Chimeric primers with hairpin conformations and methods of using same

Abstract

Methods and compositions for nucleic acid amplification, detection, and genotyping techniques are disclosed. In one embodiment, a nucleic acid molecule having a target-specific primer sequence; an anti-tag sequence 5′ of the target-specific primer sequence; a tag sequence 5′ of the anti-tag sequence; and a blocker between the anti-tag sequence and the tag sequence is disclosed. Compositions containing such a nucleic acid molecule and methods of using such a nucleic acid molecule are also disclosed.

Claims

1. A method for detecting a ligation product comprising a first oligonucleotide probe and a second oligonucleotide probe that are ligated together, the method comprising: (a) providing a third oligonucleotide probe comprising: (i) a ligation-product specific sequence, wherein the ligation-product specific sequence is complementary to at least a portion of both the first oligonucleotide probe and the second oligonucleotide probe of the ligation product; (ii) an anti-tag sequence 5′ of the ligation-product specific sequence; (iii) a tag sequence 5′ of the anti-tag sequence; (iv) a blocker between the anti-tag sequence and the tag sequence; and (v) a label; (b) hybridizing the third oligonucleotide probe to the ligation product at a temperature at which at least a portion of both the first oligonucleotide probe and the second oligonucleotide probe of the ligation product hybridizes to the third oligonucleotide probe but at which unligated subunits of the ligation product do not hybridize to the third oligonucleotide probe; and (c) detecting the hybridization of the oligonucleotide probe to the ligation product.

2. The method of claim 1, wherein the label is a Forster Resonance Energy Transfer (FRET) donor or acceptor molecule.

3. The method of claim 1, further comprising immobilizing the third oligonucleotide probe on a solid support.

4. The method of claim 3, wherein the third oligonucleotide probe is immobilized on a solid support by hybridization of the tag sequence to a complementary anti-tag sequence coupled to the solid support.

5. The method of claim 3, wherein the solid support is a bead.

6. A method for detecting a target nucleic acid, the method comprising: a) hybridizing first and second oligonucleotide probes to the target nucleic acid, wherein the first and second oligonucleotide probes are complementary to adjacent regions of the target nucleic acid: b) ligating hybridized first and second oligonucleotide probes to form a ligation product; c) denaturing the ligation product from the target nucleic acid; d) hybridizing the ligation product to a third oligonucleotide probe, the third oligonucleotide probe comprising, in a 3′ to 5′ direction, a hybridizing region that is complementary to at least a portion of the ligation product and a non-hybridizing region that is not complementary to the ligation product, wherein the third oligonucleotide hybridizes to at least a portion of both the first and second oligonucleotide probes; e) extending the ligation product along the third oligonucleotide probe to form an amplicon; and f) detecting the target nucleic acid by detecting the amplicon.

7. The method of claim 6, wherein the non-hybridizing region of the third oligonucleotide probe comprises: (i) an anti-tag sequence 5′ of the hybridizing region that is complementary to at least a portion of the ligation product; (ii) a tag sequence 5′ of the anti-tag sequence; (iii) a blocker between the anti-tag sequence and the tag sequence; and (iv) a label.

8. The method of claim 7 wherein the label is a FRET donor or a FRET acceptor molecule.

9. The method of claim 6 further comprising immobilizing the third oligonucleotide probe on a solid support.

10. The method of claim 7 wherein the third oligonucleotide probe is immobilized on a solid support by hybridizing the tag sequence to a complementary anti-tag sequence coupled to a solid support.

11. The method of claim 9 wherein the solid support is a bead.

12. The method of claim 8 further comprising hybridizing the tag sequence to a complementary FRET probe.

13. The method of claim 2 further comprising hybridizing the tag sequence to a complementary FRET probe.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

(2) FIG. 1A shows an illustration of a hairpin-forming primer and a capture complex. FIG. 1B shows an amplification product in which the amplification opened the structure of the hairpin-forming primer such that the tag region of the primer is able to hybridize to the anti-tag region of the capture complex.

(3) FIG. 2 illustrates how when non-hairpin-forming primers are used, the tag regions of non-extended primers can compete with the tag regions of the extended primers for hybridization to the anti-tag region of the capture complex.

(4) FIGS. 3A and 3B show a hairpin-forming forward primer, a hairpin-forming reverse primer, a labeled universal anti-tag molecule, and a capture complex before the amplification product is produced (FIG. 3A) and after the amplification product is produced (FIG. 3B).

(5) FIGS. 4A to 4E show various configurations of donor and acceptor chromophores in a FRET-based labeling system.

(6) FIGS. 5A to 5B show various configurations of fluorophores and quenchers in a fluorophore/quencher-based labeling system.

(7) FIG. 6 is a graph showing that hairpin primers are more effective in the presence of excess, non-extended primers than are primers that do not form hairpins.

(8) FIG. 7 is a graph showing a comparison of 12-, 14-, and 16-mer stem hairpin primers, and non-hairpin forming primers (TIF), in a PCR with Qiagen HotStart polymerase.

(9) FIG. 8 is a graph showing a comparison of 12-, 14-, and 16-mer stem hairpin primers, and non-hairpin forming primers (TIF), in a PCR with aptaTaq exo(−) polymerase.

(10) FIG. 9 is a graph of the MFI at various PCR cycles in a pseudo real-time PCR with either a hairpin-forming forward primer or a non-hairpin forming forward primer.

(11) FIG. 10 is a graph of the MFI at various PCR cycles in a real-time PCR.

(12) FIG. 11 is a graph representing a dilution series of Neiseria Meningitidis DNA in a real-time quantitative PCR.

(13) FIG. 12 illustrates a real-time PCR assay chemistry. Upon extension of the primers the hairpin portions open up allowing binding to a labeled probe, such that Forster Resonance Energy Transfer (FRET) occurs allowing real-time detection in standard real-time thermal cyclers. An advantage of this chemistry is that the end-users need only design the primers, once they are provided with the validated hairpin sequence, making it very design friendly. No beads are required in this assay.

(14) FIG. 13 illustrates an assay format in which hairpin-forming probes are used with an Invader assay. In the Invader assay the flap portion of the probe (B) is cleaved. Flap portion (B) can then act as a primer that can open up the hairpin sequence by polymerase extension. With the tag region of the hairpin sequence now available for binding it may bind to a labeled probe in a FRET pair for beadless real-time detection or it may bind to a bead for high multiplex detection.

(15) FIG. 14 illustrates an assay that incorporates the use of a ligation mechanism, such that the assay is held at a high enough temperature so that probes A and B cannot hybridize to the hairpin primer/probe unless they are ligated. Once they are ligated, they are of sufficient binding strength to bind to the probe/primer and extend in the presence of a strand displacement polymerase. With the tag region of the hairpin sequence now available for binding it may bind to a labeled probe in a FRET pair for beadless real-time detection or it may bind to a bead for high multiplex detection.

(16) FIG. 15 illustrates an assay that incorporates the use of a mung bean or Si nuclease, which has the ability to cleave single base mismatches. Once the mismatch is cleaved, B can now act as a primer that can displace the hairpin, allowing the tag to be exposed for binding to a probe, which may or may not be attached to a solid surface.

