公开(公告)号：US20230265401A1

公开(公告)日：2023-08-24

申请号：US18160951

申请日：2023-01-27

Applicant: Element Biosciences, Inc.

Inventor： Jendrik HENTSHCEL ,  Tyler LOPEZ ,  Michael KLEIN ,  Virginia SAADE ,  Matthew KELLINGER ,  Mark AMBROSO

IPC: C12N9/12 ,  C12Q1/6869

CPC classification number: C12N9/1252 ,  C12Y207/07007 ,  C12Q1/6869

Abstract: Provided herein are engineered variants of archaeal polymerases that exhibit exonuclease-minus activity, enhanced thermostability, enhanced incorporation of 3′ modified nucleotides, improved uracil-tolerance and/or reduce sequence-specific errors in polymerase-catalyzed nucleotide binding and extension reactions relative to wild type polymerase enzymes. Also provided are uses of the engineered polymerases for forming complexed polymerases and forming binding complexes, and uses for conducting nucleic acid sequencing reactions.

公开(公告)号：US20220403445A1

公开(公告)日：2022-12-22

申请号：US17521239

申请日：2021-11-08

Applicant: Element Biosciences, Inc.

Inventor： Sinan ARSLAN ,  Junhua ZHAO ,  Molly HE ,  Samantha SNOW ,  William LIGHT ,  Matthew KELLINGER ,  Michael PREVITE ,  Michael KIM ,  Hua YU ,  Yu-Hsien HWANG-FU ,  Marco TJIOE ,  Andrew BODDICKER

IPC: C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6874

Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g., having nucleotide units), the signals emitted by the nucleotides or nucleotide units that participate in the parallel sequencing reactions along the concatemer yields an increased signal intensity for each concatemer.

公开(公告)号：US20220170919A1

公开(公告)日：2022-06-02

申请号：US17675154

申请日：2022-02-18

Applicant: Element Biosciences, Inc.

Inventor： Michael PREVITE ,  Molly HE ,  Junhua ZHAO ,  Hui Zhen MAH ,  Chunhong ZHOU ,  Sinan ARSLAN ,  Matthew KELLINGER ,  Lorenzo BERTI ,  Steve Xiangling CHEN

IPC: G01N33/53 ,  G01N33/58 ,  C12Q1/6874

Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

公开(公告)号：US20210247389A1

公开(公告)日：2021-08-12

申请号：US17245670

申请日：2021-04-30

Applicant: Element Biosciences, Inc.

Inventor： Sinan Arslan ,  Molly HE ,  Matthew KELLINGER ,  Jake LEVIEUX ,  Michael PREVITE ,  Junhua ZHAO ,  Su ZHANG

IPC: G01N33/53 ,  G01N33/58 ,  C12Q1/6874

Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

公开(公告)号：US20210139981A1

公开(公告)日：2021-05-13

申请号：US17156452

申请日：2021-01-22

Applicant: ELEMENT BIOSCIENCES, INC.

Inventor： Sinan ARSLAN ,  Chunhong ZHOU ,  Molly Min HE ,  Matthew KELLINGER ,  Adeline Huizhen MAH ,  Michael PREVITE ,  Lei SUN

IPC: C12Q1/6876 ,  G01N33/543 ,  C12N9/12 ,  G01N21/64

Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

公开(公告)号：US20210072234A1

公开(公告)日：2021-03-11

申请号：US16936121

申请日：2020-07-22

Applicant: Element Biosciences, Inc.

Inventor： Sinan Arslan ,  Molly HE ,  Matthew KELLINGER ,  Jake LEVIEUX ,  Michael PREVITE ,  Junhua ZHAO ,  Su ZHANG

IPC: G01N33/53 ,  C12Q1/6874 ,  G01N33/58

Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

公开(公告)号：US20250146068A1

公开(公告)日：2025-05-08

申请号：US18919127

申请日：2024-10-17

Applicant: Element Biosciences, Inc.

