Patents by Inventor Yuan-Jyue Chen

Yuan-Jyue Chen has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20240075655
    Abstract: Recycling information is associated with objects through the use of molecular tags. The recycling information may describe the type of material that the object is made from as well as provide instructions for recycling. The molecular tags may be polynucleotides or other types of molecules including inorganic molecules. The molecular tags may be embedded within the object or attached to the surface of the object. At the end of the object's life, the molecular tags are read and the recycling information is used to appropriately recycle the object.
    Type: Application
    Filed: September 7, 2022
    Publication date: March 7, 2024
    Inventors: Yuan-Jyue CHEN, Bichlien Hoang NGUYEN, Jake Allen SMITH, Karin STRAUSS, Ranveer CHANDRA
  • Patent number: 11873484
    Abstract: Electrically controlled hybridization is used to selectively assemble oligonucleotides on the surface of a microelectrode array. Controlled activation of individual electrodes in the microelectrode array attracts oligonucleotides in solution to specific regions of the array where they hybridize to other oligonucleotides anchored on the array. The oligonucleotides that hybridize may provide locations for subsequent oligonucleotides to hybridize. The active electrodes and the oligonucleotides in solution may be varied during each round of synthesis. This allows for multiple oligonucleotides each with different and specific sequences to be created in parallel. This is accomplished without the use of phosphoramidite chemical synthesis or template-independent DNA polymerase enzymatic synthesis. Oligonucleotides created with these techniques may be used to encode digital data. Fully assembled oligonucleotides may be separated from the array and sequenced, stored, or otherwise processed.
    Type: Grant
    Filed: November 27, 2019
    Date of Patent: January 16, 2024
    Assignee: MICROSOFT TECHNOLOGY LICENSING, LLC
    Inventors: Yuan-Jyue Chen, Bichlien Nguyen, Jake Smith, Karin Strauss
  • Publication number: 20230395198
    Abstract: Techniques for random access of particular DNA strands from a mixture of DNA strands are described. DNA strands that encode pieces of the same digital file are labeled with the same identification sequence. The identification sequence is used to selectively separate DNA strands that contain portions of the same digital file from other DNA strands. A DNA staple positions DNA strands with the identification sequence adjacent to sequencing adaptors. DNA ligase joins the molecules to create a longer molecule with the region encoding the digital file flanked by sequencing adaptors. DNA strands that include sequencing adaptors are sequenced and the sequence data is available for further analysis. DNA strands without the identification sequence are not joined to sequencing adaptors, and thus, are not sequenced. As a result, the sequencing data produced by the DNA sequencer comes from those DNA strands that included the identification sequence.
    Type: Application
    Filed: August 22, 2023
    Publication date: December 7, 2023
    Inventors: Karin STRAUSS, Yuan-Jyue CHEN
  • Publication number: 20230332208
    Abstract: Polynucleotides used for encoding information are synthesized with universal base analogs that participate in pi-stacking interactions but do not form Watson-Crick hydrogen bonds with other bases. The universal base analogs may have pyrrole-based bases such as 5-nitroindole (5NI). Inclusion of the universal base analogs in the polynucleotides prevents polymerase-based amplification such as PCR. However, the non-amplifiable polynucleotides are able to hybridize to complementary strands and the sequences may be read by nanopore sequencing. The polynucleotides may be used as molecular taggants to label items for the prevention of forgery. The ability of polynucleotides collected from an item to hybridize with known sequences can be used to establish authenticity of an item. Alternatively, the polynucleotides may be used to encode digital data in a read-only molecule that cannot be readily copied.
    Type: Application
    Filed: April 15, 2022
    Publication date: October 19, 2023
    Inventors: Bichlien Hoang NGUYEN, Yuan-Jyue CHEN, Jake Allen SMITH
  • Publication number: 20230323443
    Abstract: This disclosure describes a technique for performing random access in a pool of polynucleotides by using one unique primer and one homopolymer primer to selectively amplify some but not all of the polynucleotides in the pool. The polynucleotides are synthesized by a template independent polymerase such as terminal deoxynucleotide transferase (TdT) rather than by phosphoramidite synthesis. Enzymatic synthesis efficiently creates homopolymer sequences through unregulated synthesis. Use of one homopolymer primer instead of two unique primers decreases the complexity, time, and cost of synthesizing the polynucleotides. Use of a unique primer provides a sequence that can be varied to uniquely identify multiple different groups of polynucleotides. This enables random access by polymerase chain reaction (PCR) amplification while still benefiting from the efficiency of homopolymer synthesis. The polynucleotides may include payload regions that use a sequence of nucleotides to encode digital data.