(17) FIG. 16 illustrates an assay in which universal hairpin primers are combined with target specific hairpin primers for use as a nested real-time PCR assay chemistry. Upon extension of the primers the hairpin portions will open up allowing binding to a labeled probe, such that FRET occurs allowing real-time detection in standard real-time thermal cyclers. The advantage of this solution is that the end-users need only design the primers, making it very design friendly. No beads are required in this embodiment.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

I. Nucleic Acids

(18) A. Primers

(19) Primers used in the methods and compositions described herein are designed to provide better nucleic acid amplification and detection than previously available. Assays that use these primers require less optimization of primer concentrations; yield results more quickly; result in lower background and higher specific signal when using DNA binding dyes; provide greater sensitivity; provide a more accurate measure of product/target concentration; and allow higher multiplexing of primer sets. The term “primer,” as used herein, is meant to encompass any nucleic acid that is capable of priming the synthesis of a nascent nucleic acid in a template-dependent process. Primers may be provided in double-stranded and/or single-stranded form, although the single-stranded form is preferred.

(20) In certain embodiments, the methods and compositions disclosed herein employ a hairpin-forming primer that, in addition to the target-specific primer sequence, comprises a tag region and a region that is complimentary to the tag region (anti-tag). The tag and anti-tag regions are separated by a blocker (to prevent polymerase extension into the tag region). These primers may also be referred to as being “chimeric” because they are composed of regions that serve different purposes. Prior to amplification, the tag and anti-tag regions hybridize forming a hairpin structure, thus sequestering the tag region. Once a double-stranded amplification product is formed, the hairpin stem structure is disrupted and the tag region becomes available to bind to another anti-tag probe, such as an anti-tag probe immobilized on a substrate (e.g., a bead). An example in which the hairpin-forming primer is the forward primer is illustrated in FIGS. 1A and 1B. It will be understood by those in the art that in an alternative embodiment the reverse primer could be the hairpin-forming primer.

(21) As shown in FIG. 1A, the hairpin-forming forward primer comprises a target-specific primer region, an anti-tag region, a blocker region (a C18 spacer in this drawing), and a tag region. The anti-tag region of the primer can be the same length as the tag region or it can be a different length. In FIG. 1A the anti-tag region is shorter than its complementary tag region; thus it is referred to as a partial anti-tag region. Prior to polymerase extension and the creation of a double-stranded amplification product, the anti-tag region hybridizes with the tag region to form a hairpin structure, which prevents the tag region on the primer from hybridizing to the anti-tag region that is coupled to the bead. As shown in FIG. 1B, upon extension of the reverse primer, a polymerase with strand displacement activity will disrupt the hairpin stem and stop at the blocker allowing the tag region to hybridize to the anti-tag region on the bead.

(22) Unextended forward primers will be inhibited from binding the immobilized anti-tag probes because of sequestration of the tag regions in a hairpin structure. This is advantageous because the occupation of hybridization sites on capture complexes by unextended primers can limit the availability of capture probes for labeled amplification product and thus decrease assay sensitivity. This is particularly problematic early in an amplification reaction due to the high ratio of unextended primers to extended primers at this stage. This effect is most significant when trying to measure accumulation of amplified product in real-time. As illustrated in FIG. 2A, excess unextended tagged primers that do not form hairpins can compete with the amplification products for hybridization sites on the capture complexes. Moreover, if intercalating or DNA binding dyes are used, they will bind to the double-stranded nucleic acid created by the hybridization of the unextended primer to the probe causing an increase in background signal. In contrast, when using primers with a hairpin structure, the primers and probes will not hybridize until a PCR amplification product is formed.

(23) The use of primers as described above can provide at least the following benefits, as compared to the use of non-hairpin forming primers: (1) requires less optimization of primer concentration; (2) produces faster results because fewer PCR cycles are required to achieve detectable signal; (3) produces lower background and higher specific signal when using DNA binding dyes; (4) provides more sensitive detection in general; and (5) provides a more accurate representation of product/target concentration.

(24) In certain embodiments, both the forward and the reverse primer of a primer pair are hairpin-forming primers. This can be particularly advantageous in multiplexed reactions. In this case, one of the primers of the primer pair comprises universal tag and anti-tag sequences. The tag and anti-tag sequences are “universal” because, while the target-specific primer sequence varies for each different target in the multiplexed amplification reaction, the same (i.e. “universal”) tag and anti-tag sequences are used. An example illustrated in FIGS. 3A and 3B show a hairpin-forming forward primer comprising a target-specific primer region, and complementary anti-tag and tag regions separated by a blocker region. Also, shown is a hairpin-forming reverse primer comprising a target-specific primer region, and universal anti-tag and tag regions separated by a blocker region. The forward primer and reverse primer are designed such that they will prime the synthesis of a double-stranded nucleic acid during the polymerase chain reaction. In a multiplexed reaction, the anti-tag region and tag region of the forward primer are unique for each different forward primer in the reaction. In this way, amplification products of the extended forward primer can be identified by hybridization to a probe sequence. The universal anti-tag region and universal tag region, however, are the same for all reverse primers in the reaction. This allows the labeled, universal anti-tag probe to label all extended, reverse primers in the reaction. This greatly reduces the amount of label (e.g., fluorophore) required. For example, in a 30-plex PCR panel for infectious diseases in which 30 different reverse primers are directly labeled, 6,000 nM of fluorophore would be required, whereas only 200 nM of fluorophore would be required with a labeled, universal anti-tag. This is a 30× reduction in the amount of reporter required. These calculations are based on a 30-plex panel in which a sample is expected to test positive for 0 to 2 infectious agents. The ability to use less label reduces the background of the assay, reduces the amount of reagents needed, and can eliminate the need for a wash step to remove excess label from the assay.

(25) B. Preparation of Nucleic Acids

(26) The nucleic acids disclosed herein may be prepared by any technique known to one of ordinary skill in the art, such as for example, chemical synthesis, enzymatic production, or biological production. Non-limiting examples of a synthetic nucleic acid (e.g., a synthetic oligonucleotide), include a nucleic acid made by in vitro chemical synthesis using phosphotriester, phosphite or phosphoramidite chemistry and solid phase techniques such as described in EP 266,032, incorporated herein by reference, or via deoxynucleoside H-phosphonate intermediates as described by Froehler et al., 1986 and U.S. Pat. No. 5,705,629, each incorporated herein by reference. Various different mechanisms of oligonucleotide synthesis have been disclosed in for example, U.S. Pat. Nos. 4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is incorporated herein by reference.

(27) A non-limiting example of an enzymatically produced nucleic acid include one produced by enzymes in amplification reactions such as PCR™ (see for example, U.S. Pat. Nos. 4,683,202 and 4,682,195, each incorporated herein by reference), or the synthesis of an oligonucleotide described in U.S. Pat. No. 5,645,897, incorporated herein by reference. A non-limiting example of a biologically produced nucleic acid includes a recombinant nucleic acid produced (i.e., replicated) in a living cell, such as a recombinant DNA vector replicated in bacteria (see for example, Sambrook et al., 2001, incorporated herein by reference).

(28) Nucleic acids used as a template for amplification may be isolated from cells, tissues or other samples according to standard methodologies (Sambrook et al., 2001). In certain embodiments, analysis is performed on whole cell or tissue homogenates or biological fluid samples without substantial purification of the template nucleic acid. The nucleic acid may be genomic DNA or fractionated or whole cell RNA. Where RNA is used, it may be desired to first convert the RNA to a complementary DNA (cDNA).

