SOLID PHASE NUCLEIC ACID TARGET CAPTURE AND REPLICATION USING STRAND DISPLACING POLYMERASES

Abstract

A method and kit for the capture and purification of specific nucleic acids from a sample with affinity capture probes on a solid support and for the replication of said nucleic acids with a strand displacing polymerase, whereby a second primer complementary to a sequence in each of the target nucleic acids distinct from that bound by capture probes is also bound to the nucleic acid targets, and extension of one of the primers on each target effects the separation of the copied nucleic acid strands from the solid support. Incorporation of universal nucleic acid sequences during their replication enables the simultaneous and highly specific amplification of multiple nucleic acid target sequences with minimal production of artifacts.

Claims

1. A method for the purification and replication of target nucleic acids (1) from a sample, comprising: a) contacting said sample with reverse primer/capture probe oligonucleotides (2) having a 5′ tail comprising a sequence that can be used for amplification and incubating to anneal the reverse primer/capture probe oligonucleotides (2) that hybridize to target-specific sequences (17) on the target nucleic acids (1), whereby said incubating is performed in a buffer solution and not on a solid support (4); b) contacting said sample with reverse strand displacement primer oligonucleotides (3) and incubating to anneal the reverse strand displacement primer oligonucleotides (3) that hybridize to target-specific sequences (18) on the target nucleic acids (1) that are located on a 3′ side of the sequences (17) to which the reverse primer/capture probe oligonucleotides (2) hybridize to form soluble complexes of reverse primer/capture probe oligonucleotides (2) and reverse strand displacement primer oligonucleotides (3) bound to the target nucleic acids (1), whereby said incubating is performed in a buffer solution and not on the solid support (4); c) binding the formed soluble complexes previously formed in said incubating steps on a solid support (4) by binding a ligand on the reverse primer/capture probe oligonucleotides (2) to the solid support (4) and washing away excess reverse primer/capture probe oligonucleotides (2) and reverse strand displacement primer oligonucleotides (3) that are not bound to the target nucleic acids (1) and sample components other than the complexes; d) after the step of washing away excess reverse primer/capture probe oligonucleotides (2) and reverse strand displacement primer oligonucleotides (3) and sample components other than the complexes, extending the reverse primer/capture probe oligonucleotides (2) with 5′ tail on the target nucleic acids (1) to form strands (5), and extending the reverse strand displacement primer oligonucleotides (3) on the target nucleic acids (1) with a nucleic acid strand displacing polymerase, wherein extension of the reverse strand displacement primer oligonucleotides (3) displaces, from the target nucleic acids (1), the extended reverse primer/capture probe oligonucleotides (2) to give single-stranded copies (5), which are copies of the target nucleic acids (1) and which are attached to the solid support (4); e) washing the double-stranded copies (6) resulting from the extension of reverse strand displacement primer oligonucleotides (3) that are not attached to the solid support (4) from the solid support (4); f) contacting a medium containing the single stranded copies bound to the solid support (4) with a solution containing a mixture of forward primers (7) with a 5′ tail comprising a sequence that can be used for amplification, that hybridize to target-specific sequences (20) on the single stranded copies (5), and forward strand displacement primers (8) that hybridize to target-specific sequences (19) on the single stranded copies (5), wherein the sequence (19) to which the forward strand displacement primers (8) hybridize is located on the 3′ side of the sequence (20) to which the forward primers (7) with a 5′ tail hybridize on the single stranded copy (5), and incubating to anneal forward primers (7) and forward strand displacement primers (8) to single stranded copies (5) to form complexes and washing away excess forward primers (7) and forward strand displacement primers (8) that are not bound to the single stranded copies (5); g) after washing away the excess forward primers (7) and forward strand displacement primers (8) extending forward primers (7) with tail 5′ and the forward strand displacement primers (8) hybridized on the single stranded copies (5) immobilized on the solid support (4) with a nucleic acid strand displacing polymerase, wherein extension of the strand displacement primers (8) displaces the single-stranded extension products (9) of the forward primers with 5′ tail (7) from the single stranded copies (5) and from the solid support (4); h) recovering the single-stranded extension products (9) in the supernatant solution bathing the solid support (4) said single-stranded extension products (9) containing the tail 5′ tail sequence of the forward primers (7) and the complement of the 5′ tail of the reverse primer/capture probe oligonucleotides (2), and adding them to with an amplification reagent mix; and i) amplifying the extended forward primer strands (9) using one or both of the attached tail 5′ sequences.