Inventor： Tsung-Li LIU ,  Sinan ARSLAN ,  Michael PREVITE ,  Tuval BEN-YEHEZKEL ,  Connor THOMPSON ,  Matthew KELLINGER ,  Hui Zhen MAH ,  Molly HE ,  Andrew PRICE

IPC: C12Q1/6874 ,  C12N15/10 ,  C12Q1/6804 ,  C12Q1/6841 ,  C12Q1/6844 ,  G01N33/58

Abstract: The present disclosure provides methods for conducting in situ multiplex and multi-omics detection and identification using coded padlocks probes. The methods comprise simultaneous use of RNA-specific padlock probes and polypeptide-specific padlock probes to detect both RNA and polypeptides in a cellular sample. Both types of probes include a barcode that unique identifies the RNA or polypeptide that that padlock probe detects. Both types of probes also include a batch-specific sequencing primer binding site to enable sequencing a desired subset of concatemer template molecules. Use of the batch-specific sequencing primers reduces overcrowding signals and images, to produces optical images that are intense and resolvable. By conducting multiple rounds of sequencing on the same cellular sample using different batch-specific sequencing primers enables multiplex and multi-omics sequencing to reveal numerous target RNAs and their encoded polypeptides.

公开(公告)号：US20240191278A1

公开(公告)日：2024-06-13

申请号：US18510487

申请日：2023-11-15

Applicant: Element Biosciences, Inc.

Inventor： Sinan ARSLAN ,  Junhua ZHAO ,  Molly HE ,  Samantha SNOW ,  William LIGHT ,  Matthew KELLINGER ,  Michael PREVITE ,  Michael KIM ,  Hua YU ,  Yu-Hsien HWANG-FU ,  Marco TJIOE ,  Andrew BODDICKER ,  Mark AMBROSO ,  Tyler LOPEZ ,  Michael KLEIN ,  Virginia SAADE

IPC: C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6853 ,  C12Q1/6874 ,  G01N21/64

CPC classification number: C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6853 ,  C12Q1/6874 ,  G01N21/6428 ,  G01N21/6458 ,  C12Q2600/158

Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g., having nucleotide units), the signals emitted by the nucleotides or nucleotide units that participate in the parallel sequencing reactions along the concatemer yields an increased signal intensity for each concatemer.

公开(公告)号：US20230295692A1

公开(公告)日：2023-09-21

申请号：US18161581

申请日：2023-01-30

Applicant: ELEMENT BIOSCIENCES, INC.

Inventor： Lorenzo BERTI ,  Semyon KRUGLYAK ,  Matthew KELLINGER ,  Molly HE ,  Sinan ARSLAN ,  Junhua ZHAO ,  Michael PREVITE

IPC: C12Q1/6816 ,  C12Q1/6855

CPC classification number: C12Q1/6816 ,  C12Q1/6855

Abstract: Methods and systems for detecting the presence of a target nucleic acid sequence in one or more samples of a plurality of samples are described. The methods may comprise the use of linear barcoded nucleic acid probes that, upon hybridization to a target nucleic acid sequence, may be ligated to circularize the probe molecule, amplified, and sequenced. The use of a probe-specific barcode integrated into the nucleic acid probe molecule, and sample-specific barcodes that may be incorporated into the nucleic acid probe molecule or added during the amplification step, enable large-scale multiplexed assay and sample processing.

公开(公告)号：US20230203564A1

公开(公告)日：2023-06-29

申请号：US18166429

申请日：2023-02-08

Applicant: Element Biosciences, Inc.

Inventor： Sinan ARSLAN ,  Junhua ZHAO ,  Molly HE ,  Samantha SNOW ,  William LIGHT ,  Matthew KELLINGER ,  Michael PREVITE ,  Michael KIM ,  Hua YU ,  Yu-Hsien HWANG-FU ,  Marco TJIOE ,  Andrew BODDICKER ,  Mark AMBROSO ,  Tyler LOPEZ ,  Michael KLEIN ,  Virginia SAADE

IPC: C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6874 ,  G01N21/64 ,  C12Q1/6853

CPC classification number: C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6874 ,  G01N21/6428 ,  G01N21/6458 ,  C12Q1/6853 ,  C12Q2600/158

Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g., having nucleotide units), the signals emitted by the nucleotides or nucleotide units that participate in the parallel sequencing reactions along the concatemer yields an increased signal intensity for each concatemer.