(29) Depending upon the desired application, high stringency hybridization conditions may be selected that will only allow hybridization between sequences that are completely complementary. In other embodiments, hybridization may occur under reduced stringency to allow for amplification of nucleic acids containing one or more mismatches with the primer sequences. Once hybridized, the template-primer complex is contacted with one or more enzymes that facilitate template-dependent nucleic acid synthesis. Multiple rounds of amplification, also referred to as “cycles,” are conducted until a sufficient amount of amplification product is produced.

(30) A reverse transcriptase PCR™ amplification procedure may be performed to reverse transcribe mRNA into cDNA. Methods of RT-PCR are well known in the art (see Sambrook et al., 2001). Alternative methods for RT-PCR utilize thermostable DNA polymerases. These methods are described in WO 90/07641. Polymerase chain reaction methodologies are well known in the art. Representative methods of RT-PCR are described in U.S. Pat. No. 5,882,864.

(31) Another method for amplification is ligase chain reaction (“LCR”), disclosed in European Application No. 320 308, incorporated herein by reference in its entirety. U.S. Pat. No. 4,883,750 describes a method similar to LCR for binding probe pairs to a target sequence. A method based on PCR™ and oligonucleotide ligase assay (OLA), disclosed in U.S. Pat. No. 5,912,148, may also be used.

(32) Alternative methods for amplification of nucleic acid sequences that may be used in the practice of certain aspects of the present invention are disclosed in U.S. Pat. Nos. 5,843,650, 5,846,709, 5,846,783, 5,849,546, 5,849,497, 5,849,547, 5,858,652, 5,866,366, 5,916,776, 5,922,574, 5,928,905, 5,928,906, 5,932,451, 5,935,825, 5,939,291 and 5,942,391, GB Application No. 2 202 328, and in PCT Application No. PCT/US89/01025, each of which is incorporated herein by reference in its entirety.

(33) Qbeta Replicase, described in PCT Application No. PCT/US87/00880, may also be used as an amplification method in the present invention. In this method, a replicative sequence of RNA that has a region complementary to that of a target is added to a sample in the presence of an RNA polymerase. The polymerase will copy the replicative sequence, which may then be detected.

(34) An isothermal amplification method, in which restriction endonucleases and ligases are used to achieve the amplification of target molecules that contain nucleotide 5′-[alpha-thio]-triphosphates in one strand of a restriction site may also be useful in the amplification of nucleic acids in the present invention (Walker et al., 1992). Strand Displacement Amplification (SDA), disclosed in U.S. Pat. No. 5,916,779, is another method of carrying out isothermal amplification of nucleic acids, which involves multiple rounds of strand displacement and synthesis, i.e., nick translation.

(35) Other nucleic acid amplification procedures include transcription-based amplification systems (TAS), including nucleic acid sequence based amplification (NASBA) and 3SR (Kwoh et al., 1989; Gingeras et al., PCT Application WO 88/10315, incorporated herein by reference in their entirety). European Application No. 329 822 disclose a nucleic acid amplification process involving cyclically synthesizing single-stranded RNA (“ssRNA”), ssDNA, and double-stranded DNA (dsDNA).

(36) PCT Application WO 89/06700 (incorporated herein by reference in its entirety) disclose a nucleic acid sequence amplification scheme based on the hybridization of a promoter region/primer sequence to a target single-stranded DNA (“ssDNA”) followed by transcription of many RNA copies of the sequence. This scheme is not cyclic, i.e., new templates are not produced from the resultant RNA transcripts. Other amplification methods include “race” and “one-sided PCR™” (Frohman, 1990; Ohara et al., 1989).

(37) Amplification products may be visualized. If the amplification products are integrally labeled with radio- or fluorescent-labeled nucleotides, the amplification products can be exposed to x-ray film or visualized under the appropriate excitatory spectra. In another approach, a labeled nucleic acid probe is hybridized to the amplification product. The probe may be conjugated to, for example, a chromophore, fluorophore, radiolabel, or conjugated to a binding partner, such as an antibody or biotin.

(38) Various nucleic acid detection methods known in the art are disclosed in U.S. Pat. Nos. 5,840,873, 5,843,640, 5,843,651, 5,846,708, 5,846,717, 5,846,726, 5,846,729, 5,849,487, 5,853,990, 5,853,992, 5,853,993, 5,856,092, 5,861,244, 5,863,732, 5,863,753, 5,866,331, 5,905,024, 5,910,407, 5,912,124, 5,912,145, 5,919,630, 5,925,517, 5,928,862, 5,928,869, 5,929,227, 5,932,413 and 5,935,791, each of which is incorporated herein by reference.

(39) C. Hybridization

(40) Sequence-specific nucleic acid hybridization assays are used for the detection of specific genetic sequences as indicators of genetic anomalies, mutations, and disease propensity. In addition, they are used for the detection of various biological agents and infectious pathogens. As used herein, “hybridization,” “hybridizes” or “capable of hybridizing” is understood to mean the forming of a double or triple stranded molecule or a molecule with partial double or triple stranded nature. The term “anneal” as used herein is synonymous with “hybridize.” The term “hybridization,” “hybridizes” or “capable of hybridizing” encompasses the terms “stringent conditions” or “high stringency” and the terms “low stringency” or “low stringency conditions.”

(41) As used herein “stringent conditions” or “high stringency” are those conditions that allow hybridization between or within one or more nucleic acid strands containing complementary sequences, but preclude hybridization of non-complementary sequences. Such conditions are well known to those of ordinary skill in the art, and are preferred for applications requiring high selectivity. Stringent conditions may comprise low salt and/or high temperature conditions, such as provided by about 0.02 M to about 0.15 M NaCl at temperatures of about 50° C. to about 70° C. It is understood that the temperature and ionic strength of a desired stringency are determined in part by the length of the particular nucleic acids, the length and nucleobase content of the target sequences, the charge composition of the nucleic acids, and to the presence or concentration of formamide, tetramethylammonium chloride or other solvents in a hybridization mixture.

(42) It is also understood that these ranges, compositions and conditions for hybridization are mentioned by way of non-limiting examples only, and that the desired stringency for a particular hybridization reaction is often determined empirically by comparison to one or more positive or negative controls. Non-limiting examples of low stringency conditions include hybridization performed at about 0.15 M to about 0.9 M NaCl at a temperature range of about 20° C. to about 50° C. Of course, it is within the skill of one in the art to further modify the low or high stringency conditions to suit a particular application.

II. Detection of Nucleic Acids

(43) A. Labels

(44) To detect nucleic acids, it will be advantageous to employ nucleic acids in combination with an appropriate detection system. Recognition moieties incorporated into primers, incorporated into the amplified product during amplification, or attached to probes are useful in the identification of nucleic acid molecules. A number of different labels, also referred to as “reporters,” may be used for this purpose such as fluorophores, chromophores, radiophores, enzymatic tags, antibodies, chemi/electroluminescent labels, affinity labels, etc. One of skill in the art will recognize that these and other labels not mentioned herein can be used with success in this invention. Examples of affinity labels include, but are not limited to the following: an antibody, an antibody fragment, a receptor protein, a hormone, biotin, digoxigen, DNP, or any polypeptide/protein molecule that binds to an affinity label.