2. The method according to claim 1, wherein the reverse primer/capture probe oligonucleotides (2) that hybridize to target-specific sequences (17) on the target nucleic acids (1) and the reverse strand displacement primer oligonucleotides (3) that hybridize to target-specific sequences (18) on the target nucleic acids (1) in a position 3′ to the reverse primer/capture probe oligonucleotides (2) on the target nucleic acids (1) are hybridized simultaneously to the target nucleic acids (1).

3. The method according to claim 1, wherein the reverse primer/capture probe oligonucleotides (2) that hybridize to target-specific sequences (17) on the target nucleic acids (1) and the reverse strand displacement primer oligonucleotides (3) that hybridize to target-specific sequences (18) on the target nucleic acids (1) in a position 3′ to the reverse primer/capture probe oligonucleotides (2) on the target nucleic acids (1) are hybridized separately to the target nucleic acids (1).

4. The method according to claim 1, wherein amplification is effected with the polymerase chain reaction.

5. The method according to claim 1, wherein amplification is effected with the strand displacement reaction.

6. The method according to claim 1, wherein the tail sequences of the tail reverse primers (2) or the tailed forward primers (7) provide a promoter site for subsequent amplification.

7. The method according to claim 1, wherein products of amplification are analyzed by hybridization to probes immobilized on a microarray.

8. The method according to claim 1, wherein products of amplification are analyzed by determining a sequence of the amplification products.

9. The method according to claim 1, wherein the tail sequences of the tail reverse primers (2) or the tailed forward primers (7) contain adapter sequences required for subsequent sequencing reactions or tags to identify specific samples or target nucleic acids (1).

10. A kit comprising oligonucleotide primers and probes, nucleic acid polymerase enzymes, nucleotide triphosphates, solid supports (4), wash solutions and buffer solutions with divalent metal ions for performing any of the methods of claim 1.

11. A method for the purification and replication of target nucleic acids (1) from a sample, comprising: a) contacting said sample with reverse strand displacement primer oligonucleotides (3) and incubating to anneal the reverse strand displacement primer oligonucleotides (3) to target-specific sequences (18) on the target nucleic acids (1) whereby said incubating is performed in a buffer solution and not on a solid support (4); b) contacting said sample with reverse primer/capture probe oligonucleotides (2) having a 5′ tail comprising a sequence that can be used for amplification and incubating to anneal the reverse primer/capture probe oligonucleotides (2) to target-specific sequences (17) on the target nucleic acids (1) that are located on the 5′ side of the sequences (18) to which the reverse strand displacement primer oligonucleotides (3) hybridize to form complexes of reverse primer/capture probe oligonucleotides (2) and reverse strand displacement primer oligonucleotides (3) bound to the target nucleic acids (1); c) purifying the formed complexes on a solid support (4) by capturing the complexes and washing away excess reverse primer/capture probe oligonucleotides (2) and reverse strand displacement primer oligonucleotides (3) that are not bound to the target nucleic acids (1) and sample components other than the complexes; d) after the step of purifying said formed complexes, extending the reverse primer/capture probe oligonucleotides (2) with 5′ tail on the target nucleic acids (1) to form strands (5), and extending the reverse strand displacement primer oligonucleotides (3) on the target nucleic acids (1) with a nucleic acid strand displacing polymerase, wherein extension of the reverse strand displacement primer oligonucleotides (3) displaces, from the target nucleic acids (1), the extended reverse primer/capture probe oligonucleotides (2) to give single-stranded copies (5), which are copies of the target nucleic acids (1) and which are attached to the solid support (4); e) washing the double-stranded copies (6) resulting from the extension of reverse strand displacement primer oligonucleotides (3) that are not attached to the solid support (4) from the solid support (4); f) contacting a medium containing the single stranded copies (5) bound to the solid support (4) with solution containing a mixture of forward primers (7) with a 5′ tail comprising a sequence that can be used for amplification, that hybridize to target-specific sequences (20) on the single stranded copies (5), and forward strand displacement primers (8) that hybridize to target-specific sequences (19) on the single stranded copies (5), wherein the sequence (19) to which the forward strand displacement primers (8) hybridize is located on the 3′ side of the sequences (20) to which the forward primers (7) with a 5′ tail hybridize on the single stranded copies (5), and incubating to anneal forward primers (7) and forward strand displacement primers (8) to single stranded copies (5) to form complexes and washing away excess forward primers (7) and forward strand displacement primers (8) that are not bound to the single stranded copies (5); g) after washing away the excess forward primers (7) and forward strand displacement primers (8) extending forward primers (7) with tail 5′ and the forward strand displacement primers (8) hybridized on the single stranded copies (5) immobilized on the solid support (4) with a nucleic acid strand displacing polymerase, wherein extension of the strand displacement primers (8) displaces the single-stranded extension products (9) of the forward primers (7) with 5′ tail from the single stranded copies (5) and from the solid support (4); h) recovering the single-stranded extension products (9) in the supernatant solution bathing the solid support (4) said single-stranded extension products (9) containing the tail 5′ tail sequence of the forward primers (7) and the complement of the 5′ tail of the reverse primer/capture probe oligonucleotides (2), and adding them to with an amplification reagent mix; and i) amplifying the extended forward primer strands (9) using one or both of the attached tail 5′ sequences.

