Device and methods for epigenetic analysis

Patent metadata

Field	Value
Publication number	US-9447451-B2
Application number	US-201414260082-A
Country	US
Kind code	B2
Filing date	Apr 23, 2014
Priority date	Aug 6, 2009
Publication date	Sep 20, 2016
Grant date	Sep 20, 2016

Abstract

Provided herein are methods and devices for single object detection. The methods and devices can be used to identify a plurality epigenetic markers on a genetic material, or a chromatin, encompassing fragments thereof. The invention provides for the characterization of the genetic material flowing through a channel in a continuous body of fluid based on detection of one or more properties of the genetic material. The methods and systems provided herein allow genome-wide, high-throughput epigenetic analysis and overcome a variety of limitations common to bulk analysis techniques.

First claim

What is claimed is:

1. A method for performing epigenetic analysis of native chromatin in a channel, comprising:
(a) flowing the native chromatin through an interrogation volume in said channel that is illuminated with a beam of light, said interrogation volume being defined by walls of a submicrometer channel region that are separated by a width of less than about 1 μm of said channel and said beam of light, wherein said native chromatin is labeled with a plurality of labels, at least one of which is specifically complexed with an epigenetic marker on said native chromatin, and at least one other label is complexed with a protein and/or nucleotide of said native chromatin
(b) simultaneously detecting the at least one label and the at least one other label within the interrogation volume and
(c) analyzing said detection of the at least one label and the at least one other label, thereby performing said epigenetic analysis.

2. The method of claim 1 , comprising detecting at least three or four labels.

3. The method of claim 1 , wherein the at least one other label is complexed with a histone or is a nucleic acid binding agent selected from the group consisting of sequence specific probe, intercalating dye, minor groove binder, and DNA binding proteins.

4. The method of claim 1 , wherein the at least one other label is complexed with a binding agent that complexes with a target selected from the group consisting of a non-histone protein, a transcription factor, MBD1, RNA Pol II, and RNA.

5. The method of claim 1 , wherein the detecting step provides a time-dependent resolution of better than about 10 microseconds.

6. The method of claim 1 , wherein the native chromatin comprises a nucleic acid molecule and a histone.

7. The method of claim 1 , wherein the illuminated interrogation volume contains a single native chromatin.

8. The method of claim 1 , wherein the interrogation volume is less than about 0.5 femtoliters.

9. The method of claim 1 , wherein the genetic material is characterized in less than about 0.1 seconds.

Assignees

• Univ Cornell

Inventors

• Craighead Harold G
• Cipriany Benjamin R
• Levy Stephen
• Soloway Paul

Classifications

• B01L3/502761 Primary

  specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads or physically stretching molecules · CPC title

• C12Q1/68 Primary

  involving nucleic acids · CPC title

• C12Q2565/629

  being a microfluidic device · CPC title

• C12Q2537/164

  Methylation detection other then bisulfite or methylation sensitive restriction endonucleases · CPC title

• B01L2200/0663

  Stretching or orienting elongated molecules or particles · CPC title