Nucleic acid amplification method hybridization signal amplification method (HSAM)

• US RE38,442 E1
• Filed: 03/02/2001
• Issued: 02/24/2004
• Est. Priority Date: 06/22/1994
• Status: Expired due to Term

• Current Assignee: Mount Sinai School of Medicine (Sinai Health System)
• Original Assignee: Mount Sinai School of Medicine (Sinai Health System)
• Inventors: Zhang, David Y., Brandwein, Margaret
• Primary Examiner(s): Siew, Jeffrey
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US09/798,641
• Time in Patent Office: 1,089 Days
• Field of Search: 435/6, 435/5, 435/7.1, 435/7.9, 435/91.2, 536/23.1, 536/24.3, 536/24.32, 536/24.33
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• 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 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 1/6865 Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
• CPC Class Codes: G01N 33/536 with immune complex formed in liquid phase

Abstract

An improved method allowing for rapid sensitive and standardized detection of a target nucleic acid from a pathogenic microorganism or virus or normal or abnormal gene in a sample is provided. The method involves hybridizing a target nucleic acid to several non-overlapping oligonucleotide probes that hybridize to adjacent regions in the target nucleic acid, the probes being referred to capture/amplification probes and amplifications probes, respectively, in the presence of paramagnetic beads coated with a ligand binding moiety. Through the binding of a ligand attached to one end of the capture/amplification probe and the specific hybridization of portions of the probes to adjacent sequences in the target nucleic acid, a complex comprising the target nucleic acid, the probes and the paramagnetic beads is formed. The probes may then ligated together to form a contiguous ligated amplification sequence bound to the beads, which complex may be denatured to remove the target nucleic acid and unligated probes. Alternatively, separate capture and amplification probes may be used which form continuous full-length or circular probes, and may be directly detected or amplified using a suitable amplification technique, e.g., PCR, RAM or HSAM for detection. The detection of the ligated amplification sequence, either directly or following amplification of the ligated amplification sequence, indicates the presence of the target nucleic acid in a sample. Methods for the detection of the ligated amplification sequence, including hybridization signal amplification method and ramification- extension amplification method, are also provided.

Claims

1. A method for detecting a target nucleic acid in a sample comprising:

(a) contacting said nucleic acid in said sample in a reaction vessel under conditions that allow nucleic acid hybridization between complementary sequences in nucleic acids with oligonucleotide probes in the presence of a paramagnetic particles coated with a ligand binding moiety, said oligonucleotide probes comprising one or more capture probes, each having a 3′

nucleotide sequence that is neither complementary nor hybridizable to a nucleotide sequence in the target nucleic acid, and a 5′

nucleotide sequence that is complementary and hybridizable to a nucleotide sequence in the target nucleic acid, or a 5′

nucleotide sequence that is neither complementary nor hybridizable to a nucleotide sequence in the target nucleic acid, and a 3′

nucleotide sequence that is complementary and hybridizable to a nucleotide sequence in the target nucleic acid, each capture probe further having a ligand bound to the non-complementary sequence of the probe, wherein said ligand that binds to and an forms affinity pair with said ligand binding moiety coated onto said paramagnetic particles;

, wherein said oligonucleotide probes further comprising comprise a circularizable probe having 3′ and

5′

regions that are complementary to adjacent but noncontiguous sequences in the target nucleic acid, said 3′ and

5′

regions separated by a linker region that is neither complementary nor hybridizable to a nucleotide sequence in the target nucleic acid and wherein said linker region comprises at least one pair of adjacent nucleotide sequences each pair of which is complementary and hybridizable to the 5′ and

3′

nucleotide sequences of a signal probe, such that a complex is formed comprising the target nucleic acid, and the circularizable probe, capture probes and said paramagnetic particles, wherein the capture probes are hybridized to the complementary nucleotide sequences in the target nucleic acid and are bound to the paramagnetic particles through the binding of the ligand on the capture probe to the ligand binding moiety on the paramagnetic particles, and wherein the circularizable probe is bound on its 3′ and

5′

ends to adjacent but noncontiguous sequences in the target nucleic acid;

(b) separating the complex from unbound reactants and washing the complex;

(c) adding a ligating agent that joins the 3′

end and 5′

end of said circularizable probe and adding a multiplicity of circularizable nucleic acid signal probes having 3′ and

5′

nucleotide sequences that are complementary and hybridizable to adjacent regions of the linker region of the circular probe bound to the target, or of other signal probes, and having linker regions comprising at least one pair of adjacent nucleotide sequences that are complementary and hybridizable to the 5′ and

3′

nucleotide sequences of one of the multiplicity of signal probe, such that a cluster of circular molecules is formed on the target nucleic acid;

(d) washing the target bound cluster to remove probes not bound to the target nucleic acid; and

(e) detecting said target bound cluster, wherein the detection thereof indicates the presence of the target nucleic acid in the sample.

