Redox labeled oligonucleotide probes and their use

1. A method of identifying the presence or absence of a plurality of target nucleic acid sequences in a sample, said method comprising:

performing isothermal nucleic acid amplification on a sample to provide a nucleic acid amplification mixture;

contacting the nucleic acid amplification mixture with a first oligonucleotide probe, a second oligonucleotide probe, and at least one nuclease, wherein:

the first oligonucleotide probe comprises a first sequence complementary to a first target nucleic acid sequence, a first modified internal residue conjugated to a first redox moiety, and a 3′ blocking group to prevent polymerase extension, wherein the first oligonucleotide probe is cleavable by a nuclease selected from the group consisting of AP endonuclease, DNA glycosylase/lyase, and DNA glycosylase at the first modified internal residue when said first oligonucleotide probe is hybridized to a complementary nucleic acid;

the second oligonucleotide probe comprises a second sequence complementary to a second target nucleic acid sequence, a second modified internal residue conjugated to a second redox moiety, and a 3′ blocking group to prevent polymerase extension, wherein the second oligonucleotide probe is cleavable by a nuclease selected from the group consisting of AP endonuclease, DNA glycosylase/lyase, and DNA glycosylase at the second modified internal residue when said second oligonucleotide probe is hybridized to a complementary nucleic acid; and

the first redox label conjugated to the first modified internal residue does not generate an electrical current in response to an electrical potential applied to the nucleic acid amplification mixture and the second redox label conjugated to the second modified internal residue does not generate an electrical current in response to an electrical potential applied to the nucleic acid amplification mixture;

detecting a first electrochemical signal produced by a first cleaved redox moiety, wherein said first electrochemical signal is indicative of the presence of the first target nucleic acid sequence; and

detecting a second electrochemical signal produced by a second cleaved redox moiety, wherein said second electrochemical signal is indicative of the presence of the second target nucleic acid sequence.

2. The method of claim 1 , wherein detecting the first electrochemical signal comprises using differential pulse voltammetry, amperometry, or impedance measurement; and detecting the second electrochemical signal comprises using differential pulse voltammetry, amperometry, or impedance measurement.

3. The method of claim 1 , wherein the first cleaved redox moiety and the second cleaved redox moiety have a difference (ΔE) of approximately −50 mV in their peak potentials.

4. The method of claim 1 , wherein contacting the nucleic acid amplification mixture further comprises contacting the nucleic acid amplification mixture with a third oligonucleotide probe comprising a third sequence complementary to a third target nucleic acid sequence, a third modified internal residue conjugated to a third redox moiety, and a 3′ blocking group to prevent polymerase extension, wherein the third oligonucleotide probe is cleavable by a nuclease selected from the group consisting of AP endonuclease, DNA glycosylase/lyase, and DNA glycosylase at the third modified internal residue when said third oligonucleotide probe is hybridized to a complementary nucleic acid.

5. The method of claim 4 , wherein contacting the nucleic acid amplification mixture further comprises contacting the nucleic acid amplification mixture with a fourth oligonucleotide probe comprising a fourth sequence complementary to a fourth target nucleic acid sequence, a fourth modified internal residue conjugated to a fourth redox moiety, and a 3′ blocking group to prevent polymerase extension, wherein the fourth oligonucleotide probe is cleavable by a nuclease selected from the group consisting of AP endonuclease, DNA glycosylase/lyase, and DNA glycosylase at the fourth modified internal residue when said fourth oligonucleotide probe is hybridized to a complementary nucleic acid.

6. The method of claim 5 , wherein contacting the nucleic acid amplification mixture further comprises contacting the nucleic acid amplification mixture with a fifth oligonucleotide probe comprising a fifth sequence complementary to a fifth target nucleic acid sequence, a fifth modified internal residue conjugated to a fifth redox moiety, and a 3′ blocking group to prevent polymerase extension, wherein the fifth oligonucleotide probe is cleavable by a nuclease selected from the group consisting of AP endonuclease, DNA glycosylase/lyase, and DNA glycosylase at the fifth modified internal residue when said fifth oligonucleotide probe is hybridized to a complementary nucleic acid.