12. The method according to claim 11, wherein after step (a), steps (b) and (c) are preformed simultaneously.

13. The method according to claim 11, wherein amplification is effected with the polymerase chain reaction.

14. The method according to claim 11, wherein amplification is effected with the strand displacement reaction.

15. The method according to claim 11, wherein the tail sequences of the tail reverse primers (2) or the tailed forward primers (7) provide a promoter site for subsequent amplification.

16. The method according to claim 11, wherein products of amplification are analyzed by hybridization to probes immobilized on a microarray.

17. The method according to claim 11, wherein products of amplification are analyzed by determining a sequence of the amplification products.

18. The method according to claim 11, wherein the tail sequences of the tail reverse primers (2) or the tailed forward primers (7) contain adapter sequences required for subsequent sequencing reactions or tags to identify specific samples or target nucleic acids (1).

19. A kit comprising oligonucleotide primers and probes, nucleic acid polymerase enzymes, nucleotide triphosphates, solid supports (4), wash solutions and buffer solutions with divalent metal ions for performing any of the methods of claim 11.

20. A method for the purification and replication of target nucleic acids (1) from a sample, comprising: a) contacting said sample with reverse primer/capture probe oligonucleotides (2) having a 5′ tail comprising a sequence that can be used for amplification and incubating to anneal the reverse primer/capture probe oligonucleotides (2) to target-specific sequences (17) on the target nucleic acids (1); b) purifying said target nucleic acids (1) on a solid support (4) by capturing the complexes and washing away and sample components other than the complexes; c) hybridizing reverse strand displacement primer oligonucleotides (3) to target-specific sequences (18) on the target nucleic acids (1) that are located on the 3′ side of the sequences (17) to which the reverse primer/capture probe oligonucleotides (2) hybridize; d) washing the solid support (4) to remove excess strand displacement oligonucleotides (3) that are not bound to the target nucleic acids (1); e) extending the reverse primer/capture probe oligonucleotides (2) with 5′ tail on the target nucleic acids (1) to form strands (5), and extending the reverse strand displacement primer oligonucleotides (3) on the target nucleic acids (1) with a nucleic acid strand displacing polymerase, wherein extension of the reverse strand displacement primer oligonucleotides (3) displaces, from the target nucleic acids (1), the extended reverse primer/capture probe oligonucleotides (2) to give single-stranded copies (5), which are copies of the target nucleic acids (1) and which are attached to the solid support (4); f) washing the double-stranded copies (6) resulting from the extension of reverse strand displacement primer oligonucleotides (3) from the solid support (4); g) contacting a medium containing the single stranded copies (5) bound to the solid support (4) with solution containing a mixture of forward primers (7) with a 5′ tail comprising a sequence that can be used for amplification, that hybridize to target-specific sequences (20) on the single stranded copies (5), and forward strand displacement primers (8) that hybridize to target-specific sequences (19) on the single stranded copies (5), wherein the sequence (19) to which the forward strand displacement primers (8) hybridize is located on the 3′ side of the sequence (20) to which the forward primers (7) with a 5′ tail hybridize on the single stranded copies (5), and incubating to anneal forward primers (7) and forward strand displacement primers (8) to single stranded copies (5) to form complexes and washing away excess forward primers (7) and forward strand displacement primers (8) that are not bound to the single stranded copies (5); h) after washing away the excess forward primers (7) and forward strand displacement primers (8) extending forward primers (7) with tail 5′ and the forward strand displacement primers (8) hybridized on the single stranded copies (5) immobilized on the solid support (4) with a nucleic acid strand displacing polymerase, wherein extension of the strand displacement primers (8) displaces the single-stranded extension products (9) of the forward primers with 5′ tail (7) from the single stranded copies (5) and from the solid support (4); i) recovering the single-stranded extension products (9) in the supernatant solution bathing the solid support (4) said single-stranded extension products (9) containing the tail 5′ tail sequence of the forward primers (7) and the complement of the 5′ tail of the reverse primer/capture probe oligonucleotides (2), and adding them to with an amplification reagent mix; and j) amplifying the extended forward primer strands (9) using one or both of the attached tail 5′ sequences.