(45) Examples of enzyme tags include enzymes such as urease, alkaline phosphatase or peroxidase to mention a few. Colorimetric indicator substrates can be employed to provide a detection means visible to the human eye or spectrophotometrically, to identify specific hybridization with complementary nucleic acid-containing samples. All of these examples are generally known in the art and the skilled artisan will recognize that the invention is not limited to the examples described above.

(46) Examples of fluorophores include, a red fluorescent squarine dye such as 2,4-Bis[1,3,3-trimethyl-2-indolinylidenemethyl] cyclobutenediylium-1,3-dioxolate, an infrared dye such as 2,4 Bis [3,3-dimethyl-2-(1H-benz[e]indolinylidenemethyl)] cyclobutenediylium-1,3-dioxolate, or an orange fluorescent squarine dye such as 2,4-Bis [3,5-dimethyl-2-pyrrolyl] cyclobutenediylium-1,3-diololate. Additional non-limiting examples of fluorophores include quantum dots, Alexa Fluor® dyes, AMCA, BODIPY® 630/650, BODIPY® 650/665, BODIPY®-FL, BODIPY®-R6G, BODIPY®-TMR, BODIPY®-TRX, Cascade Blue®, CyDye™, including but not limited to Cy2™, Cy3™, and Cy5™, a DNA intercalating dye, 6-FAM™, Fluorescein, HEX™, 6-JOE, Oregon Green® 488, Oregon Green® 500, Oregon Green® 514, Pacific Blue™, REG, phycobilliproteins including, but not limited to, phycoerythrin and allophycocyanin, Rhodamine Green™, Rhodamine Red™, ROX™ TAMRA™, TET™, Tetramethylrhodamine, or Texas Red®. A signal amplification reagent, such as tyramide (PerkinElmer), may be used to enhance the fluorescence signal.

(47) It is contemplated that FRET-based detection systems may be used with the methods and compositions disclosed herein. FRET (fluorescence resonance energy transfer or Forster resonance energy transfer) makes use of the transfer of energy between donor and acceptor chromophores. In certain embodiments, a chromophore is attached to the hairpin sequence or the blocker and another chromophore is attached to the capture complex, such that upon attachment of the primer to the capture complex, an increase in signal will be observed by virtue of the energy transfer between the donor and acceptor chromophores. Various, non-limiting examples of the configurations of the donor and acceptor chromophores are shown in FIGS. 4A to 4E. FRET-based detection reduce background and therefore allow for higher multiplexing of primer sets compared to free floating chromophore methods, particularly in closed tube and real-time detection systems.

(48) It is also contemplated that fluorophore/quencher-based detection systems may be used with the methods and compositions disclosed herein. When a quencher and fluorophore are in proximity to each other, the quencher quenches the signal produced by the fluorophore. A conformational change in the nucleic acid molecule separates the fluorophore and quencher to allow the fluorophore to emit a fluorescent signal. Various, non-limiting examples of the configurations of the fluorophore and quencher are shown in FIGS. 5A to 5B. Like FRET-based detection, fluorophore/quencher-based detection systems reduce background and therefore allow for higher multiplexing of primer sets compared to free floating fluorophore methods, particularly in closed tube and real-time detection systems.

(49) B. Gene Chips and Microarrays

(50) Certain embodiments of the present invention involve a solid support. The solid support may be a planar array, such as a gene chip or microarray. Arrays and gene chip technology provide a means of rapidly screening a large number of nucleic acid samples for their ability to hybridize to a variety of single stranded oligonucleotide probes immobilized on a solid substrate. These techniques involve quantitative methods for analyzing large numbers of genes rapidly and accurately. The technology capitalizes on the complementary binding properties of single stranded DNA to screen DNA samples by hybridization (Pease et al., 1994; Fodor et al., 1991). Basically, an array or gene chip consists of a solid substrate upon which an array of single stranded DNA or RNA molecules have been attached. For screening, the chip or array is contacted with a single stranded DNA or RNA sample, which is allowed to hybridize under stringent conditions. The chip or array is then scanned to determine which probes have hybridized. The identity of the probes on the chip or planar array is known by its spatial location (i.e., x, y coordinate) on the chip or planar array.

(51) The ability to directly synthesize on or attach polynucleotide probes to solid substrates is well known in the art. See U.S. Pat. Nos. 5,837,832 and 5,837,860, both of which are expressly incorporated by reference. A variety of methods have been utilized to either permanently or removably attach the probes to the substrate. Exemplary methods include: the immobilization of biotinylated nucleic acid molecules to avidin/streptavidin coated supports (Holmstrom, 1993), the direct covalent attachment of short, 5′-phosphorylated primers to chemically modified polystyrene plates (Rasmussen et al., 1991), or the precoating of the polystyrene or glass solid phases with poly-L-Lys or poly L-Lys, Phe, followed by the covalent attachment of either amino- or sulfhydryl-modified oligonucleotides using bi-functional crosslinking reagents (Running et al., 1990; Newton et al., 1993). When immobilized onto a substrate, the probes are stabilized and therefore may be used repeatedly. In general terms, hybridization is performed on an immobilized nucleic acid target or a probe molecule that is attached to a solid surface such as nitrocellulose, nylon membrane or glass. Numerous other matrix materials may be used, including reinforced nitrocellulose membrane, activated quartz, activated glass, polyvinylidene difluoride (PVDF) membrane, polystyrene substrates, polyacrylamide-based substrate, other polymers such as poly(vinyl chloride), poly(methyl methacrylate), poly(dimethyl siloxane), photopolymers (which contain photoreactive species such as nitrenes, carbenes and ketyl radicals capable of forming covalent links with target molecules.

(52) C. Bead Arrays

(53) In some embodiments, the solid support may be a microsphere. Microsphere-based assays may also be analyzed by technologies known to those in the art. For example, in certain embodiments, Luminex xMAP® technology may be used. The Luminex technology allows the detection of nucleic acid products immobilized on fluorescently encoded microspheres. By dyeing microspheres with 10 different intensities of each of two spectrally distinct fluorochromes, 100 fluorescently distinct populations of microspheres are produced. These individual populations (sets) can represent individual detection sequences and the magnitude of hybridization on each set can be detected individually. The magnitude of the hybridization reaction is measured using a third reporter, which is typically a third spectrally distinct fluorophore. The reporter molecule signals the extent of the reaction by attaching to the molecules on the microspheres. As both the microspheres and the reporter molecules are labeled, digital signal processing allows the translation of signals into real-time, quantitative data for each reaction. The Luminex technology is described, for example, in U.S. Pat. Nos. 5,736,330, 5,981,180, and 6,057,107, all of which are specifically incorporated by reference.

