BIOAGENT DETECTION OLIGONUCLEOTIDES

• US 20150184231A1
• Filed: 12/27/2012
• Published: 07/02/2015
• Est. Priority Date: 12/27/2011
• Status: Active Grant

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Ecker, David J., Hofstadler, Steven A., Sampath, Rangarajan, Blyn, Lawrence B., Hall, Thomas A., Eshoo, Mark W.
• Granted Patent: US 9,970,061 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/166 Oligonucleotides used as internal standards, controls or normalisation probes

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.

Claims

1. A composition comprising a purified oligonucleotide configured to hybridize to a broad range of bacterial genomes while discriminating against hybridizing to non-bacterial DNA.

2. The composition of claim 1, wherein said oligonucleotide is between 10 and 20 nucleotides in length.

3. The composition of claim 1, wherein said oligonucleotide hybridizes to over 100 different bacterial genomes.

4. The composition of claim 1, wherein said oligonucleotide comprises, consists essentially of, or consists of a sequence selected from SEQ ID NOs 1-18.

5. The composition of claim 1, wherein said oligonucleotide wherein said non-bacterial DNA comprises human genomic DNA.

6. A method comprising:

a) providing;

i) one or more purified oligonucleotides configured to hybridize to a broad range of bacterial genomes while discriminating against hybridizing to human genomic DNA; and

ii) a sample comprising human genomic DNA, contaminants, and possibly bacterial DNA;

b) contacting said sample with said oligonucleotides;

c) allowing said oligonucleotides to hybridize to bacterial DNA, if bacterial DNA is present in said sample; and

d) detecting said bacterial DNA, if bacterial DNA is present in said sample, based upon hybridization to said oligonucleotides.

7. The method of claim 6, wherein said broad range of bacterial genomes comprises over 100 different bacterial genomes.

8. The method of claim 6, further comprising quantifying said bacterial DNA.

9. The method of claim 6, further comprising using SCODA to separate said bacterial DNA from said human genomic DNA.

10. A kit comprising a plurality of purified oligonucleotides configured to hybridize to a broad range of bacterial genomes while discriminating against hybridizing to non-bacterial DNA.

11. The kit of claim 10, wherein said oligonucleotides are between 10 and 20 nucleotides in length.

12. The kit of claim 10, wherein said non-bacterial DNA comprises human genomic DNA.

13. The kit of claim 10, further comprising a gel suitable for use in SCODA purification.

14. The kit of claim 10, further comprising a component for generating an electric field.

15. An isolated oligonucleotide comprising, consisting essentially of, or consisting of a sequence selected from SEQ ID NOs:

1-18.

16. The isolated oligonucleotide of claim 15, wherein said isolated oligonucleotide comprises SEQ ID NO:

1.

17. The isolated oligonucleotide of claim 15, wherein said isolated oligonucleotide comprises SEQ ID NO:

2.