21. The method according to claim 20, wherein steps (a) and (b) are performed simultaneously.

22. The method according to claim 20, wherein amplification is effected with the polymerase chain reaction.

23. The method according to claim 20, wherein amplification is effected with the strand displacement reaction.

24. The method according to claim 20, wherein the tail sequences of the tail reverse primers (2) or the tailed forward primers (7) provide a promoter site for subsequent amplification.

25. The method according to claim 20, wherein products of amplification are analyzed by hybridization to probes immobilized on a microarray.

26. The method according to claim 20, wherein products of amplification are analyzed by determining a sequence of the amplification products.

27. The method according to claim 20, wherein the tail sequences of the tail reverse primers (2) or the tailed forward primers (7) contain adapter sequences required for subsequent sequencing reactions or tags to identify specific samples or target nucleic acids (1).

28. A kit comprising oligonucleotide primers and probes, nucleic acid polymerase enzymes, nucleotide triphosphates, solid supports (4), wash solutions and buffer solutions with divalent metal ions for performing any of the methods of claim 20.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0052] Embodiments will now be described, by way of example only, with reference to the drawings, in which:

[0053] FIG. 1 is a diagram illustrating an embodiment of the present disclosure in which two strand displacement steps are utilized to produce single stranded copies of target sequences with incorporated universal priming sequences at both ends of each copy and to separate them from a solid support for subsequent processing.

[0054] FIG. 2 is a diagram illustrating an embodiment of the present disclosure in which one strand displacement step is utilized to produce single stranded copies of target sequences with an incorporated universal priming sequence at one end of each copy and separate them from a solid support for subsequent processing.

[0055] FIG. 3 presents results of an experiment in which the method disclosed herein was used to detect small quantities of three synthetic RNA molecules.

[0056] FIG. 4 presents results of an experiment in which the method disclosed herein was used to detect small quantities of HIV RNA.

[0057] FIG. 5 presents results of an experiment in which the method disclosed herein was used to detect small amounts (33 to 300 pg) of human messenger RNA from cultured breast cancer cells.

[0058] FIG. 6 presents results of an experiment in which the method disclosed herein was used to detect messenger RNA from small numbers of breast cancer cells isolated from blood. Specifically, signal intensities for four genes, using log10 scale. Six replicates of three sample types: control harvested blood cells (least dense hatching), harvested blood cells with 10 SKBR3 cells (more dense hatching) and harvested blood cells with 100 SKBR3 cells (most dense hatching). The solid bars indicate the means of replicates.

[0059] FIG. 7 presents results of an experiment in which the method disclosed herein was used to quantify small amounts (0.05 to 500 pg) of human messenger RNA from cultured breast cancer cells.

DETAILED DESCRIPTION

[0060] Various embodiments and aspects of the disclosure will be described with reference to details discussed below. The following description and drawings are illustrative of the disclosure and are not to be construed as limiting the disclosure.

[0061] Numerous specific details are described to provide a thorough understanding of various embodiments of the present disclosure. However, in certain instances, well-known or conventional details are not described in order to provide a concise discussion of embodiments of the present disclosure.

[0062] As used herein, the terms, “comprises” and “comprising” are to be construed as being inclusive and open ended, and not exclusive. Specifically, when used in the specification and claims, the terms, “comprises” and “comprising” and variations thereof mean the specified features, steps or components are included. These terms are not to be interpreted to exclude the presence of other features, steps or components.

[0063] As used herein, the term “exemplary” means “serving as an example, instance, or illustration,” and should not be construed as preferred or advantageous over other configurations disclosed herein.

[0064] As used herein, the terms “about” and “approximately” are meant to cover variations that may exist in the upper and lower limits of the ranges of values, such as variations in properties, parameters, and dimensions. In one non-limiting example, the terms “about” and “approximately” mean plus or minus 10 percent or less.

