US 9,428,791 B2 · Probes of RNA structure and methods for using the same

Abstract

Methods for obtaining structural data from RNA in a sample, and RNA probes for performing the same, are provided. Methods of reversibly modifying RNA is a sample, in vitro or in vivo, and reversible probes for performing the same, are provided. The RNA probes may be SHAPE probes that include aryl or heteroaryl acyl imidazoles. The RNA probes may be reversible probes that include an aryl or heteroaryl ring substituted with a hydroxyl-reactive group and an azido-containing group. Also provided are methods of comparing in vitro and in vivo RNA structural data. Also provided are methods of diagnosing a cellular proliferative disease condition, e.g., by probing HOTAIR RNA. Aspects of the invention further include compositions, e.g., probes and kits, etc., that find use in methods of the invention.

Claims16

Dependent claims

A method for obtaining structural data from a RNA in a sample, the method comprising:

contacting the sample with a SHAPE probe to acylate one or more unconstrained nucleotides of the RNA to produce a 2′-acylated RNA, wherein the SHAPE probe is described by formula (II):
wherein:
A is selected from a phenyl, a pyridyl, a pyrrolyl, a furanyl, a thienyl, a thiazolyl, an imidazolyl, an oxazolyl, a pyrimidinyl, a pyrazinyl and a pyridazinyl ring;
R1 is H or a lower alkyl;
R2 is H or a lower alkyl;
and
analyzing the 2′-acylated RNA to obtain structural data.

4 more elements

Dependencies are inferred from the claim text.

Facts

Application

13/967,161Filed 14 Aug 2013 · us provisional application

Priority

14 Aug 2012

Published

US 2014/0154673 A15 Jun 2014

Granted

30 Aug 2016

Term ends

Not estimatedThe source records don’t support an estimate.

Classification4 codes

C12Q 1/68
Measuring or testing processes involving enzymes, nucleic acids or microorganisms ; Compositions therefor; Processes of preparing such…
Y10T 436/143333
Hetero-O [e.g., ascorbic acid, etc.]: saccharide [e.g., DNA, etc.]
C12Q
Measuring or testing processes involving enzymes, nucleic acids or microorganisms
Y10T
Technical subjects covered by former us classification

Probes of RNA structure and methods for using the same

Life of this patent

Probes of RNA structure and methods for using the same

Life of this patent

Abstract

Claims16