9. The method of claim 116 or 17, wherein said ligand is selected from the group consisting of biotin, antigens, haptens, antibodies, heavy metal derivatives, and polynucleotides including poly dG, polydT, polydC, polydA and polyU.

10. The method of claim 116 or 17, wherein said ligand binding moiety is selected from the group consisting of streptavidin, avidin, antibodies, antigens, thio groups and polynucleotides including poly dC, poly dA, poly dG, poly dT and poly U.

11. The method of claim 116 or 17, wherein said ligand is biotin and said ligand binding moiety is streptavidin.

12. The method of claim 1or 17, wherein said ligating agent is a DNA or RNA ligase.

13. The method of claim 116further comprising subjecting thesaid paramagnetic particles to a magnetic field sufficient to prevent loss of the particles from the reaction vessel during the separating and washing steps.

16. The method of claim 1, wherein

(i) the contacting recited in step (a) occurs in the presence of paramagnetic particles coated with a ligand binding moiety, wherein the oligonucleotide probes comprise one or more capture probes each having a 3′ nucleotide sequence that is neither complementary nor hybridizable to a nucleotide sequence in the target nucleic acid, and a 5′

nucleotide sequence that is complementary and hybridizable to a nucleotide sequence in the target nucleic acid, or a 5′

nucleotide sequence that is neither complementary nor hybridizable to a nucleotide sequence in the target nucleic acid, and 3′

nucleotide sequence that is complementary and hybridizable to a nucleotide sequence in the target nucleic acid, each capture probe further having a ligand bound to the non-complementary sequence of the probe, wherein said ligand binds to and forms an affinity pair with the ligand binding moiety; and

(ii) wherein the complex formed in step (a) further includes the capture probes and the paramagnetic particles.

2. A method for in situ detection of a target nucleic acid in a sample comprising the steps of:

(a) preparing a tissue sample from a histological specimen to be analyzed for the presence of the target nucleic acid;

(b) washing said tissue sample;

(c) adding a circularizable nucleic acid probe having 3′ and

5′

regions that are complementary to adjacent but noncontiguous sequences in the target nucleic acid, said 3′ and

5′

regions separated by a linker region that is neither complementary nor hybridizable to a nucleotide sequence in the target nucleic acid wherein said linker region is labeled with a ligand, such that a complex is formed comprising the target nucleic acid and circularizable probe;

(d) ligating the 3′ and

5′

ends of said circularizable probe with a ligating agent that joins nucleotide sequences such that a circular probe is formed;

(e) washing the complex;

(f) adding a ligand binding moiety that binds to and forms an affinity pair with said ligand and an oligonucleotide signal probe internally labeled with said ligand whereby said ligand binding moiety binds to said ligand on said circular probe and also to said ligand on said oligonucleotide signal probe to form a labeled complex;

(g) washing said labeled complex to remove unbound signal probe and ligand binding moieties; and

(h) detecting said labeled complex, wherein the detection thereof indicates the presence of the target nucleic acid in the sample.

4. The method of claim 2 wherein said ligand is selected from the group consisting of biotin, antigens, haptens, antibodies, heavy metal derivatives, and polynucleotides including poly dG, polydT, polydC, polydA and polyU.

5. The method of claim 2 wherein said ligand binding moiety is selected from the group consisting of streptavidin, avid, antibodies, antigens, thio groups and polynucleotides including poly dC, poly dA, poly dG, poly dT and poly U.