[0065] Unless defined otherwise, all technical and scientific terms used herein are intended to have the same meaning as commonly understood to one of ordinary skill in the art. For example, reference to the 5′ or 3′ end of oligonucleotides or of 5′ tails on oligonucleotides refers to the numbering of the carbon atoms on the sugar moieties making up the backbone of the polymer chains and indicate the directionality of the chains. A preferred embodiment of the present disclosure is illustrated in FIG. 1. Components of the method illustrated in are identified as follows:

[0066] (1)—Target nucleic acid to be purified and amplified

[0067] (2)—Reverse primer/capture probe oligonucleotide which is both a reverse primer and a capture probe with tail 5′ which includes a ligand for immobilization

[0068] (3)—Reverse strand displacement primer oligonucleotide

[0069] (4)—Solid support with ligand binding agent

[0070] (5)—Single-stranded DNA copy immobilized on the solid support

[0071] (6)—Displaced extension product/target hybrid

[0072] (7)—Forward primer with 5′ tail

[0073] (8)—Forward strand displacement primer

[0074] (9)—Displaced DNA copy with forward and reverse tail sequences

[0075] (10)—Double stranded DNA remaining bound to the solid support

[0076] (17)—A target-specific sequence on the target nucleic acid (1) to which a reverse primer/capture probe oligonucleotide (2) hybridizes

[0077] (18)—A target-specific sequence distinct from the sequence (17) and positioned in the 5′ direction relative to the sequence (17) on the target nucleic acid (1). A reverse strand displacement primer oligonucleotide (3) hybridizes to this sequence.

[0078] (19)—A sequence on the single-stranded DNA copy (5) that is immobilized on the solid support (4)

[0079] (11)—A sequence on the single-stranded DNA copy (5) immobilized on the solid support (4) distinct from the sequence (19)

[0080] (12)—The extension of the forward primer (7) with tail 5′ on the single-stranded DNA copy (5) which includes the complement of the sequence of the reverse primer oligonucleotide capture probe with 5′ tail (2)

[0081] Steps in the method illustrated in FIG. 1 are as follows: [0082] A. Add a mixture of two oligonucleotides (2, 3) for each target nucleic acid (1) to be purified and amplified to the sample lysate and incubate to anneal oligonucleotides (2, 3) to the target nucleic acid (1) to form complexes. [0083] B. Capture the complexes on the solid support (4) by binding the ligand on the reverse primer (2) to solid support (4) and wash away excess oligonucleotides (2, 3) and sample components other than the target sequences. The binding of the ligand on the reverse primer (2) to the solid support (4) may occur spontaneously due to inherent affinity between the ligand on reverse primer (2) and a chemical entity previously immobilized on the solid support (4)—e.g., biotin on the oligonucleotide and streptavidin on the solid support (4). Alternatively, the reverse primer (2) may be previously attached to the solid support (4) by covalent or non-covalent means. It will be appreciated by those skilled in the art that this capture could be done either way. [0084] C. Extend the reverse primer (2) with 5′ tail on the target nucleic acid (1) to form strand (5), and extend the reverse strand displacement primer (3) on the target nucleic acid (1) with a strand displacing polymerase. The strand displacing polymerase accomplishes this due to its inherent activity. This activity is a property of certain nucleic acid polymerases that are found in nature or in polymerases engineered from them. Extension of the reverse strand displacement primer (3) displaces the extended reverse primer (2) (i.e., strand (5) which is the copy of target (1)) which is attached to the solid support (4) from the target nucleic acid (1). The double stranded extension product/target hybrid (6) is accordingly displaced from the solid support (4), and it is washed away after the polymerase reaction. The double stranded extension product/target hybrid (6) consists of the target nucleic acid (1) and the extension of oligonucleotide primer (3) on the target nucleic acid (1). One of the two strands is the target (1), and the other strand (5) is the copy of the target (1) due to the extension of primer (3). [0085] D. Anneal the forward primer (7) with tail 5′ and the forward strand displacement primer (8) to the single stranded copy of the target nucleic acid (5) immobilized on the solid support (4), and wash away the excess oligonucleotides (7, 8) after annealing. [0086] E. Extend the forward primer (7) with 5′ tail and the forward strand displacement primer (8) on the single stranded DNA copy (5) immobilized on the solid support (4) with a strand displacing polymerase. Extension of the strand displacement primer (8) displaces the extended forward primer strand (9) from the single stranded DNA copy (5). The extended forward primer strand (9), which contains the tail 5′ tail sequence of the forward primer (7) and the complement of the 5′ tail of the reverse primer capture probe (2), is recovered from the medium bathing the solid support (4) and can be amplified using one or both of the attached tail sequences 5′. Strand (9) is shown in FIG. 1 with a 5′ tail at the left side and a 3′ tail on the right side. The 3′ tail on the right side is the complement of the 5′ tail of the primer (2).