7. A composition comprising:

a recombinase agent;

one or more nucleic acid primers;

a nuclease;

a first oligonucleotide probe comprising:

a first modified internal residue conjugated to a first redox moiety; and

a 3′ blocking group to prevent polymerase extension,

wherein the first oligonucleotide probe is cleavable by a nuclease selected from the group consisting of AP endonuclease, DNA glycosylase/lyase, and DNA glycosylase at the first modified internal residue when said first oligonucleotide probe is hybridized to a complementary nucleic acid; and

a second oligonucleotide probe comprising:

a second modified internal residue conjugated to a second redox moiety; and

a 3′ blocking group to prevent polymerase extension,

wherein the second oligonucleotide probe is cleavable by a nuclease selected from the group consisting of AP endonuclease, DNA glycosylase/lyase, and DNA glycosylase at the second modified internal residue when said second oligonucleotide probe is hybridized to a complementary nucleic acid,

wherein the first redox label conjugated to the first modified internal residue does not generate an electrical current in response to an electrical potential applied to the nucleic acid amplification mixture and the second redox label conjugated to the second modified internal residue does not generate an electrical current in response to an electrical potential applied to the nucleic acid amplification mixture.

8. The composition of claim 7 , wherein the first modified internal residue is an abasic residue and/or the second modified internal residue is an abasic residue.

9. The composition of claim 7 , wherein the first modified internal residue comprises a tetrahydrofuran and/or the second modified internal residue comprises a tetrahydrofuran.

10. The composition of claim 7 , wherein the first modified internal residue is an abasic residue comprising a sugar covalently linked at a 1′ carbon to an oxygen atom, said oxygen atom is covalently linked to a carbon atom of a linker containing n carbon atoms, and said linker is conjugated to the redox moiety; and/or the second modified internal residue is an abasic residue comprising a sugar covalently linked at a 1′ carbon to an oxygen atom, said oxygen atom is covalently linked to a carbon atom of a linker containing n carbon atoms, and said linker is conjugated to the redox moiety.

11. The composition of claim 7 , wherein the first redox moiety is selected from the group consisting of a phenothiazine, a phenoxazine, a ferrocene, ruthenium (II), osmium (II), an anthraquinone, a phenazine, and derivatives thereof; and the second redox moiety is selected from the group consisting of a phenothiazine, a phenoxazine, a ferrocene, ruthenium (II), osmium (II), an anthraquinone, a phenazine, and derivatives thereof.

12. The composition of claim 11 , wherein the first redox moiety is a phenothiazine derivative comprising methylene blue or PZ9; and/or the second redox moiety is a phenothiazine derivative comprising methylene blue or PZ9.

13. The composition of claim 7 , wherein the first redox moiety and the second redox moiety is each independently selected from the group consisting of the following structures:

14. The composition of claim 7 , wherein the first modified internal residue conjugated to the first redox moiety and the second modified internal residue conjugated to the second redox moiety each has a structure independently selected from the group consisting of:

15. The composition of claim 7 , wherein the first oligonucleotide probe or the second oligonucleotide probe comprises a nucleotide sequence at least 90% identical to a nucleotide sequence selected from the group consisting of:

CATCAGCTTTTGGAGCTTGAGAGTCAT[T(methylene blue)]A[dSpacer]GTTTTTGAGCTTCAC (SEQ ID NO: 5);

GAACCAAGAAGCATTRAGCAAAACCCAGGGA[T(methylene blue)][dSpacer]ATTAATCAGGCACTC (SEQ ID NO: 6); and

ACTGATGATATTCAGC[T(methylene blue)]ACAA[T(methylene blue)]CAAGAC[T(methylene blue)]A[dSpacer] TCGTTAAGTAATGAA (SEQ ID NO: 7),

wherein dSpacer is a tetrahydrofuran.

16. The composition of claim 7 , wherein the first oligonucleotide probe comprises a first modified internal residue conjugated to a first redox moiety at a first internal site and a third modified internal residue conjugated to a third redox moiety at a second internal site and the second oligonucleotide probe comprises a second modified internal residue conjugated to a second redox moiety at a second internal site and a fourth modified internal residue conjugated to a fourth redox moiety at a fourth internal site.

17. The composition of claim 16 , wherein the first redox moiety and the third redox moiety are the same or are different and the second redox moiety and the fourth redox moiety are the same or different.

18. The composition of claim 7 , wherein the first oligonucleotide probe comprises a first plurality of modified residues, wherein each modified residue of said first plurality of modified residues is conjugated to a redox moiety and wherein the second oligonucleotide probe comprises a second plurality of modified residues, wherein each modified residue of said second plurality of modified residues is conjugated to a redox moiety.

19. The composition of claim 7 , wherein the first oligonucleotide probe is 12 to 30, 12 to 40, or 12 to 60 residues in length or the second oligonucleotide probe is 12 to 30, 12 to 40, or 12 to 60 residues in length.