Solution phase nucleic acid sandwich assays having reduced background noise

• US 5,635,352 A
• Filed: 04/26/1995
• Issued: 06/03/1997
• Est. Priority Date: 12/08/1993
• Status: Expired due to Term

• Current Assignee: Siemens Healthcare Diagnostics Incorporated (Siemens AG)
• Original Assignee: Chiron Corporation (Novartis Ag)
• Inventors: Collins, Mark, Fultz, Timothy, Urdea, Michael S., Warner, Brian D.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/429,181
• Time in Patent Office: 769 Days
• Field of Search: 435/6, 435/91.1, 435/808, 435/810, 436/501, 536/22.1, 536/23.1, 536/24.1, 536/24.3-0.33, 935/77, 935/78
• US Class Current: 435/6.18
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: F02B 2075/027 four
• CPC Class Codes: Y10S 435/808 Optical sensing apparatus
• CPC Class Codes: Y10S 435/81 Packaged device or kit

Abstract

New techniques are provided for substantially reducing background signals encountered in solution phase hybridization assays. The techniques are premised on eliminating or significantly reducing the phenomena of nonspecific hybridization and nonspecific binding, so as to provide a detectable signal which is produced only in the presence of the target polynucleotide of interest. In certain embodiments, methods are provided for increasing the signal which can otherwise be diminished in noise reduction. Kits for carrying out the novel assays are provided as well.

Claims

1. In a solution phase sandwich hybridization assay for detecting a nucleic acid analyte in a sample, comprising:

(a) binding the analyte indirectly to a solid support;

(b) labelling the analyte;

(c) detecting the presence of label on the support; and

(d) correlating the presence of the label on the support with the presence of the nucleic acid analyte in the sample,

the improvement which comprises incorporating a first capture extender molecule and a distinct second capture extender molecule into the assay both of which must hybridize to the analyte in order for the assay to result in the detectable signal, said first and second capture extender molecules each comprising a polynucleotide containing an analyte-binding segment capable of hybridizing to a nucleic acid sequence present in the analyte and a support-binding segment capable of hybridizing to a nucleic acid sequence present within a capture probe bound to a solid support,

wherein the analyte-binding segment of the first capture extender molecule is distinct from the analyte-binding segment of the second capture extender molecule, and further wherein the capture probe contains a first capture extender binding sequence capable of hybridizing to the support-binding segment of the first capture extender molecule, and a second capture extender binding sequence capable of hybridizing to the support-binding segment of the second capture extender molecule, such that two distinct capture extender molecules can bind to a single capture probe.

2. The assay of claim 1, wherein the melt temperature T_m1 at which the nucleic acid analyte dissociates from the capture probe in the hybrid complex formed between the capture probe, capture extender molecules and nucleic acid analyte is at least about 5°

C. greater than the melt temperature T_m2 of hybrid complexes formed between the capture probe and capture extender molecules.

3. The assay of claim 2 wherein at least one step is carried out under stringency conditions which favor the T_m1 complex formation, but disfavor the T_m2 complex formation.

4. The assay of claim 3 wherein stringency is controlled by controlling at least one step parameter selected from the group consisting of formamide concentration, chaotropic salt concentration, salt concentration, pH (hydrogen ion concentration), organic solvent content, and temperature.

5. The assay of claim 4 wherein the at least one step is carried out at a temperature greater than T_m2 and less than T_m1.