[0087] Thus, there is disclosed herein a method for the purification and replication of at least one target nucleic acid (1) from a sample which includes contacting the sample with at least one oligonucleotide capture probe (2) complementary to a sequence (17) in the target nucleic acid (1), purifying the target nucleic acid (1) on a solid support (4), hybridizing a second oligonucleotide (3) to a nucleic acid sequence (18) of the target nucleic acid (1) distinct from the sequence (17) to which the capture probe (2) is bound, and contacting the complex comprised of the target nucleic acid (1) and the two oligonucleotides (2, 3) with a strand displacing nucleic acid polymerase (not shown in FIG. 1), thereby separating a duplex (6) comprised of a newly synthesized strand (19) and its template strand (1) from a separate newly synthesized nucleic acid strand (5) complementary to the template (1).

[0088] The capture probe (2) and second oligonucleotide (3) may be hybridized simultaneously to the target nucleic acid (1). The solid support (4) may be washed to remove the excess of the second oligonucleotide (3) that is not hybridized to the target nucleic acid (1) captured on the solid support (4) before contacting the complex consisting of the target nucleic acid (1), the capture probe (2) and the second oligonucleotide (3) with a nucleic acid polymerase (not shown). The capture probe (2) may be extended on the target nucleic acid sequence (1), and the second oligonucleotide (3) may displace the target nucleic acid (1) from the extension product (5) of the capture probe (2), resulting in a single stranded replica (5) of the target nucleic acid (1) immobilized on the solid support (4). The capture probe (2) may include a tail sequence 5′ of the target-specific sequence complementary to a sequence (17) of the target nucleic acid (1).

[0089] The second oligonucleotide (3) may displace the capture probe (2) from the target nucleic acid (1), resulting in the displacement from the solid support (4) of a double stranded hybrid (6) comprised of the target nucleic acid (1) and a replica (19) of the target (1).

[0090] In the method the third oligonucleotide (7) may be hybridized to a sequence (20) the single stranded replica (5) of the target nucleic acid (1) and may be extended by a nucleic acid polymerase, the polymerase is not shown in FIG. 1. The solid support (4) may be washed to remove the excess of the third oligonucleotide (7) that is not hybridized to the single stranded replica (5) of the target nucleic acid (1) before contacting the complex with the nucleic acid polymerase.

[0091] The third oligonucleotide (7) may include a tail sequence 5′ of the target-specific portion of the oligonucleotide which is the complement of a sequence (20) of the single stranded replica (5) of the target nucleic acid (1). In the method a fourth oligonucleotide (8) may be hybridized to a sequence (19) on the single stranded replica (5) of the target nucleic acid (1) that is distinct from the sequence (20) to which the third oligonucleotide (7) is bound, and this fourth oligonucleotide (8) can be extended by a strand displacing nucleic acid polymerase to displace a single stranded nucleic acid molecule (9) consisting of the extension product (21) of the third oligonucleotide (7) from the solid support (4).

[0092] Another embodiment is illustrated in FIG. 2. Components of the method illustrated in are identified as follows:

[0093] 1—Target nucleic acid

[0094] 4—Solid support

[0095] 7—Forward primer with tail 5′

[0096] 11—Reverse primer with tail 5′

[0097] 12—Reverse primer/capture probe with its end 3′ complementary to a target nucleic acid sequence and its tail end 5′ capable of attaching to a solid support matrix (4). The primer/capture probe (12) in FIG. 2 has a different number than the primer/capture probe (2) in FIG. 1, since primer/capture probe (12) in FIG. 2 is positioned to the right of the tailed primer (11) and displaces the extension product of the tailed primer (11) from the solid support (4).

[0098] 13—Double-stranded extension product/target hybrid retained on the solid support (4)

[0099] 14—Single stranded DNA copy displaced from the solid support (4)

[0100] 15—Reverse universal primer

[0101] 16—Forward universal primer

[0102] 22—A target-specific sequence on the target nucleic acid (1) to which a reverse primer (11) hybridizes

[0103] 23—A sequence on the target nucleic acid distinct from the sequence (22) and positioned in the 3′ direction relative to the target-specific sequence (22) on the target nucleic acid (1). This sequence (23) may be a sequence present on more than one target sequence in a sample, e.g., the poly-A site on eukaryotic mRNA.