(54) Flow cytometry can be used for simultaneous sequence identification and hybridization quantification in microsphere-based assays. Internal dyes in the microspheres are detected by flow cytometry and used to identify the specific nucleic acid sequence to which a microsphere is coupled. The label on the target nucleic acid molecule is also detected by flow cytometry and used to quantify target hybridization to the microsphere. Methods of flow cytometry are well know in the art and are described, for example, in U.S. Patents, all of which are specifically incorporated by reference. 5,981,180, 4,284,412; 4,989,977; 4,498,766; 5,478,722; 4,857,451; 4,774,189; 4,767,206; 4,714,682; 5,160,974; and 4,661,913

(55) Microspheres may also be analyzed on array platforms that image beads and analytes distributed on a substantially planar array. In this way, imaging of bead arrays is similar to the gene chips discussed above. However, in contrast to gene chips where the analyte is identified by its spatial position on the array, bead arrays typically identify the analyte by the encoded microsphere to which it is bound. Examples of commercially available bead array systems include Illumina's BeadXpress™ Reader and BeadStation 500™.

(56) D. Competitive Binding Assays

(57) Embodiments of the present invention may also be used in conjunction with a competitive binding assay format. In general, this format involves a sequence coupled to a solid surface, and a labeled sequence, which is complementary to the sequence coupled to the solid surface, in solution. With this format, the target sequence in the sample being assayed does not need to be labeled. Rather, the target sequence's presence in the sample is detected because it competes with the labeled complement for hybridization with the immobilized detection sequence. Thus, if the target sequence is present in the sample, the signal decreases as compared to a sample lacking the target sequence. The Luminex xMAP technology described above can be used in a competitive binding assay format. The use of the Luminex technology in a competitive binding assay format is described in U.S. Pat. Nos. 5,736,330 and 6,057,107, incorporated herein by reference.

(58) E. Tag Sequences

(59) As mentioned above, various aspects of the present invention use complementary tag sequences (i.e., tags and anti-tags). A number of approaches have been developed that involve the use of oligonucleotide tags attached to a solid support that can be used to specifically hybridize to their tag complements that are coupled to primers, probe sequences, target sequences, etc. The proper selection of non-cross hybridizing tag and anti-tag sequences is useful in assays, particularly assays in a highly parallel hybridization environment, that require stringent non-cross hybridizing behavior.

(60) Certain thermodynamic properties of forming nucleic acid hybrids are considered in the design of tag and anti-tag sequences. The temperature at which oligonucleotides form duplexes with their complementary sequences known as the T.sub.m (the temperature at which 50% of the nucleic acid duplex is dissociated) varies according to a number of sequence dependent properties including the hydrogen bonding energies of the canonical pairs A-T and G-C (reflected in GC or base composition), stacking free energy and, to a lesser extent, nearest neighbor interactions. These energies vary widely among oligonucleotides that are typically used in hybridization assays. For example, hybridization of two probe sequences composed of 24 nucleotides, one with a 40% GC content and the other with a 60% GC content, with its complementary target under standard conditions theoretically may have a 10° C. difference in melting temperature (Mueller et al., 1993). Problems in hybridization occur when the hybrids are allowed to form under hybridization conditions that include a single hybridization temperature that is not optimal for correct hybridization of all oligonucleotide sequences of a set. Mismatch hybridization of non-complementary probes can occur forming duplexes with measurable mismatch stability (Santalucia et al., 1999). Mismatching of duplexes in a particular set of oligonucleotides can occur under hybridization conditions where the mismatch results in a decrease in duplex stability that results in a higher T.sub.m than the least stable correct duplex of that particular set. For example, if hybridization is carried out under conditions that favor the AT-rich perfect match duplex sequence, the possibility exists for hybridizing a GC-rich duplex sequence that contains a mismatched base having a melting temperature that is still above the correctly formed AT-rich duplex. Therefore, design of families of oligonucleotide sequences that can be used in multiplexed hybridization reactions must include consideration for the thermodynamic properties of oligonucleotides and duplex formation that will reduce or eliminate cross hybridization behavior within the designed oligonucleotide set.

(61) There are a number of different approaches for selecting tag and anti-tag sequences for use in multiplexed hybridization assays. The selection of sequences that can be used as zip codes or tags in an addressable array has been described in the patent literature in an approach taken by Brenner and co-workers (U.S. Pat. No. 5,654,413, incorporated herein by reference). Chetverin et al. (WO 93/17126, U.S. Pat. Nos. 6,103,463 and 6,322,971, incorporated herein by reference) discloses sectioned, binary oligonucleotide arrays to sort and survey nucleic acids. These arrays have a constant nucleotide sequence attached to an adjacent variable nucleotide sequence, both bound to a solid support by a covalent linking moiety. Parameters used in the design of tags based on subunits are discussed in Barany et al. (WO 9731256, incorporated herein by reference). A multiplex sequencing method has been described in U.S. Pat. No. 4,942,124, incorporated herein by reference. This method uses at least two vectors that differ from each other at a tag sequence.

(62) U.S. Pat. No. 7,226,737, incorporated herein by reference, describes a set of 210 non-cross hybridizing tags and anti-tags. U.S. Published Application No. 2005/0191625, incorporated herein by reference, discloses a family of 1168 tag sequences with a demonstrated ability to correctly hybridize to their complementary sequences with minimal cross hybridization.

(63) A population of oligonucleotide tag or anti-tag sequences may be conjugated to a population of primers or other polynucleotide sequences in several different ways including, but not limited to, direct chemical synthesis, chemical coupling, ligation, amplification, and the like. Sequence tags that have been synthesized with primer sequences can be used for enzymatic extension of the primer on the target for example in PCR amplification. A population of oligonucleotide tag or anti-tag sequences may be conjugated to a solid support by, for example, surface chemistries on the surface of the support.

(64) 8. Blocker Moieties

(65) Blocker moieties prevent the polymerase from extending through the tag sequence region during second strand synthesis, thus allowing the tag sequence to remain single-stranded during amplification and therefore free to hybridize to its complementary anti-tag sequence in the capture complex.

(66) A blocker moiety refers to any moiety that when linked (e.g., covalently linked) between a first nucleotide sequence and a second nucleotide sequence is effective to inhibit and preferably prevent extension of either the first or second nucleotide sequence but not both the first and second nucleotide sequence. There are a number of molecules that may be used as blocker moieties. Non-limiting examples of blocker moieties include C6-20 straight chain alkylenes and iSp18 (which is an 18-atom hexa-ethyleneglycol). Blocker moieties may include, for example, at least one deoxy ribofuranosyl naphthalene or ribofuranosyl naphthalene moiety, which may be linked to the adjacent nucleotides via a 3′-furanosyl linkage or preferably via a 2′-furanosyl linkage. A blocker moiety may be an oligonucleotide sequence that is in the opposite orientation as the target specific sequence. Various blocker moieties and their use are described in U.S. Pat. No. 5,525,494, which is incorporated herein by reference.

III. Examples

(67) The following examples are included to demonstrate certain embodiments of the invention. Those of skill in the art should, in light of the present disclosure, will appreciate that many changes can be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

A. Example 1

(68) A side by side study was performed to compare hairpin-forming primers comprising tag and anti-tag regions with non-hairpin forming primers comprising a tag region but not an anti-tag region. These “tagged” primers were used as forward primers. Cy3-labeled reverse primers (400 nM) were added along with the respective forward primer (hairpin forming or non-hairpin forming) as well as a detection bead prior to PCR amplification. The target was a thrombophilia gene, MTHFR Exon 7. After 27 cycles, the samples were analyzed on an LX200 (Luminex Corp.) at room temperature without any other addition of buffer or reporter, thus representing a simulated closed-tube detection format.