6. The assay of claim 3 wherein the at least one step comprises step (a).

7. A solution phase sandwich hybridization assay for detecting the presence of a nucleic acid analyte in a sample, comprising:

(a) providing a solid support having capture probes thereon, capture extender molecules having a first segment C-1 capable of hybridizing to a nucleic acid sequence in the analyte and a second segment C-2 capable of hybridizing to a nucleic acid sequence in the capture probes, label extender molecules having a first segment L-1 capable of hybridizing to a nucleic acid sequence in the analyte and a second segment L-2 capable of hybridizing to a label probe system, a label probe system comprising a nucleic acid sequence M-1 capable of hybridizing to L-2 and which, directly or indirectly, gives rise to a detectable signal;

(b) incubating the nucleic acid analyte under hybridization conditions with the capture extender molecules at least two of which must hybridize to the analyte in order for the assay to result in a detectable signal, label extender molecules, and the capture probes on the solid support, simultaneously or sequentially in any order, to form a support-bound hybrid complex;

(c) thereafter optionally separating materials not bound to the solid support;

(d) thereafter contacting the support-bound hybrid complex with the label probe system under hybridizing conditions, to provide a labeled, support-bound hybrid complex;

(e) thereafter separating materials not bound to the solid support;

(f) detecting the presence of label in the support-bound hybrid complex; and

(g) correlating the presence of the label in the support-bound hybrid complex with the presence of the nucleic acid analyte in the sample,

wherein the melt temperature T_m1 at which the nucleic acid analyte dissociates from the capture probe in the hybrid complex formed between the capture probe, capture extender molecules and nucleic acid analyte is at least about 5°

C. greater than the melt temperature T_m2 of hybrid complexes formed between the capture probe and capture extender molecules.

8. The assay of claim 7, wherein the label probe system comprises (i) an amplification multimer containing the nucleic acid sequence M-1 and a plurality of identical oligonucleotide subunits containing nucleic acid sequences M-2 capable of hybridizing to label probes, and (ii) label probes containing a nucleic acids sequence L-3 which is capable of hybridizing to M-2 and which, directly or indirectly, gives rise to a detectable signal, and wherein step (d) of the assay comprises the following steps:

(d₁) contacting the support-bound hybrid complex under hybridizing conditions with the amplification multimer, to produce a second support-bound hybrid complex;

(d₂) thereafter optionally separating materials not bound to the solid support; and

(d₃) thereafter contacting the second support-bound hybrid complex with the label probes under hybridization conditions, to produce a labeled support-bound hybrid complex.

9. The assay of claim 7, wherein at least one step is carried out under stringency conditions which favor the T_m1 complex formation, but disfavor the T_m2 complex formation.

10. The assay of claim 9 wherein stringency is controlled by controlling at least one step parameter selected from the group consisting of formamide concentration, chaotropic salt concentration, salt concentration, pH (hydrogen ion concentration), organic solvent content, and temperature.

11. The assay of claim 10 wherein the at least one step is carried out at a temperature greater than T_m2 and less than T_m1.

12. The assay of claim 9 wherein the at least one step comprises step (b).

13. A solution phase sandwich hybridization assay for detecting the presence of a nucleic acid analyte in a sample, comprising:

(a) providing a solid support having capture probes thereon, capture extender molecules having a first segment C-1 capable of hybridizing to a nucleic acid sequence in the analyte and a second segment C-2 capable of hybridizing to a nucleic acid sequence in the capture probes, label extender molecules having a first segment L-1 capable of hybridizing to a nucleic acid sequence in the analyte and a second segment L-2 capable of hybridizing to a nucleic acid sequence P-1 in a preamplifier probe, a preamplifier probe having a nucleic acid sequence P-1 and capable of binding a plurality of amplification multimers through nucleic acid sequences P-2, amplification multimers containing a nucleic acid sequence M-1 capable of hybridizing to P-2 and a plurality of identical oligonucleotide subunits containing nucleic acid sequences M-2 capable of hybridizing to label probes, and label probes containing a sequence L-3 which is capable of hybridizing to M-2 and which, directly or indirectly, gives rise to a detectable signal;

(b) incubating the nucleic acid analyte under hybridization conditions with the capture extender molecules at least two of which must hybridize to the analyte in order for the assay to result in a detectable signal, label extender molecules, and the capture probes on the solid support, simultaneously or sequentially in any order, to form a support-bound, first hybrid complex;

(c) thereafter optionally separating materials not bound to the solid support;

(d) contacting the support-bound, first hybrid complex under hybridization conditions with the preamplifier probe and the amplification multimer, to produce a support-bound, second hybrid complex;