[0104] 24—A sequence on the single stranded DNA copy (14) displaced from the solid support (4) to which the forward primer (7) with tail 5′ hybridizes

[0105] Steps in the method illustrated in FIG. 2 are as follows: [0106] I. Add a mixture of tailed reverse primers (11) to the sample containing the target (1) (one primer for each target) and anneal them to sequences (22) target nucleic acids (1). [0107] J. Capture the complexes on the solid support (4) with capture probe/primers (12) that hybridize to sequences (23) on the targets in 3′ positions relative to the sequences (22) bound by the tailed reverse primers (11), and wash away the excess primers (11) and sample components other than the target sequences (1). [0108] K. Extend the reverse primers (11) and the capture probe/primers (12) on the target nucleic acid (1) with a strand displacing polymerase (not shown), thereby displacing single-stranded copies (14) of the nucleic acid target (1) from the solid support (4). The target nucleic acid/capture probe/primers hybrid (13) remains on the solid support (4). [0109] L. Add a mixture of target-specific tailed forward primers (7) that hybridize to sequences (24) on the single-stranded copies (14) and two universal primers (15 and 16) to the single-stranded copies (14) of the nucleic acid targets (1) and amplify the extension products (14) of the target nucleic acids (1) with a polymerase reaction.

[0110] The forward target-specific tailed primers (7) in FIG. 2 may be present at a substantially lower concentration than the forward universal primer (16) in FIG. 2. The target-specific 5′ portions of the forward tailed primers (7) in FIG. 2 may also have lower melting temperatures compared to the forward universal primer (16).

[0111] In the embodiments disclosed herein, the displaced single or double stranded replicas of the target nucleic acid sequence (1) and incorporated 5′ tail sequences may be recovered in the solution bathing the solid support (4) without the use of denaturing conditions to disrupt nucleic acid hybrids.

[0112] Further, the displaced single or double stranded replicas of the target nucleic acid sequence and incorporated 5′ tail sequences may be recovered in the solution bathing the solid support (4) without the use of chemical cleavage methods.

[0113] The tail 5′ sequences of the forward and reverse target-specific primers (7 and 2 in FIGS. 1 and 7 and 11 in FIG. 2) may provide priming sites for subsequent amplification. This amplification may be effected with the polymerase chain reaction. Alternatively, the amplification may be effected with the strand displacement amplification reaction.

[0114] The tail sequence may provide a promoter site for subsequent amplification, and this amplification may be effected by transcription mediated amplification or NASBA.

[0115] The products of the amplification may be analyzed by a variety of methods including by hybridization on multiple different probes immobilized on a solid support such as a microarray or on different beads, by real-time PCR, or by determining the complete sequences of the products. For sequencing of the products, the 5′ tails on the primers may contain adapter sequences required for subsequent sequencing reactions or tags to identify specific samples or nucleic acid targets.

[0116] The solid support (4) may be magnetic beads, a membrane or a porous flow-through chip.

[0117] The capture probe/primers (12) hybridized to the sequence (23) may comprise the poly-adenylated sites of messenger RNA. The capture probe/primers (12) hybridized to the sequence (23) comprise target-specific sequences that are different for each target nucleic acid.

[0118] In the present method nucleic acid target sequences may be isolated from crude lysates containing detergent and/or chaotropic agents, so that target nucleic acids may be isolated by the method disclosed herein without prior purification of nucleic acids.

[0119] The method in FIG. 2 is simpler than the method in FIG. 1, but the method in FIG. 1 may be more resistant to the effects of primer-dimers than the method in FIG. 2. The method in FIG. 2 requires fewer oligonucleotides for each target sequence, and it involves fewer steps than the method in FIG. 1. The forward primers in the method in FIG. 1 are hybridized to a single stranded copy of the target nucleic acid while it is immobilized on the solid support, so that the excess forward primers can be washed away before the subsequent polymerase reaction. The forward primers in the method in FIG. 2 are hybridized to the single stranded copy of the target nucleic acid after it has been displaced from the solid support, so that the excess primers cannot be washed away. In this case primer-dimers may form between different gene-specific forward primers. However, the formation of these primer-dimer artifacts will be limited by minimizing their concentration. Furthermore, their amplification will be limited because all of the primer-dimers formed from the forward gene-specific primers will have the same tail sequence on their 5′ ends and the complement of the 5′ tail sequence on their 3′ ends, so they will form hairpin structures and will not be efficiently amplified.

[0120] A kit may be produced comprising reagents for performing the present method.

EXAMPLES

[0121] The method outlined in FIG. 1 was tested with different types of samples including synthetic RNAs (arbitrary random and HIV sequences) and total RNA from breast cancer cells and whole blood. The method of the present disclosure outlined in FIG. 2 was tested with total RNA from breast cancer cells.