    Type: Application
    Filed: June 1, 2023
    Publication date: October 12, 2023
    Inventors: Yuan-Jyue CHEN, Bichlien NGUYEN
  • Patent number: 11783918
    Abstract: Techniques for random access of particular DNA strands from a mixture of DNA strands are described. DNA strands that encode pieces of the same digital file are labeled with the same identification sequence. The identification sequence is used to selectively separate DNA strands that contain portions of the same digital file from other DNA strands. A DNA staple positions DNA strands with the identification sequence adjacent to sequencing adaptors. DNA ligase joins the molecules to create a longer molecule with the region encoding the digital file flanked by sequencing adaptors. DNA strands that include sequencing adaptors are sequenced and the sequence data is available for further analysis. DNA strands without the identification sequence are not joined to sequencing adaptors, and thus, are not sequenced. As a result, the sequencing data produced by the DNA sequencer comes from those DNA strands that included the identification sequence.
    Type: Grant
    Filed: October 30, 2017
    Date of Patent: October 10, 2023
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Karin Strauss, Yuan-Jyue Chen
  • Publication number: 20230313276
    Abstract: An authentication assay using embedded deoxyribonucleic acid (DNA) taggants includes a substrate and a sample of an authenticity label collected from a product. The substrate has a plurality of assay locations, each of which includes a reporter oligonucleotide bound to the substrate. The reporter oligonucleotide includes a first region with a single-stranded toehold sequence, a second region with a universal sequence, and a third region with a unique sequence, the second and third regions being prehybridized with a complementary strand. The sample includes at least one fluorophore-labeled DNA taggant complementary to the first and second regions of the reporter oligonucleotide. Incubation of the substrate with the sample results in a toehold-mediated DNA strand displacement reaction that exchanges the complementary strand for the fluorophore-labeled DNA taggant. Excitation of the fluorophore molecule attached to the DNA taggant produces a pattern of light emitted at one or more assay locations.
    Type: Application
    Filed: March 29, 2022
    Publication date: October 5, 2023
    Applicant: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue CHEN, Karin STRAUSS, Ranveer CHANDRA
  • Publication number: 20230257789
    Abstract: Sequential assembly of oligonucleotide hairpins is used to create oligonucleotides with specific sequences. Each oligonucleotide hairpin includes a payload region containing one or more nucleotides that are added to the end of an anchor strand. Overhang regions on the oligonucleotide hairpins hybridize to anchor strands attached to a substrate. The hybridized oligonucleotide hairpins are covalently attached to the anchor strands by the activity of ligase. The oligonucleotide hairpins include an enzyme cleavage region which, when cleaved, separates the payload region from the remainder of the oligonucleotide hairpin. The oligonucleotide hairpin is separated from the anchor strand by denaturation and washed away. This process is repeated with additional oligonucleotide hairpins to add additional nucleotides to the ends of the anchor strands. A microelectrode array may be used to control the location of hybridization and create multiple oligonucleotides in parallel.
    Type: Application
    Filed: February 11, 2022
    Publication date: August 17, 2023
    Inventors: Yuan-Jyue CHEN, Bichlien Hoang NGUYEN, Karin STRAUSS
  • Publication number: 20230257788
    Abstract: Sequential assembly of oligonucleotide hairpins is used to create oligonucleotides that encode a specific sequence of arbitrary information. Each oligonucleotide hairpin includes a payload region in the loop region of the hairpin. The payload region encodes arbitrary information such as a binary digit. Overhang regions on the oligonucleotide hairpins hybridize to anchor strands attached to a substrate. The hybridized oligonucleotide hairpins are covalently attached to the anchor strands by ligase. Invading strands are used to open the hairpin structures by also hybridizing to the anchor strand and displacing the double-stranded stem region of the hairpin. This process is repeated with another oligonucleotide hairpin that hybridizes to the end of the previously added oligonucleotide hairpin. A microelectrode array may be used to control the location of hybridization and create multiple different oligonucleotides in parallel.
    Type: Application
    Filed: February 11, 2022
    Publication date: August 17, 2023
    Inventors: Yuan-Jyue CHEN, Bichlien Hoang NGUYEN, Karin STRAUSS
  • Publication number: 20230245720
    Abstract: This disclosure describes an efficient method to copy all polynucleotides encoding digital data of digital files in a polynucleotide storage container while maintaining random access capabilities over a collection of files or data items in the container. The disclosure further describes a process whereby random-access and sequencing of the polynucleotides are combined in a single step.