(e) thereafter optionally separating materials not bound to the solid support;

(f) contacting the support-bound, second hybrid complex with the label probes under hybridizing conditions, to produce a labeled, support-bound, third hybrid complex;

(g) thereafter separating materials not bound to the solid support;

(h) detecting the presence of label in the support-bound, third hybrid complex; and

(i) correlating the presence of the label in the support-bound, third hybrid complex with the presence of the nucleic acid analyte in the sample,

wherein the melt temperature T_m1 at which the nucleic acid analyte dissociates from the capture probe in the hybrid complex formed between the capture probe, capture extender molecules and nucleic acid analyte is at least about 5°

C. greater than the melt temperature T_m2 of hybrid complexes formed between the capture probe and capture extender molecules.

14. A solution phase sandwich hybridization assay for detecting the presence of a nucleic acid analyte in a sample, comprising:

(a) providing a solid support having capture probes thereon, a first capture extender molecule comprising a polynucleotide containing an analyte-binding segment capable of hybridizing to a nucleic acid sequence present in the analyte and a support-binding segment capable of hybridizing to a nucleic acid sequence present within the capture probes, a distinct second capture extender molecule comprising a polynucleotide containing an analyte-binding segment capable of hybridizing to a nucleic acid sequence present in the analyte and a support-binding segment capable of hybridizing to a nucleic acid sequence present within the capture probes, label extender molecules having a first segment L-1 capable of hybridizing to a nucleic acid sequence in the analyte and a second segment L-2, an amplification multimer containing a nucleic acid sequence M-1 capable of hybridizing to L-2 and a plurality of identical oligonucleotide subunits containing nucleic acid sequences M-2, and label probes containing a sequence L-3 which is capable of hybridizing to M-2 and which, directly or indirectly, gives rise to a detectable signal;

(b) incubating the nucleic acid analyte under hybridization conditions with the capture extender molecules, label extender molecules, and the capture probes on the solid support, simultaneously or sequentially in any order, to form a support-bound, first hybrid complex;

(c) thereafter optionally separating materials not bound to the solid support;

(d) contacting the support-bound, first hybrid complex under hybridization conditions with the amplification multimer, to produce a support-bound, second hybrid complex;

(e) thereafter optionally separating materials not bound to the solid support;

(f) contacting the support-bound, second hybrid complex with the label probes under hybridizing conditions, to produce a labeled, support-bound, third hybrid complex;

(g) thereafter separating materials not bound to the solid support;

(h) detecting the presence of label in the support-bound, third hybrid complex; and

(i) correlating the presence of the label in the support-bound, third hybrid complex with the presence of the nucleic acid analyte in the sample,

wherein the capture extender molecules are configured such that the support-bound, second hybrid complex of step (b) will form only when both first and second capture extender molecules have bound to the analyte.

16. The assay of claim 14, wherein the capture probe contains a first capture extender binding sequence capable of hybridizing to the support-binding segment of the first capture extender molecule, and a second capture extender binding sequence capable of hybridizing to the support-binding segment of the second capture extender molecule, such that two capture extender molecules can bind to a single capture probe.

15. A solution phase sandwich hybridization assay for detecting the presence of a nucleic acid analyte in a sample, comprising:

(a) providing a solid support having capture probes thereon, a first capture extender molecule comprising a polynucleotide containing an analyte-binding segment capable of hybridizing to a nucleic acid sequence present in the analyte and a support-binding segment capable of hybridizing to a nucleic acid sequence present within the capture probes, a distinct second capture extender molecule comprising a polynucleotide containing an analyte-binding segment capable of hybridizing to a nucleic acid sequence present in the analyte and a support-binding segment capable of hybridizing to a nucleic acid sequence present within the capture probes, label extender molecules having a first segment L-1 capable of hybridizing to a nucleic acid sequence in the analyte and a second segment L-2 capable of hybridizing to a nucleic acid sequence P-1 in a preamplifier probe, a preamplifier probe having the nucleic acid sequence P-1 and capable of binding a plurality of amplification multimers through nucleic acid sequences P-2, amplification multimers containing a nucleic acid sequence M-1 capable of hybridizing to P-2 and a plurality of identical oligonucleotide subunits containing nucleic acid sequences M-2 capable of hybridizing to label probes, and label probes containing a sequence L-3 which is capable of hybridizing to M-2 and which, directly or indirectly, gives rise to a detectable signal;

