公开(公告)号：US20240191225A1

公开(公告)日：2024-06-13

申请号：US18465687

申请日：2023-09-12

Applicant: Element Biosciences, Inc.

Inventor： Junhua ZHAO ,  Xiaodong QI ,  Kelly BLEASE ,  Hua YU ,  Matthew KELLINGER

IPC: C12N15/10

CPC classification number: C12N15/1093

Abstract: The present disclosure provides compositions comprising nucleic acid double-stranded splint adaptors, including kits, and methods that employ the double-stranded splint adaptors. The double-stranded splint adaptors (200) can be used in a one-pot, multi-enzyme reaction to introduce one or more new adaptor sequences into a library molecule. The double-stranded splint adaptor (200) comprises a first splint strand (long splint strand (300)) and a second splint strand (short splint strand (400)), where the first and second splint strands are hybridized together to form the double-stranded splint adaptor (200) having a double-stranded region and two flanking single-stranded regions. The second splint strand (400) carries the new adaptor sequence(s) to be introduced, such as for example a universal binding sequence, an index sequence and/or a random sequence.

公开(公告)号：US20240084380A1

公开(公告)日：2024-03-14

申请号：US18450302

申请日：2023-08-15

Applicant: Element Biosciences, Inc.

Inventor： Sinan ARSLAN ,  Michael KIM ,  Ramreddy TIPANNA ,  Chunhong ZHOU ,  William LIGHT ,  Hua YU ,  Junhua ZHAO ,  Tsung-Li LIU

IPC: C12Q1/6874 ,  C12Q1/6844

CPC classification number: C12Q1/6874 ,  C12Q1/6844 ,  C12Q1/6806

Abstract: The present disclosure provides compositions and related methods, e.g., for preparing immobilized nucleic acid nanostructures using compaction oligonucleotides. In some embodiments, rolling circle amplification reaction can be conducted with compaction oligonucleotides on-support or in-solution to generate concatemer molecules having multiple copies of a polynucleotide unit arranged in tandem. Each polynucleotide unit comprises a sequence-of-interest and at least one universal adaptor sequence that binds one end of a compaction oligonucleotide. The 5′ and 3′ regions of the compaction oligonucleotide can hybridize to the concatemer to pull together distal portions of the concatemer causing compaction of the concatemer to form a nanostructure. Nanostructures having tighter size and shape compared to concatemers generated in the absence of the compaction oligonucleotides. The compact and stable characteristics of the nucleic acid nanostructures improves sequencing accuracy by increasing signal intensity and they retain their shape and size during multiple sequencing cycles.

公开(公告)号：US20230392201A1

公开(公告)日：2023-12-07

申请号：US18330279

申请日：2023-06-06

Applicant: Element Biosciences, Inc.

Inventor： James A. STAPLETON ,  Timothy WHITEHEAD ,  Michael PREVITE ,  Molly HE ,  Tuval BEN-YEHEZKEL ,  Matthew KELLINGER ,  Kyle METCALFE

IPC: C12Q1/6869 ,  C12Q1/686 ,  C12N15/10 ,  C12Q1/6813

CPC classification number: C12Q1/6869 ,  C12Q1/686 ,  C12N15/1065 ,  C12Q1/6813

Abstract: The disclosure relates to methods for obtaining nucleic acid sequence information by constructing a nucleic acid library and reconstructing longer nucleic acid sequences by assembling a series of shorter nucleic acid sequences.

公开(公告)号：US11788075B2

公开(公告)日：2023-10-17

申请号：US18160947

申请日：2023-01-27

Applicant: Element Biosciences, Inc.

Inventor： Jendrik Hentschel ,  Tyler Lopez ,  Michael Klein ,  Virginia Saade ,  Matthew Kellinger ,  Mark Ambroso

IPC: C12N9/12 ,  C12Q1/6869

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

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：US20230296593A1

公开(公告)日：2023-09-21

申请号：US18202247

申请日：2023-05-25

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 ,  C12Q1/6874 ,  G01N33/58

CPC classification number: G01N33/5308 ,  C12Q1/6874 ,  G01N33/582

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：US20230279483A1

公开(公告)日：2023-09-07

申请号：US17725065

申请日：2022-04-20

Applicant: Element Biosciences, Inc.