6. The method of claim 2 wherein said ligand is biotin and said ligand binding moiety is streptavidin.

7. The method of claim 2 wherein said ligating agent is a DNA or RNA ligase.

3. A method for in situ detection of a target nucleic acid in a sample comprising the steps of:

(a) preparing a tissue sample from a histological specimen to be analyzed for the presence of the target nucleic acid;

(b) washing said tissue sample;

(c) adding a circularizable nucleic acid probe having 3′ and

5′

regions that are complementary to adjacent but noncontiguous sequences in the target nucleic acid, said 3′ and

5′

regions separated by a linker region that is neither complementary nor hybridizable to a nucleotide sequence in the target nucleic acid and wherein said linker region comprises at least one pair of adjacent nucleotide sequences each pair of which is complementary and hybridizable to the 5′ and

3′

nucleotide sequences of a signal probe, such that a complex is formed comprising the target nucleic acid and circularizable probe, wherein the circularizable probe is bound on its 3′ and

5′

ends to adjacent but noncontiguous sequences in the target nucleic acid;

(d) adding a ligating agent that joins nucleotides sequences and adding a multiplicity of signal probes having 3′ and

5′

nucleotide sequences that are complementary and hybridizable to adjacent regions of the linker region of the circular probe bound to the target, or of other signal probes, and having linker regions comprising at least one pair of adjacent nucleotide sequences that are complementary and hybridizable to the 5′ and

3′

nucleotide sequences of one of the multiplicity of signal probes, such that a cluster of circular molecules is formed on the target nucleic acid;

(e) washing the target bound cluster to remove probes not bound to the target nucleic acid; and

(f) detecting said target bound cluster, wherein the detection thereof indicates the presence of the target nucleic acid in the sample.

8. The method of claim 3 wherein said ligating agent is a DNA or RNA ligase.

14. A method for detecting an antigen in a sample comprising:

(a) contacting said antigen in said sample with an antibody to said antigen wherein said antibody is labeled with a ligand under conditions whereby an antigen/antibody complex is formed;

(b) washing said complex to remove unbound antibody;

(c) adding ligand-binding molecules that are at least divalent for said ligand and a ligand-labeled nucleic acid probe labeled with at least two molecules of ligand under conditions whereby ligand-binding molecules bind to said ligand-labeled antibody and said ligand-labeled nucleic acid probe such that a complex of antigen, ligand-labeled antibody, ligand-binding molecules, and ligand-labeled nucleic acid probes is formed; and

(d) detecting said complex in the absence of nucleic acid amplification, wherein detection thereof is indicative of the presence of said antigen in said sample.

15. A method for detecting an antibody in a sample comprising:

(a) contacting said antibody in said sample with an antigen to said antibody wherein said antigen is labeled with a ligand under conditions whereby an antigen/antibody complex is formed;

(b) washing said complex to remove unbound antigen;

(c) adding ligand-binding molecules that are at least divalent for said ligand and a ligand-labeled nucleic acid probe labeled with at least two molecules of ligand under conditions whereby ligand-binding molecules bind to said ligand-labeled antigen and said ligand-labeled nucleic acid probe such that a complex of antibody, ligand-labeled antigen, ligand-binding molecules, and ligand-labeled nucleic acid probes is formed; and

(d) detecting said complex in the absence of nucleic acid amplification, wherein detection thereof is indicative of the presence of said antibody in said sample.

17. A method for detecting a target nucleic acid in a sample comprising:

(a) contacting the nucleic acid in the sample under conditions that allow nucleic acid hybridization between complementary sequences in nucleic acids with oligonucleotide probes, wherein said oligonucleotide probes comprise circularizable probes having 3′ and

5′

regions that are complementary to adjacent but noncontiguous sequences in the target nucleic acid, said 3′ and

5′

regions separated by a linker region that is neither complementary nor hybridizable to a nucleotide sequence in the target nucleic acid and wherein said linker region is labeled with a ligand, such that a complex is formed comprising the target nucleic acid and the circularizable probe;

(b) ligating the 3′ and

5′

end of the circularizable probe with a ligating agent such that circular probe is formed;

(c) washing the complex;

(d) adding a ligand binding moiety that binds to and forms an affinity pair with the ligand and an oligonucleotide signal probe internally labeled with the ligand whereby the ligand binding moiety binds to the ligand on the circular probe and also to the ligand on the oligonucleotide signal probe to form a labeled complex;

(e) washing the labeled complex to remove the unbound signal probe and the ligand binding moieties; and

(f) detecting the labeled complex, wherein the detection thereof indicates the presence of the target nucleic acid in the sample.