(b) incubating the nucleic acid analyte under hybridization conditions with the capture extender molecules, label extender molecules, and the capture probes on the solid support, simultaneously or sequentially in any order, to form a support-bound, first hybrid complex;

(c) thereafter optionally separating materials not bound to the solid support;

(d) contacting the support-bound, first hybrid complex under hybridization conditions with the preamplifier probe and the amplification multimer, to produce a support-bound, second hybrid complex;

(e) thereafter optionally separating materials not bound to the solid support;

(f) contacting the support-bound, second hybrid complex with the label probes under hybridizing conditions, to produce a labeled, support-bound, third hybrid complex; and

(h) thereafter separating materials not bound to the solid support;

(i) detecting the presence of label in the support-bound, third hybrid complex; and

(j) correlating the presence of the label in the support-bound, third hybrid complex with the presence of the nucleic acid analyte in the sample,

wherein the capture extender molecules are configured such that the support-bound, second hybrid complex of step (b) will form only when both first and second capture extender molecules have bound to the analyte.

17. The assay of claim 15, wherein the capture probe contains a first capture extender binding sequence capable of hybridizing to the support-binding segment of the first capture extender molecule, and a second capture extender binding sequence capable of hybridizing to the support-binding segment of the second capture extender molecule, such that two capture extender molecules can bind to a single capture probe.

18. A solution phase sandwich hybridization assay for detecting the presence of a nucleic acid analyte in a sample, comprising:

(a) providing a solid support having capture probes thereon, capture extender molecules comprising polynucleotides containing an analyte-binding segment capable of hybridizing to a nucleic acid sequence present in the analyte and a support-binding segment capable of hybridizing to a nucleic acid sequence present within the capture probes, a first label extender molecule having a first segment capable of hybridizing to a nucleic acid sequence in the analyte and a second segment capable of hybridizing to a label probe system, a distinct second label extender molecule having a first segment capable of hybridizing to a nucleic acid sequence in the analyte and a second segment capable of hybridizing to a label probe system, a label probe system comprising nucleic acid sequences capable of hybridizing to the second segments of the first label extender molecule and the second label extender molecule, and which, directly or indirectly, gives rise to a detectable signal;

(b) incubating the nucleic acid analyte under hybridization conditions with the capture extender molecules, label extender molecules and the capture probes on the solid support, simultaneously or sequentially in any order, to form a support-bound hybrid complex;

(c) thereafter optionally separating materials not bound to the solid support;

(d) thereafter contacting the support-bound hybrid complex with the label probe system under hybridizing condition, to produce a labeled, support-bound hybrid complex; and

(e) thereafter separating materials not bound to the solid support;

(f) detecting the presence of label in the labeled support-bound hybrid complex; and

(g) correlating the presence of the label in the support-bound, third hybrid complex with the presence of the nucleic acid analyte in the sample,

wherein the label extender molecules are configured such that the support-bound, third hybrid complex of step (d) will form only when both first and second label extender molecules have bound to the analyte.

19. The assay of claim 18, wherein the label probe system comprises (i) an amplification multimer containing the nucleic acid sequence M-1 and a plurality of identical oligonucleotide subunits containing nucleic acid sequences M-2 capable of hybridizing to label probes, and (ii) label probes containing a nucleic acids sequence L-3 which is capable of hybridizing to M-2 and which, directly or indirectly, gives rise to a detectable signal, and wherein step (d) of the assay comprises the following steps:

(d₁) contacting the support-bound hybrid complex under hybridizing conditions with the amplification multimer, to produce a second support-bound hybrid complex;

(d₂) thereafter optionally separating materials not bound to the solid support; and

(d₃) thereafter contacting the second support-bound hybrid complex with the label probes under hybridization conditions, to produce a labeled support-bound hybrid complex.

