公开(公告)号：US20240158778A1

公开(公告)日：2024-05-16

申请号：US18280653

申请日：2022-04-01

Applicant: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY ,  THE UNIVERSITY OF CHICAGO

Inventor： Georgi MARINOV ,  William J. GREENLEAF ,  Tong WU ,  Chuan HE

IPC: C12N15/10 ,  C12Q1/686

CPC classification number: C12N15/102 ,  C12Q1/686

Abstract: The disclosure pertains to a method for isolating DNA fragments that contain a binding site for a guide-RNA of an RNA-guided endonuclease. The method comprises contacting the RNA-guided endonuclease with a target double-stranded DNA, thereby producing a single stranded DNA (ss-DNA) at the site to which the guide-RNA binds. The ssDNA is then reacted with kethoxal or an analog thereof modified by a chemoselective group, thereby adding the chemoselective group to any unpaired guanine based within the ssDNA. A first binding member of a specific binding pair is linked to the chemoselective group, for example, via a cycloaddition reaction. The DNA is fragmented and the DNA fragments that contain the binding sites for the guide-RNA are enriched using a support that comprises a second binding member of the specific binding pair. The method can be used to identify binding sites for a guide-RNA thereby identifying off-target binding sites.

公开(公告)号：US20220143198A1

公开(公告)日：2022-05-12

申请号：US17595477

申请日：2020-05-22

Applicant: The University of Chicago

Inventor： Chuan HE ,  Tong WU ,  Pingluan WANG

IPC: A61K47/54 ,  A61K31/121 ,  A61K47/55

Abstract: Embodiments are directed to therapeutic, diagnostic, or functional complexes comprising a kethoxal derivative.

公开(公告)号：US20210310062A1

公开(公告)日：2021-10-07

申请号：US17250365

申请日：2019-07-26

Applicant: The University of Chicago

Inventor： Chuan HE ,  Ji NIE ,  Xiao-Long CUI

IPC: C12Q1/6865

Abstract: The methods, compositions, and kits of the disclosure provide a novel approach for a whole genome, unbiased DNA analysis method that can be performed on limited amounts of DNA. can be used to analyze DNA to determine its modification status. Aspects of the disclosure relate to a method for amplifying bisulfite-treated deoxyribonucleic acid (DNA) molecules comprising: (a) ligating an adaptor to the DNA molecules, wherein the adaptor comprises a RNA polymerase promoter comprising bisulfite-protected cytosines; (b) treating the ligated DNA molecules with bisulfite; (c) hybridizing the bisulfite-treated DNA molecules with a primer; (d) extending the hybridized primer to make double stranded DNA; and (e) in vitro transcribing the double-stranded DNA to make RNA.

公开(公告)号：US20200032330A1

公开(公告)日：2020-01-30

申请号：US16491278

申请日：2018-03-08

Applicant: The University of Chicago

Inventor： Chuan HE ,  Boxuan Simen ZHAO ,  Pradnya NARKHEDE ,  Chang LIU ,  Xiaolong CUI

IPC: C12Q1/6844 ,  C12Q1/6806

Abstract: Methods, compositions and kits are provided to amplify the amount of genomic methylated DNA can by subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

公开(公告)号：US20250092449A1

公开(公告)日：2025-03-20

申请号：US18954222

申请日：2024-11-20

Applicant: THE UNIVERSITY OF CHICAGO

Inventor： Chuan HE ,  Boxuan Simen ZHAO ,  Pradnya NARKHEDE ,  Chang LIU ,  Xiaolong CUI

IPC: C12Q1/6844 ,  C12Q1/6806

Abstract: Methods, compositions and kits are provided to amplify an amount of genomic methylated DNA that can be subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

公开(公告)号：US20210214773A1

公开(公告)日：2021-07-15

申请号：US17250023

申请日：2019-05-08

Applicant: The University of Chicago

Inventor： Chuan HE ,  Xiaocheng WENG ,  Tong WU

IPC: C12Q1/6806 ,  C07C69/003

Abstract: Embodiments are directed to N3-kethoxal reagents and derivatives thereof, and related methods that allow fast and reversible labeling of single-stranded nucleic acids in live cells. By way of example, one aspect is directed to a process for reversible labeling of single-stranded guanine bases in live cells, which results in an effective in vivo method for transcriptome-wide RNA secondary structure mapping and RNA G-quadruplex prediction.

公开(公告)号：US20250154187A1

公开(公告)日：2025-05-15

申请号：US18556842

申请日：2022-04-27

Applicant: THE UNIVERSITY OF CHICAGO

Inventor： Chuan HE ,  Qing DAI ,  Lisheng ZHANG ,  Chang YE

IPC: C07H1/00 ,  C12N9/12 ,  C12Q1/6806 ,  C12Q1/6869

Abstract: Aspects of the present disclosure are directed to methods and compositions for modification, detection, and quantification of pseudouridine and 5-hydroxymethylcytosine. Disclosed are methods for modification of pseudouridine and/or 5-hydroxymethylcytosine comprising bisulfite treatment under particular conditions. Further disclosed are compositions and kits comprising a bisulfite solution and instructions for use.

公开(公告)号：US20220364173A1

公开(公告)日：2022-11-17

申请号：US17754622

申请日：2020-10-09

Applicant: The University of Chicago

Inventor： Chuan HE ,  Lulu HU

IPC: C12Q1/6883

Abstract: Aspects of the present disclosure relate to methods for modification and detection of methylated nucleotides. Embodiments are directed to detection of RNA methylation. Disclosed are methods and compositions for transcriptome-wide detection of N6-methyladenosine in mRNA. In some cases, methods for modifying a methylated nitrogenous base are described. Also disclosed are enzymes and other molecules useful for RNA methylation detection.

公开(公告)号：US20220033890A1

公开(公告)日：2022-02-03

申请号：US17448958

申请日：2021-09-27

Applicant: The University of Chicago

Inventor： Chuan HE ,  Boxuan Simen ZHAO ,  Pradnya NARKHEDE ,  Chang LIU ,  Xiaolong CUI

IPC: C12Q1/6844 ,  C12Q1/6806

Abstract: Methods, compositions and kits are provided to amplify the amount of genomic methylated DNA can by subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

公开(公告)号：US20210317506A1

公开(公告)日：2021-10-14

申请号：US17250024

申请日：2019-05-08

Applicant: The University of Chicago

Inventor： Chuan HE ,  Qiancheng YOU

IPC: C12Q1/6806

Abstract: Certain embodiments are directed to compositions and methods for capture of elements in physical proximity. In certain aspects the methods comprise (a) contacting a target with a functionalized scaffold or capture agent that comprises activatable cross-linking moieties to form a target/scaffold mixture; (b) exposing the target/scaffold mixture to an activator to activate the cross-linking moieties of the dendrimer and form a cross-linked target/scaffold complex; (c) isolating the target/scaffold complexes; and (d) identify portions of the target or targets that are cross linked with the scaffold.