Enzyme amplified electrochemical DNA detection

• US 20060199187A1
• Filed: 03/02/2005
• Published: 09/07/2006
• Est. Priority Date: 03/02/2005
• Status: Abandoned Application

• Current Assignee: HandyLab Incorporated (Becton, Dickinson & Co), Board of Regents of the University of Michigan (University of Michigan)
• Original Assignee: HandyLab Incorporated (Becton, Dickinson & Co)
• Inventors: Wheeler, Lara M., Meyerhoff, Mark E., Althaus, John S., Yim, Hyoungsik, Lee, Kyong-Hoon, Lee, Youngmi
• Application Number:
  US11/070,570
• Publication Number:
  US 20060199187A1
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical

Abstract

An oligonucleotide probe for DNA detection is disclosed. The oligonucleotide probe includes a site-specific sequence. Either a co-factor or a mediator is conjugated to the site-specific sequence. The co-factor is adapted to produce an enzymatic signal that is electrochemically detectable. The mediator is adapted to enhance an enzymatic signal that is electrochemically detectable.

Claims

1. An oligonucleotide probe for enzyme amplified electrochemical target DNA detection, the oligonucleotide probe comprising:

a site-specific sequence; and

a co-factor conjugated to the site-specific sequence or a mediator conjugated to the site-specific sequence;

wherein the co-factor is adapted to produce an enzymatic signal that is electrochemically detectable and the mediator is adapted to enhance an enzymatic signal that is electrochemically detectable.

2. The oligonucleotide probe as defined in claim 1 wherein the co-factor comprises one of a prosthetic group, a metal-ion activator, and a do-enzyme.

3. The oligonucleotide probe as defined in claim 1 wherein the co-factor is one of pyrroloquinoline quinone, flavin adenine dinucleotide, nicotinamide adenine dinucleotide phosphate, and heme.

4. The oligonucleotide probe as defined in claim 1 wherein the mediator is one of ferrocene, ferrocene derivatives, dichlorophenol indolphenol, ubiquinone, Ru(III) complexes, Os(III) complexes, and phenazoinum methosulfate.

5. The oligonucleotide probe as defined in claim 1 wherein the site specific sequence is 5′

-amino-hexyl-AGAAGTACATGCTGATCAAGTGACAACTCCACA-3′

, the prosthetic group is pyrroloquinoline quinone, and the target DNA is from group beta streptococcus.

6. The oligonucleotide probe as defined in claim 1 wherein the enzymatic signal is electrochemically detectable via voltammetry, amperometry, coulometry, potentiometry, conductivity, and combinations thereof.

7. The oligonucleotide probe as defined in claim 1 wherein the co-factor is adapted to release from the site-specific sequence and to bind to and activate an apo-enzyme, thereby forming a holo-enzyme that is adapted to catalyze a reaction to produce electrons.

8. The oligonucleotide probe as defined in claim 1 wherein the mediator is adapted to release from the site-specific sequence and to react with a holo-enzyme.

9. A method of detecting target DNA in a sample, the method comprising:

performing a DNA amplification process on the sample;

exposing an oligonucleotide probe to exonuclease activity, the oligonucleotide probe including a site-specific sequence and a co-factor conjugated to the site-specific sequence or a mediator conjugated to the site-specific sequence, the exposing thereby releasing a probe fragment including the co-factor or the mediator;

combining the probe fragment with an apo-enzyme or a holo-enzyme, wherein combining the probe fragment having co-factor with the apo-enzyme produces an enzymatic signal that is electrochemically detectable or wherein combining the probe fragment having the mediator with the holo-enzyme enhances an enzymatic signal that is electrochemically detectable; and

electrochemically detecting the enzymatic signal, thereby detecting the target DNA.

10. The method as defined in claim 9 wherein the DNA amplification process is at least one of real time PCR, end-point PCR, and RCA.

11. The method as defined in claim 10 wherein the DNA amplification process is real time PCR and wherein the enzymatic signal is detected at predetermined intervals during the amplification process.

12. The method as defined in claim 10 wherein the DNA amplification process is end-point PCR and wherein the enzymatic signal is detected prior to and after the amplification process.

13. The method as defined in claim 10 wherein the DNA amplification process includes exposing the sample to a PCR mixture including at least one of substrates, co-substrates, buffers, mediators, stabilizers, and mixtures thereof.

14. The method as defined in claim 9 wherein the performing, exposing, combining, and detecting occur one of substantially simultaneously and sequentially.

15. The method as defined in claim 9 wherein the apo-enzyme or the holo-enzyme is immobilized on a surface of an electrode.

16. The method as defined in claim 15 wherein the electrode comprises a film layer covering the apo-enzyme or the holo-enzyme.

17. The method as defined in claim 15, further comprising establishing a barrier membrane between the oligonucleotide probe and the electrode, the barrier membrane adapted to diffuse the probe fragment and prohibit diffusion of the oligonucleotide probe.

