Detection of nucleic acids

Patent metadata

Field	Value
Publication number	US-2019032120-A1
Application number	US-201816154045-A
Country	US
Kind code	A1
Filing date	Oct 8, 2018
Priority date	Aug 12, 2014
Publication date	Jan 31, 2019
Grant date	—

Abstract

Provided herein is technology relating to detecting and identifying nucleic acids and particularly, but not exclusively, to compositions, methods, kits, and systems for detecting, identifying, and quantifying target nucleic acids with high confidence at single-molecule resolution.

First claim

1 - 19 . (canceled)

20 . A system for detecting an analyte in a sample comprising:
a) a detectably labeled query probe specific for an analyte; b) a detector configured to detect transient binding of the detectably labeled query probe to said analyte; and c) a processor configured to:
i) count the number and/or rate of transient binding events between the detectably labeled query probe and the analyte; and
ii) indicate the presence of the analyte in the sample based on the number and/or rate of said transient binding events.

21 . The system of claim 20 wherein said processor is configured to indicate the presence of the analyte in the sample when the number and/or rate of said transient binding events falls within an empirically determined range characteristic of the detectably labeled query probe and the analyte.

22 . The system of claim 20 wherein said detectably labeled query probe binds to the analyte with a rate constant k on that is greater than 1 per minute and/or said detectably labeled query probe dissociates from the analyte with a k off that is greater than 1 per minute.

23 . The system of claim 20 further comprising an analyte.

24 . The system of claim 20 further comprising an analyte immobilized to a discrete region of a solid support.

25 . The system of claim 24 wherein said solid support comprises a microscope slide, a bead, a coverslip, or a cell.

26 . The system of claim 24 wherein said solid support comprises an immobilized capture probe.

27 . The system of claim 20 wherein said detectably labeled query probe comprises a fluorescent label.

28 . The system of claim 20 wherein said processor is configured to produce a kinetic fingerprint characterizing transient binding events between the detectably labeled query probe and the analyte.

29 . The system of claim 20 wherein said processor is configured to compare the number and/or rate of said transient binding events with the number and/or rate of said transient binding events detected for a positive and/or a negative control.

30 . The system of claim 20 further comprising a component configured to control the temperature of a sample.

31 . The system of claim 20 wherein said detectably labeled query probe comprises a nucleic acid.

32 . The system of claim 20 wherein said detectably labeled query probe comprises a protein.

33 . The system of claim 20 wherein said processor is configured to apply a statistical treatment to the number and/or rate of transient binding events between the detectably labeled query probe and the analyte.

34 . The system of claim 20 wherein said processor is configured to apply a Poisson statistical treatment to the number and/or rate of transient binding events between the detectably labeled query probe and the analyte.

35 . The system of claim 20 wherein said empirically determined range characteristic of the detectably labeled query probe and the analyte is provided by hidden Markov modeling.

36 . The system of claim 20 wherein said detector detects said transient binding with single-molecule resolution.

37 . The system of claim 23 further comprising a ligand of said analyte that produces a detectable change in said transient binding of the detectably labeled query probe to said analyte.

38 . The system of claim 20 further comprising a first analyte and a second analyte.

39 . The system of claim 38 wherein the processor is configured to distinguish between the first analyte and the second analyte.

Assignees

• Univ Michigan Regents

Inventors

• Walter Nils
• Johnson-Buck Alexander
• Blanco Mario
• Rinaldi Arlie

Classifications

• C12Q1/6816

  characterised by the detection means (C12Q1/6804 takes precedence) · CPC title

• C12Q1/6837 Primary

  using probe arrays or probe chips (C12Q1/6874 takes precedence) · CPC title

• C12Q1/6886

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12Q2600/178

  miRNA, siRNA or ncRNA · CPC title

• C12Q2565/519

  characterised by the capture moiety being a single stranded oligonucleotide · CPC title