    Type: Application
    Filed: April 7, 2023
    Publication date: August 3, 2023
    Inventors: Karin STRAUSS, Yuan-Jyue CHEN
  • Patent number: 11702689
    Abstract: This disclosure describes a technique for performing random access in a pool of polynucleotides by using one unique primer and one homopolymer primer to selectively amplify some but not all of the polynucleotides in the pool. The polynucleotides are synthesized by a template independent polymerase such as terminal deoxynucleotide transferase (TdT) rather than by phosphoramidite synthesis. Enzymatic synthesis efficiently creates homopolymer sequences through unregulated synthesis. Use of one homopolymer primer instead of two unique primers decreases the complexity, time, and cost of synthesizing the polynucleotides. Use of a unique primer provides a sequence that can be varied to uniquely identify multiple different groups of polynucleotides. This enables random access by polymerase chain reaction (PCR) amplification while still benefitting from the efficiency of homopolymer synthesis. The polynucleotides may include payload regions that use a sequence of nucleotides to encode digital data.
    Type: Grant
    Filed: April 24, 2020
    Date of Patent: July 18, 2023
    Assignee: MICROSOFT TECHNOLOGY LICENSING, LLC
    Inventors: Yuan-Jyue Chen, Bichlien Nguyen
  • Publication number: 20230167485
    Abstract: A multiplex assay for nucleic acid detection includes a substrate, a sample, and a fluorophore-labeled oligonucleotide. The substrate has a plurality of physically separated assay locations, each of which includes a nucleotide-targeting enzyme configured to cleave nucleic acids, a guide ribonucleic acid (gRNA), and a quencher-labeled oligonucleotide. A portion of the sample is distributed to each assay location. The gRNA recognizes target nucleic acid in the sample, thereby activating the nucleotide-targeting enzyme to cleave nucleic acids, including the quencher-labeled oligonucleotide. The fluorophore-labeled oligonucleotide is subsequently added to each assay location, which facilitates identification of a presence of the target nucleic acid in the sample via detection of unquenched light emitted by the fluorophore in one or more of the plurality of assay locations.
    Type: Application
    Filed: November 29, 2021
    Publication date: June 1, 2023
    Applicant: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue CHEN, Karin STRAUSS, Bichlien H. NGUYEN
  • Patent number: 11651836
    Abstract: This disclosure describes an efficient method to copy all polynucleotides encoding digital data of digital files in a polynucleotide storage container while maintaining random access capabilities over a collection of files or data items in the container. The disclosure further describes a process whereby random-access and sequencing of the polynucleotides are combined in a single step.
    Type: Grant
    Filed: June 29, 2018
    Date of Patent: May 16, 2023
    Assignee: MICROSOFT TECHNOLOGY LICENSING, LLC
    Inventors: Karin Strauss, Yuan-Jyue Chen
  • Publication number: 20230125457
    Abstract: Synthetic molecular tags are placed on an item at various points in a supply chain to create a molecular record of movement through the supply chain. Associations between each unique synthetic molecular tag and individual locations in the supply chain are stored in an electronic record which may be maintained in the cloud. The synthetic molecular tags are collected from the item and sequenced to determine movement of the item through the supply chain by reference to the electronic record. The synthetic molecular tags can be used for identifying recalled items based on locations in the supply chain associated with a recall. The synthetic molecular tags may be polynucleotides such as deoxyribose nucleic acid (DNA). The item may be any type of item including food.
    Type: Application
    Filed: October 26, 2021
    Publication date: April 27, 2023
    Inventors: Yuan-Jyue CHEN, Karin STRAUSS, Bichlien Hoang NGUYEN, Jonathan Bernard LESTER, Hari Krishnan SRINIVASAN, Upendra SINGH, Peeyush KUMAR, Ranveer CHANDRA, Anirudh BADAM, Michael McNab BASSANI
  • Publication number: 20230101409
    Abstract: Large numbers of polynucleotides with random sequences are used collectively as a molecular anti-counterfeiting tag. The polynucleotides are sequenced, placed on an item, and the sequences stored in an electronic record. Authenticity is determined by collecting the polynucleotides from a labeled item, sequencing those polynucleotides, and comparing the sequence to that stored in the electronic record. The number of polynucleotides used as the tag may be adjusted by aliquoting the original batch of randomly synthesized polynucleotides. Complexity of the polynucleotide tags may be increased by assembling individual polynucleotides from multiple dilutions to create longer assembled polynucleotides. Even if the sequences of the polynucleotides are known, the complexity of the tag can make the forgery of the tag itself technically difficult and prohibitively expensive.