(69) The forward primers were:

(70) TABLE-US-00001 12snap: (SEQ ID NO: 1) 5′CAAACAAACATTCAAATATCAATC/iSp18/CTATCTATACATAATGT TTGTTTGCAAGGAGGAGCTGCTGAAGATG3′ 12isoSNAP: (SEQ ID NO: 2) 5′CAAACAAACATTCAAATATCAATC/ie-isodC//iMeisodC/CTAT CTATACATAATGTTTGTTTGCAAGGAGGAGCTGCTGAAGATG3′. Snap1: (SEQ ID NO: 3) 5′CAAACAAACATTCAAATATCAATC/iSp18/GATTGATATTGAATGTT TGTTTGCAAGGAGGAGCTGCTCAACATG3′ NoSnap (SEQ ID NO: 4) 5′CAAACAAACATTCAAATATCAATC/iSp18/CTATCTATACATTTACA AACATTCCAAGGAGGAGCTGCTGAAGATG3′ TIF (SEQ ID NO: 5) 5′CAAACAAACATTCAAATATCAATC/iSp18/CAAGGAGGAGCTGCTCA ACATG3′
The sequence of the Cy3-labeled reverse primer was:

(71) TABLE-US-00002 (SEQ ID NO: 6) /5Cy3/CACTTTGTGACCATTCCGGTTTG

(72) 12snap and 12isoSNAP differed from each other in that 12snap contains an iSp18 blocker and 12isoSNAP contains an isodC blocker. The 12snap and 12isoSNAP were calculated to be in the hairpin conformation 99.9% of the time in solution (37° C.; [monovalent]=0.0500 mol/L; [Mg.sup.2+]=0.0015 mol/L; [Betaine]=1.00 mol/L) by Visual OMP software. Snap1 was similar to 12snap except that it had 24-base tag hybridizing to its complimentary anti-tag in the hairpin, rather than 12 bases as in 12snap. NoSnap was as long as 12snap but without a hairpin structure. The TIF primer included a tag sequence but no complementary anti-tag sequence.

(73) All PCR reactions were performed in the same cocktail. These were analyzed after 27 cycles of amplification and 36 cycles of amplification. A PCR cocktail was prepared using the following concentrations and reagents:

(74) TABLE-US-00003 TABLE 1 1x Volume Master Mix 25 μl HotStart TAQ Plus Master Mix 2X (Qiagen) H.sub.2O 21 μl RNASE FREE Water (Qiagen) Primer 1 μl IDT (400 nM final concentration each) Template 1 μl Purified Human DNA Sample from UCLA (100 ng) Beads 2 μl MagPlex Microspheres (Luminex) (5000 per set) Total 50 μl

(75) These formulations were used along with the downstream primer:

(76) TABLE-US-00004 (SEQ ID NO: 7) LUA-MED-TF/5Cy3/CACTTTGTGACCATTCCGGTTTG.

(77) Each primer was at 400 nM concentration. The cycling conditions for this reaction were as follows:

(78) Heat Denaturation Step; 95° C. for 5 min.

(79) Cycling Steps (for 36 cycles): 94° C. for 30 s, 55° C. for 30 s, 72° C. for 30 s.

(80) After amplification the reactions were stored until all reactions were completed and were then placed in a v-bottom plate and analyzed on a Luminex 200 analyzer after 3 minutes at 96° C. and 12 minutes at 37° C.

(81) Results are shown in Table 2 below. Analyte 27 is the positive bead set with the anti-tag region coupled to the bead. Analyte 33 is the negative control with a non-specific sequence coupled to the bead. Median values are shown.

(82) TABLE-US-00005 TABLE 2 Analyte 27 Analyte 33 Location Sample MFI MFI Cycles  1(1, A1) 12isoSNAP 77 11 36  2(1, B1) 12isoSNAP 86 4  3(1, C1) 12snap 113 14  4(1, D1) 12snap 120 9.5  5(1, E1) NoSnap 107 13  6(1, F1) NoSnap 111.5 9.5  7(1, G1) snap1 98.5 10  8(1, H1) snap1 98.5 8  9(1, A2) TIF 118 12 10(1, B2) TIF 108 15 11(1, C2) TIF 36 10.5 27 12(1, D2) TIF 32.5 7 13(1, E2) snap1 24.5 7 14(1, F2) snap1 21 13.5 15(1, G2) NoSnap 20 8 16(1, H2) NoSnap 26.5 12.5 17(1, A3) 12snap 58 12 18(1, B3) 12snap 53 15.5 19(1, C3) 12isoSNAP 25 9 20(1, D3) 12isoSNAP 31.5 13

(83) The high signal (MFIs of 58 and 53) from the 12snap primer at the 27.sup.th cycle as compared to the signal (MFIs of 20 and 26.5) from the NoSnap primer indicates that the 12snap primer is folding when it is supposed to and not interfering with hybridization at the stage of the reaction where excess primer would be expected.

B. Example 2

(84) Another study was performed in which after amplification to 27 cycles as described in Example 1, the samples were spiked with more of the same forward primer (400 nM) that they were originally amplified with. Addition of excess primer prior to hybridization, but after amplification, was done to test whether the non-extended hairpin primers were interfering with hybridization to the bead, and whether the TIF primers were interfering with hybridization. If there was interference, one would expect that the spiked primers would decrease the MFI value.

(85) TABLE-US-00006 TABLE 3 Analyte 27 Analyte 33 Total Location Sample MFI MFI Events 1(1, A1) TIF 91.5 8 203 2(1, B1) TIF 94 5.5 201 3(1, C1) 12snap 115.5 11 211 4(1, D1) 12snap 119 8 206 5(1, E1) TIF spiked 400 nM 63 13.5 208 6(1, F1) TIF spiked 400 nM 64 8.5 208 7(1, G1) 12snap spiked 400 nM 106 13 207 8(1, H1) 12snap spiked 400 nM 109 15 203

(86) As shown in Table 3 and FIG. 6, the MFI for the TIF primer sample dropped to 68% of its original value when excess TIF primer was added, whereas the 12snap primer only dropped to 92% of its original value when excess 12snap primer was added. The slight drop in signal observed with the 12snap primer could be due to incomplete hairpin structure formation by these primers, as only 12 base pairs are available for hairpin formation.

C. Example 3

(87) Varying amounts of primer concentration were tested in PCR reactions stopped at 27 cycles to determine whether the signal would increase or decrease with additional amounts of TIF primer or 12snap primer. The results are shown in Tables 4 and 5 below.

(88) TABLE-US-00007 TABLE 4 12snap primer Analyte 27 Analyte 33 Total Location Primer Concentration MFI MFI Events 1(1, A1) 100 nM 96 4 213 2(1, B1) 100 nM 99 4 203 3(1, C1) 100 nM 101.5 7 211 4(1, D1) 200 nM 111.5 8 220 5(1, E1) 200 nM 103 7 212 6(1, F1) 200 nM 108 10 200 7(1, G1) 400 nM 121 12 206 8(1, H1) 400 nM 114 8 205 9(1, A2) 400 nM 118.5 14.5 214

(89) TABLE-US-00008 TABLE 5 TIF primer Analyte 27 Analyte 33 Total Location Primer Concentration MFI MFI Events 1(1, A1) 100 nM 53 2 234 2(1, B1) 100 nM 63.5 5 214 3(1, C1) 100 nM 62 3.5 206 4(1, D1) 200 nM 60 5.5 209 5(1, E1) 200 nM 63 11 207 6(1, F1) 200 nM 62 7.5 216 7(1, G1) 400 nM 55 13 209 8(1, H1) 400 nM 43 8.5 209 9(1, A2) 400 nM 52 14 203

(90) The data show that one can gain greater signal with the hairpin primer by increasing the concentration, whereas greater signal cannot be obtained by increasing the TIF primer. This indicates that the hairpin primer does not interfere as much with hybridization to the bead as does the TIF primer.