Inventor： William LIGHT ,  Samantha SNOW ,  Junhua ZHAO

IPC: C12Q1/6869 ,  C12N15/10

CPC classification number: C12Q1/6869 ,  C12N15/1065 ,  C12N15/1068 ,  C12Q1/682

Abstract: The present disclosure provides compositions comprising nucleic acid double-stranded splint adaptors, including kits, and methods that employ the double-stranded splint adaptors. The double-stranded splint adaptors (200) can be used in a one-pot, multi-enzyme reaction to introduce one or more new adaptor sequences into a library molecule. The double-stranded splint adaptor (200) comprises a first splint strand (long splint strand (300)) and a second splint strand (short splint strand (400)), where the first and second splint strands are hybridized together to form the double-stranded splint adaptor (200) having a double-stranded region and two flanking single-stranded regions. The second splint strand (400) carries the new adaptor sequence(s) to be introduced, such as for example a universal binding sequence and/or an index sequence.

公开(公告)号：US20230279382A1

公开(公告)日：2023-09-07

申请号：US17725042

申请日：2022-04-20

Applicant: Element Biosciences, Inc.

Inventor： William LIGHT ,  Ryan KELLEY ,  Junhua ZHAO

IPC: C12N15/10 ,  C12Q1/6874

CPC classification number: C12N15/1065 ,  C12N15/1068 ,  C12Q1/6874 ,  C12Q1/6853

Abstract: The present disclosure provides compositions comprising nucleic acid single-stranded splint strands, including kits, and methods that employ the single-stranded splint strands. The single-stranded splint strands can hybridize to portions of linear library molecules to form circularized library-splint complexes having a nick, where the nick can be ligated to form covalently closed circular molecules which can be subjected to downstream amplification and sequencing workflows.

公开(公告)号：US20230265402A1

公开(公告)日：2023-08-24

申请号：US18160952

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

CPC classification number: C12N9/1252 ,  C12Y207/07007

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：US20220101039A1

公开(公告)日：2022-03-31

申请号：US17547602

申请日：2021-12-10

Applicant: Element Biosciences, Inc.

Inventor： Chunhong ZHOU ,  Semyon KRUGLYAK ,  Francisco GARCIA ,  Minghao GUO ,  Haosen WANG ,  Ryan KELLY

IPC: G06K9/62 ,  G06K9/00 ,  G06T7/30

Abstract: Methods and systems for image analysis are provided, and in particular for identifying a set of base-calling locations in a flow cell for DNA sequencing. These include capturing flow cell images after each sequencing step performed on the flow cell, and identifying candidate cluster centers in at least one of the flow cell images. Intensities are determined for each candidate cluster center in a set of flow cell images. Purities are determined for each candidate cluster center based on the intensities. Each candidate cluster center with a purity greater than the purity of the surrounding candidate cluster centers within a distance threshold is added to a template set of base-calling locations.

公开(公告)号：US20220025457A1

公开(公告)日：2022-01-27

申请号：US17496710

申请日：2021-10-07

Applicant: Element Biosciences, Inc.

Inventor： Steve Xiangling CHEN ,  Minghao GUO ,  Michael PREVITE ,  Chunhong ZHOU ,  Derek FULLER

IPC: C12Q1/6869 ,  G01N21/64 ,  G01N15/14

Abstract: Methods and systems for sequencing a nucleic acid molecule are described that comprise imaging a first surface and an axially-displaced second surface using a compensation-free optical system, the system comprising an objective lens and at least one image sensor, wherein said optical system has a numerical aperture (NA) of less than 0.6 and a field-of-view (FOV) of greater than 1.0 mm2; and) processing the images of the first surface and the axially-displaced second surface to correct for optical aberration such that the images of the first surface and the axially-displaced second surface have substantially the same optical resolution.