公开(公告)号：US20240158870A1

公开(公告)日：2024-05-16

申请号：US18509884

申请日：2023-11-15

Applicant: New England Biolabs, Inc.

Inventor： Chaithanya Ponnaluri ,  Hang-Gyeong Chin ,  Pierre O. Esteve ,  Sriharsa Pradhan

IPC: C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6841 ,  C12Q1/6869

CPC classification number: C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q2521/301 ,  C12Q2521/331 ,  C12Q2525/117 ,  C12Q2527/156 ,  C12Q2531/119 ,  C12Q2535/122 ,  C12Q2543/10 ,  C12Q2563/131 ,  C12Q2565/133 ,  C12Q2600/154

Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.

公开(公告)号：US11492667B2

公开(公告)日：2022-11-08

申请号：US17342216

申请日：2021-06-08

Applicant: New England Biolabs, Inc.

Inventor： Sriharsa Pradhan ,  Hang Gyeong Chin ,  George R. Feehery ,  Shuang-Yong Xu ,  Vishnu Udayakumaran Nair Sunitha Kumary ,  Julie Beaulieu ,  Pierre O. Esteve

IPC: C12Q1/6869 ,  C07K14/31 ,  C12N9/22

Abstract: Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.

公开(公告)号：US11198910B2

公开(公告)日：2021-12-14

申请号：US16327698

申请日：2017-08-31

Applicant: New England Biolabs, Inc.

Inventor： Chaithanya Ponnaluri ,  Hang-Gyeong Chin ,  Pierre O. Esteve ,  Sriharsa Pradhan

IPC: C12Q1/68 ,  C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q1/6827

Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.

公开(公告)号：US11840741B2

公开(公告)日：2023-12-12

申请号：US17454082

申请日：2021-11-09

Applicant: New England Biolabs, Inc.

Inventor： Chaithanya Ponnaluri ,  Hang-Gyeong Chin ,  Pierre O. Esteve ,  Sriharsa Pradhan

IPC: C12Q1/68 ,  C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q1/6827

CPC classification number: C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q2521/301 ,  C12Q2521/331 ,  C12Q2525/117 ,  C12Q2527/156 ,  C12Q2531/119 ,  C12Q2535/122 ,  C12Q2543/10 ,  C12Q2563/131 ,  C12Q2565/133 ,  C12Q2600/154 ,  C12Q1/6806 ,  C12Q2521/301 ,  C12Q2521/331 ,  C12Q2525/117 ,  C12Q2527/156 ,  C12Q2531/119 ,  C12Q2535/122 ,  C12Q2543/10 ,  C12Q2563/131 ,  C12Q2565/133 ,  C12Q1/6841 ,  C12Q2521/301 ,  C12Q2521/331 ,  C12Q2525/117 ,  C12Q2527/156 ,  C12Q2531/119 ,  C12Q2535/122 ,  C12Q2543/10 ,  C12Q2563/131 ,  C12Q2565/133 ,  C12Q1/6869 ,  C12Q2521/301 ,  C12Q2521/331 ,  C12Q2525/117 ,  C12Q2527/156 ,  C12Q2531/119 ,  C12Q2535/122 ,  C12Q2543/10 ,  C12Q2563/131 ,  C12Q2565/133

Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.

公开(公告)号：US20220056537A1

公开(公告)日：2022-02-24

申请号：US17454082

申请日：2021-11-09

Applicant: New England Biolabs, Inc.

Inventor： Chaithanya Ponnaluri ,  Hang-Gyeong Chin ,  Pierre O. Esteve ,  Sriharsa Pradhan

IPC: C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q1/6827

Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.

公开(公告)号：US20190211404A1

公开(公告)日：2019-07-11

申请号：US16327698

申请日：2017-08-31

Applicant: New England Biolabs, Inc.

Inventor： Chaithanya Ponnaluri ,  Hang-Gyeong Chin ,  Pierre O. Esteve ,  Sriharsa Pradhan

IPC: C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q1/6827

CPC classification number: C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6841 ,  C12Q1/6869 ,  C12Q2521/301 ,  C12Q2521/331 ,  C12Q2525/117 ,  C12Q2527/156 ,  C12Q2531/119 ,  C12Q2535/122 ,  C12Q2543/10 ,  C12Q2563/131 ,  C12Q2565/133 ,  C12Q2600/154

Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.

公开(公告)号：US20230089237A1

公开(公告)日：2023-03-23

申请号：US17933943

申请日：2022-09-21

Applicant: New England Biolabs, Inc.

Inventor： Sriharsa Pradhan ,  Hang Gyeong Chin ,  George R. Feehery ,  Shuang-Yong Xu ,  Vishnu Udayakumaran Nair Sunitha Kumary ,  Julie Beaulieu ,  Pierre O. Esteve

IPC: C12Q1/6869 ,  C07K14/31 ,  C12N9/22

Abstract: Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.

公开(公告)号：US20210388434A1

公开(公告)日：2021-12-16

申请号：US17342216

申请日：2021-06-08

Applicant: New England Biolabs, Inc.

Inventor： Sriharsa Pradhan ,  Hang Gyeong Chin ,  George R. Feehery ,  Shuang-Yong Xu ,  Vishnu Udayakumaran Nair Sunitha Kumary ,  Julie Beaulieu ,  Pierre O. Esteve

IPC: C12Q1/6869 ,  C12N9/22 ,  C07K14/31

Abstract: Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.

公开(公告)号：US09963705B2

公开(公告)日：2018-05-08

申请号：US15034092

申请日：2014-11-10

Applicant: New England Biolabs, Inc.

Inventor： Sriharsa Pradhan ,  Pierre O. Esteve ,  Guoqiang Zhang

IPC: C12N15/113 ,  A61K31/7105

CPC classification number: C12N15/1137 ,  A61K31/7105 ,  C12N2310/11 ,  C12N2310/141 ,  C12N2310/151 ,  C12N2320/30 ,  C12Y201/01037

Abstract: RNA molecules inhibiting a DNMT and methods and compositions incorporating or generating the RNA molecules are described.

公开(公告)号：US20160272977A1

公开(公告)日：2016-09-22

申请号：US15034092

申请日：2014-11-10

Applicant: NEW ENGLAND BIOLABS INC.

Inventor： Sriharsa Pradhan ,  Pierre O. Esteve ,  Guoqiang Zhang

IPC: C12N15/113 ,  A61K31/7105

CPC classification number: C12N15/1137 ,  A61K31/7105 ,  C12N2310/11 ,  C12N2310/141 ,  C12N2310/151 ,  C12N2320/30 ,  C12Y201/01037

Abstract: RNA molecules inhibiting a DNMT and methods and compositions incorporating or generating the RNA molecules are described.

Abstract translation: 描述了抑制DNMT的RNA分子以及掺入或产生RNA分子的方法和组合物。