D. Example 4

(91) Two additional studies were performed to confirm: (1) that the Cy3-labeled reverse primer was not hybridizing to the forward primers; and (2) that primer dimers were not forming.

(92) The primers (the Cy3-labeled reverse primer and either 12snap or TIF) were mixed with the anti-tagged beads in PCR solution and heated to 96° C. for 3 minutes followed by 37° C. for 12 minutes. As shown in Table 6, no non-specific binding of the reverse primer to either forward primer was detected.

(93) TABLE-US-00009 TABLE 6 Analyte Analyte Total Location Sample 27 MFI 33 MFI Events 1(1, A1) 12snap 14.5 24.5 204 2(1, B1) 12snap 12 14 204 3(1, C1) no forward primer 3 3.5 203 4(1, D1) TIF 12 10.5 205 5(1, E1) TIF 11 6 215 6(1, F1) no forward primer 2 2.5 200

(94) PCR reactions with the upstream primers 12snap and TIF and the Cy3-labeled reverse primer were performed in the absence of template to check for the formation of primer dimers. The reactions were run in duplicate on RD18 after a 3 minute 96° C. and 12 minute 37° C. hyb protocol. The results shown in Table 7 indicate that no primer dimers were formed and hybridized to the beads.

(95) TABLE-US-00010 TABLE 7 Analyte Analyte Total Location Sample 27 MFI 33 MFI Events 1(1, A1) TIF, no template 0.5 2 205 1(1, B1) TIF, no template 0.5 0 209 6(1, F1).sup.  12snap, no template 5 0.5 203 5(1, E1).sup.  12snap, no template 2 0 212 9(1, A2) TIF 102.5 0 200 10(1, B2)  TIF 104 0 207 14(1, F2) .sup.  12snap 132 3.5 208 13(1, E2) .sup.  12snap 120 0 224

E. Example 5

(96) Forward primers that formed 16-mer and 14-mer stem structures in the hairpins were also studied. An additional tagged, but non-hairpin forming primer, TIF, was also included in these studies.

(97) TABLE-US-00011 16snap: (SEQ ID NO: 8) CAA ACA AAC ATT CAA ATA TCA ATC /iSp18/CTC TCT ATT TTG AAT GTT TGT TTG CAA GGA GGA GCT GCT GAA GAT G 14snap: (SEQ ID NO: 9) CAA ACA AAC ATT CAA ATA TCA ATC /iSp18/CTC AAC TAT TTT GAA TGT TTG TTT GCA AGG AGG AGC TGC TGA AGA TG

(98) 16snap and 14snap were tested in PCR reactions and in PCR solution using oligos complimentary to the primer region. The following PCR set up was designed to test the oligos in Qiagen Hotstart Master Mix with no extra MgCl.sub.2 added.

(99) TABLE-US-00012 TABLE 8 Master Mix 25 μl H.sub.2O 19.75 μl Primer 2 μl Template 0.25 μl Beads (2) 3 μl Total 50 μl

(100) The reaction was stopped at 27 cycles and hybridized for 2 minutes at 96° C. followed by 37° C. for 12 minutes. The results were as follows:

(101) TABLE-US-00013 TABLE 9 Analyte Analyte Location Sample 27 MFI 33 MFI 1(1, A1) 16snap 33 0 2(1, B1) 16snap 34 1 3(1, C1) 16snap 35 2 4(1, E1) 14snap 32 2 5(1, F1).sup.  14snap 31 0 6(1, G1) 14snap 34.5 3.5 7(1, A2) 12snap 52.5 3 8(1, B2) 12snap 59 0 9(1, C2) 12snap 62.5 1 10(1, E2)  TIF 47.5 0 11(1, F2) .sup.  TIF 47 0 12(1, G2)  TIF 48 2

(102) The data from Table 9 is also represented graphically in FIG. 7. The 16snap and 14snap primers produced lower signals than 12snap. They also produced lower signals than TIF. It was postulated that the exonuclease activity of the polymerase in the Qiagen Hotstart Master Mix was degrading the stem structure on the 16snap and 14snap primers. Accordingly, another PCR, which was also stopped at 27 cycles, was performed using the exo (−) polymerase apta taq. The cocktail for this PCR was as follows:

(103) TABLE-US-00014 TABLE 10 10x Buffer 5 μl H.sub.2O 29.5 μl Primer 4 μl Template 0.25 μl Beads (2) 2 μl dNTPs 1 μl apta taq 0.25 μl MgCl.sub.2 8 μl Total 50 μl

(104) The results of the reaction with apta taq were as follows:

(105) TABLE-US-00015 TABLE 11 Analyte Analyte Location Sample 27 MFI 33 MFI 1(1, A1) 16snap 98 0 2(1, B1) 16snap 99 2 3(1, C1) 16snap 94 4 4(1, D1) 16snap 106 2 5(1, E1).sup.  14snap 133 0 6(1, F1).sup.  14snap 127.5 0 7(1, G1) 14snap 130.5 2 8(1, H1) 14snap 125.5 0.5 9(1, A2) 12snap 170 0 10(1, B2)  12snap 157.5 2.5 11(1, C2)  12snap 162.5 1 12(1, D2)  12snap 162 0.5 13(1, E2) .sup.  TIF 34.5 5 14(1, F2) .sup.  TIF 32 0 15(1, G2)  TIF 36 0 16(1, H2)  TIF 32 3

(106) The data from Table 11 is also represented graphically in FIG. 8. All of the hairpin-forming primers (16snap, 14snap, and 12snap) significantly outperformed the non-hairpin-forming primer (TIF).

F. Example 6

(107) The PCR cocktail as described above in the apta taq PCR was used as a hybridization buffer for hybridizing a labeled oligo complimentary to the primer region for each of the 16snap, 14snap, 12snap, and TIF primers. As shown in Table 12, the hairpin structure of the 16snap, 14snap, and 12snap primers largely inhibited their ability to hybridize to the beads.

(108) TABLE-US-00016 TABLE 12 Analyte Analyte Location Sample 27 MFI 33 MFI 1(1, A1) 16snap 12.5 9 2(1, B1) 16snap 10.5 8 3(1, C1) 14snap 16 12 4(1, D1) 14snap 19 9 5(1, E1) 12snap 35 10.5 6(1, F1) 12snap 35 9.5 7(1, A2) TIF 425 12 8(1, B2) TIF 427 13.5

G. Example 7

(109) Oligos were also made for the amplification of the prothrombin gene. These oligos were as follows:

(110) TABLE-US-00017 PT TIF: (SEQ ID NO: 10) CAA TTC AAA TCA CAA TAA TCA ATC /iSp18/CTT CCT GAG CCC AGA GAG C 12SNAP/ptu: (SEQ ID NO: 11) CAA TTC AAA TCA CAA TAA TCA ATC /iSp18/ACA CTC CAC ACATGA TTT GAA TTG CTT CCT GAG CCC AGA GAG C PtdCY3: (SEQ ID NO: 12) /5Cy3/ GTC ATT GAT CAG TTT GGA GAG TAG G BeadPT: (SEQ ID NO: 13) /5AmMC12/GAT TGA TTA TTG TGA TTT GAA TTG FVmutant oligo FV506Q2: (SEQ ID NO: 14) /5AmMC12/GTATTCCTTGCCTGTCCA

(111) The BeadPT oligo was coupled to bead set 29. The Analyte 33 and Analyte 27 bead sets from the MTHFR studies described above, were used as negative controls.