Synthetic RNA (Arbitrary Random Sequences & HIV 5′LTR Sequence)

[0122] The method outlined in FIG. 1 was tested with synthetic RNA targets. A pool of three different synthetic RNA targets (˜400 bases each) were spiked into detergent-containing lysis/hybridization buffer and their respective strand displacement primers and biotinylated capture probes containing a universal sequence at the 5′ end were allowed to anneal. The complexes were captured on streptavidin magnetic beads and excess probes and primers were washed away before reverse transcription/strand displacement reaction. After reverse transcription the displaced double stranded RNA:cDNA complexes were washed away, and a second set of primers was added to the extension product of the capture probe to introduce another universal sequence at the 5′ end by a second strand displacement reaction. The supernatant was added to a PCR mix containing universal forward primers and biotinylated universal reverse primers, and the targets were amplified. The biotinylated PCR products were hybridized on flow-through oligonucleotide microarrays (Quinn et al, J Transl. Med. 7:55, 2009), followed by washes, incubation with streptavidin-HRP and further washes. The presence of targets was detected by chemiluminescence. Signals were detected down to 10 femtograms (fg) of for all three synthetic RNA targets that were spiked into the same lysis/hybridization buffer (FIG. 3).

[0123] Similarly, synthetic RNA with HIV 5′LTR sequence (˜600 bases) was used to test the method outlined in FIG. 1. In this experiment, two different sets of biotinylated capture probes and primers targeting two different regions of the HIV sequence were hybridized to the synthetic HIV RNA and processed using the aforementioned method. Signals were detected down to 100 fg for synthetic HIV RNA targets spiked into lysis/hybridization method (FIG. 4).

SKBR3 Breast Cancer Cell Line and Universal Human Reference Total RNA

[0124] Total RNA derived from mammalian SKBR3 breast cancer cell line was used to test the feasibility of multiple target detection with the present method. Universal Human Reference (UHR) total RNA, comprised of RNA derived from 10 different cell lines, was used as control. Several relevant genes associated with breast cancer (ERBB2, EPCAM, KRT9, CCND1) and a housekeeping gene ACTG1 were selected as mRNA targets. Biotinylated capture probes and primers were designed for each of these targets and samples were spiked into detergent-containing lysis/hybridization buffer and processed using method outlined in FIG. 1.

[0125] Different amounts of total RNA from SKBR3 breast cancer cells were tested and signals were detected down to 33.3 pg for housekeeping gene ACTG1 and a subset of the breast cancer genes (FIG. 5). KRT9 was not detected in any of the samples as it is not expressed in this cell line. The housekeeping gene ACTG1 was detected down to 5 pg of UHR total RNA, but none of the breast cancer genes were detected, presumably because they were not expressed in any of the cell lines used to generate this sample.

SKBR3 Breast Cancer Cells Spiked into Blood

[0126] To test the feasibility of measuring levels of mRNA in small numbers of tumour cells harvested from blood, 10 or 100 cells of SKBR3 breast cancer cells were spiked into 10 mL of blood, and tumor cells were harvested from the blood with a device that partially purified tumor cells from blood cells on the basis of the physical characteristics of the cells. Total RNA from the cells were then processed as described above (as outlined in FIG. 1). The harvested cells were predominantly white blood cells, and in some cases only RNA from white blood cells was used as control.

[0127] Six replicates of each sample were tested: blood with no tumor cells, 10 mL of blood with 10 tumor cells, and 10 mL of blood with 100 tumor cells (arranged left to right in each bar plot in FIG. 6). In addition to housekeeping genes, mRNA transcripts of three different genes (ERBB2, EPCAM and CCND1) were detected unambiguously when 100 tumor cells had been spiked into 10 mL of blood. The transcript of the ERBB2 gene was detected when only 10 cells had been spiked into 10 mL of blood at a level about ten-fold lower than when 100 tumor cells had been spiked into the blood. The ERBB2 gene is known to be expressed at a relatively high level in SKBR3 cells.

mRNA Quantification from SKBR3 Breast Cancer Cells

[0128] The method outlined in FIG. 2 was used to capture mRNA from small amounts of total RNA from SKBR3 cancer cells and to amplify and quantify specific genes using flow-through oligonucleotide microarrays. Three different regions of each of eight target genes were simultaneously amplified and quantified using oligonucleotide probe sets specific to each region of the genes. The object of this 24-plex test was to screen different oligonucleotide probe sets to discover those that provided the greatest sensitivity. The results for one probe set for each of the eight genes are presented in FIG. 7. The signal intensities depended on the amount of total RNA used in the assay. Some gene transcripts were detectable in only 1 picogram (pg) of total RNA (zero on the axis of the log10 plot). The dotted vertical lines indicate the range of total RNA expected from single mammalian cells (see Roozemond, Histochem J. 8:625, 1976; Uemura, Brain Res Bull 5, 117, 1980; Brady, Yeast 17:211, 2000). The results indicate that the method of this disclosure will enable assessment of the expression levels of multiple mRNA transcripts in single cells.