    Type: Application
    Filed: September 30, 2021
    Publication date: March 30, 2023
    Inventors: Yuan-Jyue CHEN, Bichlien Hoang NGUYEN, Jake Allen SMITH, Karin STRAUSS
  • Publication number: 20230101083
    Abstract: Multiple polynucleotides with random sequences are collectively used as a molecular anti-counterfeiting tag. The polynucleotides are placed on an item as a molecular identifier of authenticity. Each position within the random sequences is synthesized using a predetermined ratio of nucleoside bases. With this technique the sequence of each polynucleotide is random but the ratio of nucleoside bases over the collection of synthetic polynucleotides is not. Verification of authenticity is achieved by sequencing a portion of the polynucleotides collected from the item and calculating the ratio of nucleoside bases at each position. If these ratios are the same or similar to the ratios used for synthesizing the polynucleotides, then the item is identified as authentic. The ratios of nucleoside bases and a description of the item may be stored in an electronic record that is used for validating authenticity of the item.
    Type: Application
    Filed: September 30, 2021
    Publication date: March 30, 2023
    Inventors: Yuan-Jyue CHEN, Karin STRAUSS
  • Publication number: 20220389483
    Abstract: Electrode controlled hybridization is used to change local pH and selectively assemble oligonucleotide complexes on the surface of a microelectrode array. The oligonucleotide complexes have sticky ends that provide locations for subsequent oligonucleotide complexes to hybridize. The order in which specific oligonucleotide complexes are joined together encodes information. Controlled activation of individual electrodes in the microelectrode array creates negative voltages that reduces a buffer solution and raises the pH in proximity to the electrodes. At higher pH levels double-stranded oligonucleotides de-hybridize. Nicks between oligonucleotide complexes and oligonucleotides anchored to the microelectrode array are closed creating covalent attachments. De-hybridized single-stranded oligonucleotides are removed leaving only the oligonucleotides connected to microelectrode array.
    Type: Application
    Filed: June 3, 2021
    Publication date: December 8, 2022
    Inventors: Yuan-Jyue CHEN, Bichlien Hoang NGUYEN, Karin STRAUSS, Jake Allen SMITH
  • Publication number: 20220347645
    Abstract: A system includes a synthesizer unit having a fluid input to receive fluids and a communication input to receive commands to synthesize data-encoded DNA sequences and cleave the DNA. A first flexible chemistry reaction chamber module may be fluidically coupled to the synthesizer unit to receive the data-encoded DNA sequences and amplify the sequences. A deposition unit may be fluidically coupled to the first flexible chemistry reaction chamber module to receive the amplified DNA sequences and encapsulate the amplified DNA sequences into one or more wells in a storage plate for storage and retrieval to and from a plate storage unit. Retrieved DNA may be processed and read by further units.
    Type: Application
    Filed: July 12, 2022
    Publication date: November 3, 2022
    Inventors: Bichlien H. NGUYEN, Douglas P. KELLEY, Karin STRAUSS, Robert CARLSON, Hsing-Yeh PARKER, John MULLIGAN, Luis H. CEZE, Yuan-Jyue CHEN, Douglas CARMEAN
  • Patent number: 11439970
    Abstract: A system includes a synthesizer unit having a fluid input to receive fluids and a communication input to receive commands to synthesize data-encoded DNA sequences and cleave the DNA. A first flexible chemistry reaction chamber module may be fluidically coupled to the synthesizer unit to receive the data-encoded DNA sequences and amplify the sequences. A deposition unit may be fluidically coupled to the first flexible chemistry reaction chamber module to receive the amplified DNA sequences and encapsulate the amplified DNA sequences into one or more wells in a storage plate for storage and retrieval to and from a plate storage unit. Retrieved DNA may be processed and read by further units.
    Type: Grant
    Filed: May 22, 2018
    Date of Patent: September 13, 2022
    Assignee: MICROSOFT TECHNOLOGY LICENSING, LLC
    Inventors: Bichlien H Nguyen, Douglas P Kelley, Karin Strauss, Robert Carlson, Hsing-Yeh Parker, John Mulligan, Luis H Ceze, Yuan-Jyue Chen, Douglas Carmean
  • Publication number: 20220282243
    Abstract: This disclosure provides techniques and systems for efficient random access to digital data encoded in oligonucleotides (e.g., DNA). Random access to DNA-encoded data is provided by amplification using polymerase chain reaction (PCR) and primer pairs that selectively amplify only the oligonucleotides encoding a desired set of digital data. Multiple separate random-access requests are prepared for multiplex DNA sequencing by generating copy-normalized amplification products. Copy-normalized amplification products are efficiently created by performing multiple singleplex PCR reactions in parallel and measuring the quantity of oligonucleotides in each reaction. The PCR reactions are performed in parallel through the use of multiple isolated reaction volumes such as water-in-oil microdroplets or individual wells on a plate.
    Type: Application
    Filed: May 20, 2022
    Publication date: September 8, 2022
    Inventors: Yuan-Jyue CHEN, Bichlien NGUYEN, Karin STRAUSS