Dynamic range methods
Methods for detecting and quantifying an analyte employ a pair of proximity probes, each comprising a proteinaceous target-binding domain coupled to a nucleic acid domain (NAD), which NADs interact when the proximity probes have bound in proximity to their respective target; and a set of markers, wherein each marker is a nucleic acid molecule comprising a binding domain and a reporter domain giving a detectable signal, can interact with said NADs to form a nucleic acid molecule from which a detectable signal is generated, or with a nucleic acid molecule generated by interaction of said NADs, cannot interact with said NADs simultaneously with another marker in the set, generates a signal that is distinguishable from another marker signal, and is present in an amount capable of detecting analyte at a range of concentrations differing from the range of concentrations detectable by other markers.
1. A method of detecting a peptide target or protein target in a sample, said method comprising:
(A) providing multiple proximity probes, wherein each of the multiple proximity probes comprises a proteinaceous binding domain and a nucleic acid domain, and said proteinaceous binding domain is coupled to the nucleic acid domain;
(B) contacting said sample with said multiple proximity probes and allowing each of the multiple proximity probes to bind, via its proteinaceous binding domain, to multiple binding sites on the target, thereby producing a binding complex comprising said target and said multiple proximity probes if the target is in the sample, wherein said multiple proximity probes in the binding complex are in proximity to one another;
(C) providing a set of at least two markers comprising a first marker and a second marker, and optionally one or more subsequent markers;
(i) wherein each marker in the set comprises one or more nucleic acid molecules comprising a binding domain and a reporter domain,
(ii) wherein the reporter domain of each marker in the set includes a detectable label and the detectable label of each marker in the set is structurally different and detectably different from the detectable label of each of the other markers in the set,
(iii) wherein the nucleic acid domain of each of at least two of the multiple proximity probes in the binding complex (a) together provide a marker binding site, or (b) generate a marker binding site by interaction of the nucleic acid domain of each of the at least two of the multiple proximity probes in the binding complex directly or indirectly with one another,
(iv) wherein each marker in the set is capable of interacting with the marker binding site such that the first marker is capable of interacting with the marker binding site to form a first interaction product comprising the detectable label of the first marker, the second marker is capable of interacting with the marker binding site to form a second interaction product comprising the detectable label of the second marker, and each of the subsequent markers in the set is capable of interacting with the marker binding site to form a subsequent interaction product comprising the detectable label if the target is in the sample,
(v) wherein all of the markers in the set compete to interact with the marker binding site if the target is in the sample,
(vi) wherein the amount of each marker in the set is different, and
(vii) wherein the first marker in the set is in an amount capable of detecting the target in a first concentration range if the target is in the sample, the second marker in the set is in an amount capable of detecting the target in a second concentration range if the target is in the sample, and the first concentration range and the second concentration range are different;
(D) after step (C), adding said set of at least two markers to the sample and allowing said markers in the set to compete with each other for interaction with the marker binding site on the binding complex, thereby forming one or more of the first interaction product, the second interaction product, and the subsequent interaction product if the target is in the sample;
(E) if the target is in the sample, separating the one or more of the first interaction product, the second interaction product, and the subsequent interaction product from the set of at least two markers which are not contained in the one or more of the first interaction product, the second interaction product, and the subsequent interaction product; and
(F) detecting the detectable label in the one or more of the first interaction product, the second interaction product, and the subsequent interaction product, wherein the presence of the detectable label in the one or more of the first interaction product, the second interaction product, and the subsequent interaction product indicates the presence of the target in the sample.
2. The method of claim 1 , wherein (i) said markers in the set are present in a pre-defined ratio; and/or (ii) the binding domain of each of said markers is capable of binding directly or indirectly to the marker binding site; and/or (iii) the binding domain of each marker in the set has the same or substantially the same binding affinity or specificity for the marker binding site.
3. The method of claim 2 , wherein each marker in the set comprises a splint oligonucleotide and a gap oligonucleotide capable of hybridizing to the splint oligonucleotide, the interaction in step (D) comprises hybridizing the splint oligonucleotide to the marker binding site and hybridizing the gap oligonucleotide to the splint oligonucleotide such that the gap oligonucleotide is located between the nucleic acid domain of one of the proximity probes and the nucleic acid domain of another of the proximity probes on the splint oligonucleotide, and ligating the nucleic acid domain of one of the proximity probes, the gap oligonucleotide, and the nucleic acid domain of another of the proximity probes on the splint oligonucleotide together.