20. A solution phase sandwich hybridization assay for detecting the presence of a nucleic acid analyte in a sample, comprising:

(a) providing a solid support having capture probes thereon, capture extender molecules comprising polynucleotides containing an analyte-binding segment capable of hybridizing to a nucleic acid sequence present in the analyte and a support-binding segment capable of hybridizing to a nucleic acid sequence present within the capture probes, a first label extender molecule having a first segment capable of hybridizing to a nucleic acid sequence in the analyte and a second segment capable of hybridizing to a preamplifier probe, a distinct second label extender molecule having a first segment capable of hybridizing to a nucleic acid sequence in the analyte and a second segment capable of hybridizing to a preamplifier probe, preamplifier probes having a first segment capable of hybridizing to a label extender molecule and a second segment capable of binding a plurality of amplification multimers, amplification multimers containing a nucleic acid sequence M-1 capable of hybridizing to the label extender molecules and containing a plurality of identical oligonucleotide subunits containing nucleic acid sequences M-2, and label probes containing a sequence which is capable of hybridizing to M-2 and which, directly or indirectly, gives rise to a detectable signal;

(b) incubating the nucleic acid analyte under hybridization conditions with the capture extender molecules, label extender molecules, and the capture probes on the solid support, simultaneously or sequentially in any order, to form a support-bound, first hybrid complex;

(c) thereafter optionally separating materials not bound to the solid support;

(d) contacting the support-bound, first hybrid complex under hybridization conditions with the preamplifier probe and the amplification multimers, to produce a support-bound, second hybrid complex;

(e) thereafter optionally separating materials not bound to the solid support;

(f) contacting the support-bound, second hybrid complex with the label probes under hybridizing conditions, to produce a labeled, support-bound, third hybrid complex; and

(g) thereafter separating materials not bound to the solid support;

(h) detecting the presence of label in the support-bound, third hybrid complex; and

(i) correlating the presence of the label in the support-bound, third hybrid complex with the presence of the nucleic acid analyte in the sample,

wherein the label extender molecules are configured such that the support-bound, second hybrid complex of step (d) will form only when both first and second label extender molecules have bound to the analyte.

21. A solution phase sandwich hybridization assay for detecting the presence of a nucleic acid analyte in a sample, comprising:

(a) providing a solid support having capture probes thereon, capture extender molecules having a first segment C-1 capable of hybridizing to a nucleic acid sequence in the analyte and a second segment C-2 capable of hybridizing to a nucleic acid sequence in the capture probes, a first label extender molecule having a first segment L-1 capable of hybridizing to a nucleic acid sequence in the analyte and a second segment L-2 capable of hybridizing to a first amplification multimer, a second label extender molecule having a first segment L-1a capable of hybridizing to a nucleic acid sequence in the analyte and a second segment L-2a capable of hybridizing to a second amplification multimer, a first amplification multimer containing a nucleic acid sequence M-1 capable of hybridizing to L-2 and a plurality of identical oligonucleotide subunits containing nucleic acid sequences M-2 capable of hybridizing to label probes, a second amplification multimer containing a nucleic acid sequence M-1a capable of hybridizing to L-2a and a plurality of identical oligonucleotide subunits containing nucleic acid sequences M-2a capable of hybridizing to label probes, and label probes capable of hybridizing to the amplification multimers and which, directly or indirectly, gives rise to a detectable signal;

(b) incubating the nucleic acid analyte under hybridization conditions with the capture extender molecules, label extender molecules and the capture probes on the solid support, simultaneously or sequentially in any order, to form a support-bound, first hybrid complex;

(c) thereafter optionally separating materials not bound to the solid support;

