Chemical platform assisted proximity capture (CAP-C)
AssigneeThe University of Chicago
InventorsChuan He, Qiancheng You
Life of this patent
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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.
Claims25
A chromatin mapping method comprising:
- (a) contacting a chromatin target structure comprising nucleic acids and histones with a functionalized dendrimer comprising cross-linking moieties to form a chromatin/dendrimer mixture;
- (b) exposing the chromatin/dendrimer mixture to an activator to activate the cross-linking moieties of the functionalized dendrimer and, thereby forming a cross-linked chromatin/dendrimer complex;
- (c) isolating the cross-linked chromatin/dendrimer complex;
- and
- (d) identifying genomic loci from the isolated chromatin/dendrimer complex.
A method comprising:
- (a) contacting a chromatin structure with a functionalized dendrimer comprising activatable cross-linking moieties to form a chromatin structure/dendrimer mixture, wherein the dendrimer is also coupled to an avidity tag;
- (b) exposing the chromatin structure/dendrimer mixture to an activator to activate the cross-linking moieties of the dendrimer and form a cross-linked chromatin structure/dendrimer complex;
- (c) contacting the cross-linked chromatin structure/dendrimer with an affinity agent that binds a chromatin associated protein, wherein the affinity agent is coupled to an avidity tag modification agent, wherein the avidity tag modification agent, when brought in proximity to an avidity tag, modifies the avidity tag forming an isolatable cross-linked chromatin/dendrimer complex;
- (d) isolating the cross-linked chromatin structure/dendrimer complex via the avidity tag;
- and
- (e) identifying portions of nucleic acid associated with the cross-linked chromatin structure/dendrimer complex isolated in (d).
A method comprising:
- (a) contacting a target in proximity to a RNA with a functionalized dendrimer comprising activatable cross-linking moieties to form a target/dendrimer mixture, wherein the target is a RNA-binding target or protein target, wherein the functionalized dendrimer is also coupled to an avidity tag;
- (b) exposing the target/dendrimer mixture to an activator to activate the cross-linking moieties of the functionalized dendrimer and form a cross-linked target/dendrimer complex;
- (c) contacting the cross-linked target/dendrimer complex with an affinity agent that binds a RNA-binding protein or protein target in proximity to the RNA, wherein the affinity agent is coupled to an avidity tag modification agent, wherein the avidity tag modification agent, when brought in proximity to an avidity tag, modifies the avidity tag forming an isolatable cross-linked target/dendrimer complex;
- (d) isolating the cross-linked target/scaffold complex via the avidity tag;
- and
- (e) identifying portions of the RNA that is associated with the cross-linked target/dendrimer complex isolated in (d).
Dependencies are inferred from the claim text.