18. The method as defined in claim 9 wherein electrochemically detecting the enzymatic signal may be accomplished via voltammetry, amperometry, coulometry, potentiometry, conductivity, and combinations thereof.

19. The method as defined in claim 9 wherein the probe fragment having the co-factor combines with the apo-enzyme, and the method further comprises:

binding the co-factor with the apo-enzyme, thereby activating the apo-enzyme and forming a holo-enzyme; and

converting a substrate in the sample to a product and free electrons via a reaction involving the holo-enzyme as a catalyst.

20. The method as defined in claim 9 wherein the holo-enzyme produces an enzymatic signal prior to being combined with the probe fragment having the mediator, and wherein the method further comprises mediating electron transfer between the holo-enzyme and an electrode, thereby enhancing the enzymatic signal of the holo-enzyme such that the signal is detectable electrochemically.

21. The method as defined in claim 9, further comprising adding a reagent to the sample after performing the DNA amplification process and prior to detecting the enzymatic signal, thereby complexing the oligonucleotide probe and prohibiting its binding with the apo-enzyme.

22. The method as defined in claim 21 wherein the reagent is one of protamine and poly-L-lysine.

23. The method as defined in claim 9, further comprising adding a reagent to the sample, thereby complexing the oligonucleotide probe and prohibiting its combining with the holo-enzyme.

24. The method as defined in claim 9 wherein the co-factor comprises one of a prosthetic group, a co-enzyme, and a metal-ion activator.

25. The method as defined in claim 24 wherein the co-factor is one of pyrroloquinoline quinone, flavin adenine dinucleotide, nicotinamide adenine dinucleotide phosphate, and heme.

26. The method as defined in claim 9 wherein the mediator is one of ferrocene, ferrocene derivatives, dichlorophenol indolphenol, ubiquinone (Qo), Ru(III) complexes, Os(III) complexes, and phenazoinum methosulfate.

27. The method as defined in claim 9 wherein the site-specific sequence is 5′

-amino-hexyl-AGAAGTACATGCTGATCAAGTGACAACTCCACA-3′

, the prosthetic group is pyrroloquinoline quinone, and the target DNA is from group beta streptococcus.

28. The method as defined in claim 9 wherein the apo-enzyme or holo-enzyme, the target DNA, and the oligonucleotide probe are mixed in a homogeneous assay system.

29. The method as defined in claim 9 wherein the mediator and the apo-enzyme or holo-enzyme coated on an electrode surface in a heterogeneous assay system and wherein a PCR solution containing multiple copies of target DNA, the fragment probe, and the oligonucleotide probe is injected on a modified electrode surface for electrochemical detection.

30. A diagnostic device for detecting target DNA, comprising:

at least one electrode having an apo-enzyme or a holo-enzyme immobilized thereon; and

an oligonucleotide probe in electrochemical contact with the at least one electrode, the probe including;

a site-specific sequence; and

one of a co-factor conjugated to the site-specific sequence and a mediator conjugated to the site-specific sequence;

wherein the co-factor or the mediator is adapted to release from the probe to form a probe fragment;

wherein the probe fragment having the co-factor binds to the apo-enzyme to produce an enzymatic signal that is electrochemically detectable;

or wherein the probe fragment having the mediator reacts with the holo-enzyme to enhance an enzymatic signal that is electrochemically detectable.

31. The diagnostic device as defined in claim 30 wherein the co-factor comprises one of a prosthetic group, a co-enzyme, and a metal-ion activator.

32. The diagnostic device as defined in claim 30 wherein the co-factor is one of pyrroloquinoline quinone, flavin adenine dinucleotide, nicotinamide adenine dinucleotide phosphate, and heme.

33. The diagnostic device as defined in claim 30 wherein the mediator is one of ferrocene, ferrocene derivatives, dichlorophenol indolphenol, ubiquinone (Qo), Ru(III) complexes, Os(III) complexes, and phenazoinum methosulfate.

34. The diagnostic device as defined in claim 30 wherein the site-specific sequence is 5′

-amino-AGAAGTACATGCTGATCAAGTGACAACTCCACA-3′

, the co-factor is pyrroloquinoline quinone, and the target DNA is from group beta streptococcus.

35. The diagnostic device as defined in claim 30 wherein the enzymatic signal is electrochemically detectable via voltammetry, amperometry, coulometry, potentiometry, conductivity, and combinations thereof.

36. The diagnostic device as defined in claim 30 wherein the at least one electrode comprises a film layer covering the apo-enzyme or the holo-enzyme, the film layer exhibiting at least one of charge and size exclusion properties to allow the probe fragment to contact the apo-enzyme or the holo-enzyme.

37. The diagnostic device as defined in claim 30, further comprising a barrier membrane established between the oligonucleotide probe and the electrode, the barrier membrane adapted to diffuse the probe fragment and prohibit diffusion of the oligonucleotide probe.