4. The method of claim 2 , wherein the binding domain of each marker in the set is the same.
5. The method of claim 1 , wherein (i) [the nucleic acid domains of the proximity probes in the bound multiple proximity probes interact by ligation to each other to generate] the marker binding site is generated by ligating the nucleic acid domain of each of the multiple proximity probes using a proximity ligation assay; or (ii) [the nucleic acid domains of the proximity probes in the bound multiple proximity probes interact by hybridisation to each other and extension of one or more of said domains to generate] the marker binding site is generated by a proximity extension assay.
6. The method of claim 1 , wherein, in each marker of the set, the binding domain and the reporter domain form two parts of a single nucleic acid molecule.
7. The method of claim 6 , wherein (i) the markers in the set are padlock probes, being circularisable oligonucleotides in which the binding domain of each marker in the set is separated into two parts, where the first part of the two parts is at the 5′ end of each of the oligonucleotides and the second part of the two parts is at the 3′ end of each of the oligonucleotides; or (ii) the markers in the set are circular oligonucleotides.
8. The method of claim 7 , wherein, for each marker in the set which interacts with the marker binding site, the interaction in step (D) comprises hybridization of the two parts of each marker in the set to the marker binding site such that the two parts of each marker in the set are brought into juxtaposition on the marker binding site after the hybridization, and ligating the two parts of each marker on the marker binding site to circularize each marker in the set, wherein the one or more of the first interaction product, the second interaction product, and the subsequent interaction product comprise a circular oligonucleotide including the detectable label.
9. The method of claim 7 , wherein the padlock probes hybridize to the marker binding site.
10. The method of claim 7 , wherein each of the circular or circularisable oligonucleotides comprises (i) a common nucleotide sequence capable of hybridising to the marker binding site, and (ii) the detectable label, wherein the detectable label comprises a detectable nucleotide sequence.
11. The method of claim 7 , wherein said markers in the set are circular oligonucleotides and the interaction in step (D) comprises binding of one or more of the markers in the set to the marker binding site, wherein the nucleic acid domain of one of the proximity probes in one or more of the first interaction product, the second interaction product, and the subsequent interaction product can serve as a primer for priming rolling circle amplification of the markers on the marker binding site.
12. The method of claim 1 , wherein the markers are padlock probes, each of the padlock probes comprises two or more oligonucleotides, and the interaction in step (D) comprises hybridization of the two or more oligonucleotides to the marker binding site such that the oligonucleotides are brought into juxtaposition on the marker binding site after said hybridization to form hybridized two or more oligonucleotides and ligating the hybridized two or more oligonucleotides together, wherein the one or more of the first interaction product, the second interaction product, and the subsequent interaction product comprise a circular oligonucleotide including the detectable label.
13. The method of claim 1 , wherein the detectable label of each marker in the set is a detectable nucleic acid molecule and is amplified.
14. The method of claim 13 , wherein the detectable nucleic acid molecule is amplified by rolling circle amplification or polymerase chain reaction.
15. The method of claim 1 , wherein the detectable label is selected from nucleic acid molecules, fluorophores, fluorescent proteins, radioactive isotopes, colorimetric detection labels, magnetic particles, particles of carbon, silver or gold, quantum dots and enzymes.
16. The method of claim 1 , wherein the detectable label of each marker in the set comprises a nucleic acid and wherein said detecting the detectable label comprises amplifying the detectable label, producing an amplified detectable label, and measuring the amplified detectable label using digital PCR.
17. The method of claim 1 , wherein:
in step (B), the multiple proximity probes comprise a pair of proximity probes;
in step (C), each marker in the set comprises a padlock probe comprising two oligonucleotides, wherein each of the oligonucleotides is capable of hybridizing to the marker binding site, the first oligonucleotide of the two oligonucleotides being common in each marker of the set and the second oligonucleotide of the two oligonucleotides being different in each marker of the set, and the second oligonucleotide of the two oligonucleotides comprising the binding domain separated into two parts, each of the two parts at each end of the second oligonucleotide, and the reporter domain;
step (D) comprises hybridizing said padlock probe of each marker of the set to bind to the marker binding site such that the oligonucleotides of said padlock probe are brought into juxtaposition on the marker binding site after said hybridization, and ligating the oligonucleotides of said padlock probe of each marker of the set together to circularize said padlock probe of each marker of the set, wherein the one or more of the first interaction product, the second interaction product, and the subsequent interaction product comprises a circular oligonucleotide including the detectable label; and
in step (F), the circular oligonucleotide of the one or more of the first interaction product, the second interaction product, and the subsequent interaction product is further subjected to rolling circle amplification (RCA) primed by the nucleic acid domain of one of the proximity probes in the binding complex to form a RCA product.
18. The method of claim 1 , wherein the detectable label of each marker in the set is a detectable nucleic acid.