Bioagent detection oligonucleotides

Patent metadata

Field	Value
Publication number	US-9970061-B2
Application number	US-201214369618-A
Country	US
Kind code	B2
Filing date	Dec 27, 2012
Priority date	Dec 27, 2011
Publication date	May 15, 2018
Grant date	May 15, 2018

Abstract

The present invention compositions, methods and systems to identify, detect, and/or quantify bacterial DNA in the presence of contaminating non-bacterial DNA. In particular, the present invention provides oligonucleotides configured to detect a relatively small amount of bacterial DNA in the presence of an overwhelmingly large amount of contaminating human DNA.

First claim

We claim:

1. A method of detecting bacterial DNA in the presence of contaminating human DNA comprising:
a) contacting a sample comprising human genomic DNA, contaminants, and possibly bacterial DNA with an oligonucleotide wherein said oligonucleotide is 1 a sequence selected from SEQ ID NOs: 1-18;
b) allowing said oligonucleotide to hybridize to bacterial DNA, if bacterial DNA is present in said sample; and
c) detecting said bacterial DNA in the presence of contaminating human DNA, if bacterial DNA is present in said sample, based upon hybridization of said oligonucleotide to said bacterial DNA.

2. The method of claim 1 , further comprising quantifying said bacterial DNA.

3. The method of claim 1 , further comprising using SCODA to separate said bacterial DNA from said human genomic DNA.

4. The method of claim 1 , wherein said oligonucleotide comprises a label.

5. The method of claim 4 , wherein said label is a fluorescent label, a luminescent label, a chemiluminescent label, radioactive label, a quencher label, an interacting label, or a mass-tagged label.

6. The method of claim 1 , wherein said oligonucleotide is a capture oligonucleotide immobilized in a SCODA gel.

7. The method of claim 6 , wherein said bacterial DNA is eluted from said SCODA gel and amplified with a primer pair comprising a sequence selected from SEQ ID NOs: 1-18 prior to detection.

8. The method of claim 6 , wherein said bacterial DNA is amplified in said SCODA gel using in situ PCR methods with a primer pair comprising a sequence selected from SEQ ID NOs: 1-18 prior to detection, or prior to elution and detection.

9. The method of claim 8 , wherein an electrical field, a magnetic field, a flow field, or combination thereof promotes hybridization and disassociation of said bacterial DNA and said immobilized primers during rounds of said PCR.

10. The method of claim 8 , wherein said bacterial DNA is detected without elution from said SCODA gel wherein a sequence of said primer pair is detectably labeled.

11. The method of claim 7 , wherein said detection comprises next-generation sequencing detection.

12. The method of claim 7 , wherein said detection comprises quantifying said bacterial DNA.

Assignees

• Ibis Biosciences Inc
• Hofstadler Nina M

Inventors

• Ecker David J
• Hofstadler Steven A
• Sampath Rangarajan
• Blyn Lawrence B
• Hall Thomas A
• Eshoo Mark W

Classifications

• C12Q1/686

  Polymerase chain reaction [PCR] · CPC title

• C12Q2600/158

  Expression markers · CPC title

• C12Q1/689 Primary

  for bacteria · CPC title

• C12Q1/6853

  using modified primers or templates · CPC title

• C12Q2600/166

  Oligonucleotides used as internal standards, controls or normalisation probes · CPC title