increases
Solution Approach 1:
The patent combines multiple functions into a single integrated system. Address oligonucleotides are designed to simultaneously provide specificity for data selection and compatibility with simple magnetic bead separation. This merging of selection and separation functions into a unified approach using nucleic acid hybridization eliminates the need for complex fluorescent sorting systems while maintaining selective access capabilities.
3Quantity of substance
If data is stored in DNA sequences, then high storage density is achieved, but repeated access causes loss in information fidelity
Solution Approach 1:
The patent employs a copying mechanism where address oligonucleotides bind to data oligonucleotides to create temporary complexes for retrieval. The original data oligonucleotides remain intact in the storage pool after retrieval, allowing repeated access without degradation. The bound and unbound oligonucleotides can be separated and the data oligonucleotides returned to the pool, preserving information fidelity across multiple access cycles.
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 accelerates data access time and increases storage stability by providing a straightforward method for random access and retrieval of data without irreversible loss, using DNAFiles that are easily addressable and physically separable.
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)
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.