Apparatus for high density information storage in molecular chains
Inventors
McFarland, Kirsty A. • Magyar, Andrew P. • Frank, Ian Ward • Kotz, Kenneth T. • Markovic, Stacey • Huang, Haiyao • Byrnes, Steven J. • Favalora, Gregg E. • Sprachman, Melissa M. • Dubay, Ryan A. • Vargo, Emma • Cavanagh, Peter • Rosenberger, Erin
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Assignees
Charles Stark Draper Laboratory Inc
Member
DraperDraper is an independent nonprofit engineering innovation company with a legacy spanning over 90 years, dedicated to delivering transformative solutions for national security, prosperity, and global challenges. Renowned for its pioneering work in guidance, navigation, and control (GN&C) systems, Draper partners with government, industry, and academia to engineer advanced technologies in space, defense, biotechnology, and electronic systems. The company leverages multidisciplinary expertise, digital engineering, and a collaborative approach to provide field-ready prototypes, mission-critical systems, and innovative research. Draper’s mission is to ensure the nation's security and prosperity by delivering sustainable, cutting-edge solutions that address the toughest problems of today and tomorrow, while fostering an inclusive and diverse workforce. Draper also invests in the next generation of innovators through robust educational programs, including internships, co-ops, and the Draper Scholars Program, integrating academic research with real-world problem-solving.
Draper is an independent nonprofit engineering innovation company with a legacy spanning over 90 years, dedicated to delivering transformative solutions for national security, prosperity, and global challenges. Renowned for its pioneering work in guidance, navigation, and control (GN&C) systems, Draper partners with government, industry, and academia to engineer advanced technologies in space, defense, biotechnology, and electronic systems. The company leverages multidisciplinary expertise, digital engineering, and a collaborative approach to provide field-ready prototypes, mission-critical systems, and innovative research. Draper’s mission is to ensure the nation's security and prosperity by delivering sustainable, cutting-edge solutions that address the toughest problems of today and tomorrow, while fostering an inclusive and diverse workforce. Draper also invests in the next generation of innovators through robust educational programs, including internships, co-ops, and the Draper Scholars Program, integrating academic research with real-world problem-solving.
Publication Number
US-11995558-B2
Publication Date
2024-05-28
Expiration Date
Abstract
A parallelized chain-synthesizing technique includes capillary tubes, where each tube provides multiple locations or addresses where a specific arbitrary sequence for polymeric chains can be synthesized. An optical addressing system selectively delivers light to the locations to mediate or control reactions in the tubes.
Core Innovation
The invention extends a parallelized chain-synthesizing approach to synthesize polymeric chains in tube(s), for example capillary tubes, rather than wells, and provides hardware and methods for synthesis, storage, retrieval, and sequencing of the chains. The tubes contain volumetric regions or locations along longitudinal and/or circumferential positions where specific arbitrary sequences for polymeric chains, often DNA, can be synthesized from immobilized seed molecules. An optical addressing system or spatial light modulator selectively delivers light to the locations to mediate or control chemical reactions for synthesis, while a microfluidic manifold and fluid control system introduce and cycle the reagents required for synthesis through the tubes.
The invention addresses challenges related to high-density information storage by enabling compact, scalable arrays of chains in tubes for encoding digital data into polymeric chains and supporting random access retrieval through inclusion of DNA indices or different seed molecules. Optical activation or deactivation of the DNA synthesis reaction enables spatially-controlled, multiplexed synthesis of a few to many strands (possibly 10^7 DNA strands) per tube and permits in situ sequencing in the tube or elution for sequencing. [procedural detail omitted for safety]
Claims Coverage
Two independent claims are identified; the following inventive features are extracted from those independent claims.
Manifold system including an input manifold and an output manifold
providing a manifold system including an input manifold and an output manifold
Internal channels in the input manifold and the output manifold
forming internal channels in the input manifold and the output manifold
Parallel tubes coupled to the internal channels
holding several tubes extending parallel to each other between the input manifold and the output manifold and coupled to the internal channels
Immobilized seed molecules in the tubes
immobilizing seed molecules in the tubes
Selective light delivery to locations of the tubes to mediate or control chemical reactions to synthesize polymeric chains to encode digital data
selectively delivering light to different locations of the tubes to mediate or control chemical reactions for synthesis of sequences from the seed molecules to thereby synthesize polymeric chains to encode digital data into the polymeric chains by the selective delivery of the light while the tubes are held between the input manifold and the output manifold
Introducing different reagents by flowing through the tubes via the manifold
introducing different reagents required for synthesis of the polymeric chains by flowing the different reagents through the tubes via the manifold system
Different seed molecules to enable random access
wherein different seed molecules are used to enable random access of the different chains
Immobilizing different types of seed molecules
immobilizing different types of seed molecules in the tubes
Introducing reagents via internal channels of the input manifold and then into the tubes
introducing different reagents required for synthesis of the polymeric chains by flowing the different reagents through internal channels of the input manifold and then into the tubes
Performing multiple readout cycles using different types of seed molecules to enable random access
performing multiple readout cycles using the different types of seed molecules to enable random access of the different chains
The independent claims collectively claim a manifold-based system holding parallel tubes coupled to internal channels, immobilized seed molecules in the tubes, selective optical delivery to tube locations to mediate synthesis of polymeric chains encoding digital data, reagent introduction via the manifold into the tubes, and the use of different or different types of seed molecules to enable random access and multiple readout cycles.
Stated Advantages
Highly dense storage of huge amounts of information at the molecular level.
Compact and scalable arrays of chains synthesized in tubes (capillary tubes) for data storage.
Exceptional longevity of polymeric chains such as DNA when stored properly.
Optical activation enables spatially-controlled, multiplexed synthesis of up to 10^7 DNA strands per tube.
Random access retrieval of individual DNA strands enabled via DNA indices at sequence ends or different seed molecules.
Data stored in this form can be copied and edited.
Documented Applications
Data encoding and storage by synthesizing polymeric chains, often DNA, that encode digital data.
Random access read/write of information to/from DNA in a tube where digital data is encoded through synthesis and decoded through sequencing.
In situ sequencing of polymeric chains in the tube, including sequencing by synthesis with fluorescently labeled nucleotides and detection of fluorescence.
Elution of polymeric chains from tubes into wells or arrays (e.g., microtiter plates) followed by sequencing with commercial sequencers.
Storage of DNA-encoded information in glass capillary tubes and retrieval via robotic handling into storage pods or sequencing instruments.
Targeted PCR amplification and retrieval using forward and reverse primer address sequences for information access.
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