(d) contacting the support-bound, first hybrid complex under hybridization conditions with the amplification multimers, to produce a support-bound, second hybrid complex;

(e) thereafter optionally separating materials not bound to the solid support;

(f) contacting the support-bound, second hybrid complex with the label probes under hybridizing conditions, to produce a labeled, support-bound, third hybrid complex;

(g) thereafter separating materials not bound to the solid support;

(h) detecting the presence of label in the support-bound, third hybrid complex; and

(i) correlating the presence of the label in the support-bound, third hybrid complex with the presence of the nucleic acid analyte in the sample,

wherein the label probes contain a first nucleic acid segment which is capable of hybridizing to the first amplification multimer, and a second nucleic acid segment which is capable of hybridizing to the second amplification multimer, such that the support-bound, third hybrid complex is not formed unless the first and second amplification multimers are linked through the label probes.

22. A kit for detecting a nucleic acid analyte in a sample, comprising:

(a) a solid support having capture probes bound thereto;

(b) a first capture extender molecule capable of hybridizing to the capture probes and to predetermined segments of the nucleic acid analyte;

(c) a distinct second capture extender molecule capable of hybridizing to the capture probes and to segments of the nucleic acid analyte other than those to which the first capture extender molecule binds;

(d) label extender molecules capable of hybridizing to segments of the nucleic acid analyte other than those to which the first and second capture extender molecules bind;

(e) a label probe system comprising a nucleic acid sequence capable of hybridizing to the label extender molecules and which provide, directly or indirectly, a detectable signal,

wherein the capture probes comprises a probe having a first capture extender binding sequence capable of hybridizing to the first capture extender molecule and a second capture extender binding sequence capable of hybridizing to the second capture extender molecule.

23. The kit of claim 22, wherein the label probe system comprises (f) an amplification multimer containing a nucleic acid sequence capable of hybridizing to the label extender molecules and a plurality of identical oligonucleotide subunits;

and

(g) label probes designed to hybridize to the identical oligonucleotide subunits and which provide, directly or indirectly, a detectable signal.

24. A kit for detecting a nucleic acid analyte in a sample, comprising:

(a) a solid support having capture probes bound thereto;

(b) capture extender molecules capable of hybridizing to the capture probes and to predetermined segments of the nucleic acid analyte;

(c) a first label extender molecule capable of hybridizing to predetermined segments of the nucleic acid analyte;

(d) a second label extender molecule capable of hybridizing to segments of the nucleic acid analyte other than those to which the first label extender molecule bind;

(e) an optional preamplifier probe capable of binding to the label extender molecules and to a plurality of amplification multimers;

(f) an amplification multimer containing a nucleic acid sequence capable of hybridizing to the label extender molecules or to the preamplifier probe, and a plurality of identical oligonucleotide subunits; and

(g) label probes designed to hybridize to the identical oligonucleotide subunits and which provide, directly or indirectly, a detectable signal.

25. A kit for detecting a nucleic acid analyte in a sample, comprising:

(a) a solid support having capture probes bound thereto;

(b) capture extender molecules capable of hybridizing to the capture probes and to predetermined segments of the nucleic acid analyte;

(c) a first label extender molecule capable of hybridizing to predetermined segments of the nucleic acid analyte;

(d) a second label extender molecule capable of hybridizing to segments of the nucleic acid analyte other than those to which the first set of label extender molecules bind;

(e) a first amplification multimer containing (i) a nucleic acid sequence capable of hybridizing to the label extender molecule, and (ii) a plurality of identical oligonucleotide subunits;

(f) a second amplification multimer containing (i) a nucleic acid sequence capable of hybridizing to the label extender molecule, and (ii) a plurality of identical oligonucleotide subunits; and

(g) label probes containing a first nucleic acid sequence capable of hybridizing with the oligonucleotide subunits of the first amplification multimer, and a second nucleic acid sequence capable of hybridizing with the oligonucleotide subunits of the second amplification multimer, and which provide, directly or indirectly, a detectable signal.