公开(公告)号：US20230392144A1

公开(公告)日：2023-12-07

申请号：US18328650

申请日：2023-06-02

Applicant: Element Biosciences, Inc.

Inventor： Andrew PRICE ,  Junhua ZHAO ,  Semyon KRUGLYAK ,  Kelly BLEASE ,  Hua YU ,  Andrew ALTOMARE ,  Ryan KELLEY ,  Juan MORENO

IPC: C12N15/10 ,  C12Q1/6834

CPC classification number: C12N15/1093 ,  C12Q1/6834

Abstract: The present disclosure provides compositions comprising reagents employed in a nucleic acid library preparation workflow for removing deaminated bases, and methods for using the reagents. The compositions and methods described herein reduce base call errors, such as C:G to T:A transitions, in nucleic acid sequencing workflows.

公开(公告)号：US20230296592A1

公开(公告)日：2023-09-21

申请号：US18202246

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：US20220403463A1

公开(公告)日：2022-12-22

申请号：US17377279

申请日：2021-07-15

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

IPC: 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：US20210318295A1

公开(公告)日：2021-10-14

申请号：US17358507

申请日：2021-06-25

Applicant: Element Biosciences, Inc.

Inventor： Sinan Arslan ,  Molly Min 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：US20210318294A1

公开(公告)日：2021-10-14

申请号：US17356929

申请日：2021-06-24

Applicant: Element Biosciences, Inc.

Inventor： Michael PREVITE ,  Molly Min 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：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：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.