(112) Two PCR cocktails were prepared sharing all the same reagents with the exception of the forward primers (PT TIF and 12SNAP/ptu). A no template control was added as well as 3 template added samples for each condition. The PCR cocktail is shown in Table 13. Results are shown in Table 14.

(113) TABLE-US-00018 TABLE 13 10x ThermoPol Buffer  5 μl H.sub.2O 34.7 μl   Primer 2 μl (400 nM) Template #24 0.3 μl (100 ng) Beads 2 μl (5,000 beads) dNTPs 1 μl (0.2 mM) Deep Vent Polymerase 2 μl (10 Units) (New England BioLabs) MgSO.sub.4 3 μl (8 mM) Total 50 μl

(114) TABLE-US-00019 TABLE 14 Analyte Analyte Analyte Total Location Sample 27 MFI 29 MFI 33 Events 1(1, A1) 12SNAP/ptu, 14.5 10 23 184 no template 2(1, B1) 12SNAP/ptu 10.5 78 12.5 415 3(1, C1) 12SNAP/ptu 6.5 84 14 322 4(1, D1) PT TIF, 7 16 17 346 5(1, E1) PT TIF 15 38 14 336 6(1, F1) PT TIF 6 36.5 10.5 193

(115) From the results in Table 14, it can be seen that the signal difference of the 12SNAP/ptu primer is about double that of the PT TIF primer after 27 cycles using 400 nM primer concentrations with a PCR protocol of: 97° C., 5 minutes; (97° C., 30 seconds; 55° C., 30 seconds; 72° C., 30 seconds)×27 cycles; followed by 7 minutes at 72° C. These results also demonstrated that the PT primers will not cross hybridize with the MHFTR primer sets if combined into a multiplex reaction.

H. Example 8

(116) A pseudo real-time PCR was performed in which a PCR cocktail (with DeepVent exo (−) polymerase) was divided into 16 aliquots for each primer set. Each aliquot was removed from the thermal cycler at progressive cycles to measure the signal levels at each cycle. This was done using a fast 2-step PCR reaction, and aliquots were measured on an LX200 (Luminex) at room temperature at the end of the PCR protocol of 36 cycles total.

(117) As shown in FIG. 9 signal was observable at just 22 cycles (44 minutes) for the 12SNAP/ptu primer compared to 29 cycles (58 min.) for the PT TIF primer. In addition to producing an observable signal earlier, it can be seen in FIG. 9 that the hairpin forming primer also was more sensitive. At cycle 22 the PT TIF primer was only 16% of the signal compared to the 12SNAP/ptu primer, and only 75% at peak cycle 33.

I. Example 9

(118) A real-time PCR experiment was performed on a glass slide with the lens and hex-illuminator directly over the slide for the duration of the experiment. Glass slide chambers were constructed, and the glass was chemically modified using DMDCS followed by a dip in Polyadenylic Acid Potassium salt. A glass slide and a cover slip were joined together with a sticky gasket (BioRad) using an in situ PCR kit. These were placed onto a BioRad DNA Engine thermal cycler equipped with a slide griddle. This particular slide griddle had a hole drilled in it, directly over one of the 96 wells. The exposed well was painted black. The glass chamber was placed directly over the hole in the griddle to reduce background reflection light. A real-time PCR unit was constructed by coupling a CCD camera and light source to the DNA Engine thermal cycler. The Hex-illuminator was placed directly over the glass slide and remained there for the duration of the PCR reaction. The following cocktail was placed in the 25 μL volume glass chamber:

(119) TABLE-US-00020 TABLE 15 10x ThermoPol Buffer  5 μl H.sub.2O 34.7 μl   Primer 200 nM each 12SNAP/ptu & PtdCY3 Template #24 0.3 μl (100 ng) Beads 2 μl (5,000 beads) dNTPs 1 μl (0.2 mM each) Deep Vent Polymerase 2 μl (10 Units) (New England BioLabs) MgSO.sub.4 3 μl (8 mM) Total 50 μl

(120) The following PCR Cycling conditions were run: 1) 97° C. for 5 min; 2) 105° C. for 15 s; 3) 96° C. for 30 s; 4) 50° C. for 5 s; 5) 68° C. for 30 s; 6) Go to 2, 5 times; 7) 15° C. for 10 s; 8) 24° C. for 5 min; 9) Go to 2, 6 times; 10) End. These conditions included extra ramp times to account for the heating delay of the griddle.

(121) Images of the beads were taken at exactly 4 minutes at each 5 cycle interval at 24° C. The glass chamber was not agitated in between runs. The data are shown in Table 16 and FIG. 10.

(122) TABLE-US-00021 TABLE 16 Cycle before Bead MFI 6 1 251 2 232 12 1 246 2 248 18 1 235 2 241 24 1 276 2 220 30 1 316 2 183 36 1 281 2 154 42 1 299 2 178

J. Example 10

(123) Optimization of the length of the stem region of the hairpin used in the primer that contains the universal Tag sequence that binds to the universal labeled probe upon extension of the opposite strand was evaluated. In order to find the optimal length of the reverse primer hairpin stem region length, and the length of the universal reporter probes, a series of primers with different stem lengths and universal reporter probes with different lengths were reacted for comparison.

(124) In these reactions reverse hairpin primers with 11mer, 14mer, 16mer and 0 mer stem lengths were used. These were hybridized with beads that were coupled to probes that were complimentary to the target specific primer regions of each of these hairpin primers. Each 50 uL reaction contained:

(125) 8 mM MgCl.sub.2

(126) 1× Qiagen PCR buffer

(127) 5000 beads

(128) 200 nM of primer

(129) 200 nM of universal reporter probe

(130) All reagents were hybridized at 95° C. for 5 min. followed by 37° C. for 15 minutes. The Luminex magnetic beads were then analyzed on a Luminex Lx200 analyzer.

(131) The following oligos were used in this reaction:

(132) TABLE-US-00022 BeadTagantiprime (SEQ ID NO: 15) /5AmMC12/TAG TTG CAA ATC CGC GAC AA NoSnaprevNei (SEQ ID NO: 16) ATG ATG ATG TAT TGT AGT TAT GAA /iSp18/AGG TAT TGA AGT TTT GTC GCG GAT TTG CAA CTA Univlabeled13 (SEQ ID NO: 17) /5Cy3/AAT ACA TCA TCA T/3InvdT/ UnivLabeled 15 (SEQ ID NO: 18) /5Cy3/ACA ATA CAT CAT CAT /3InvdT/ Snap11revNei (SEQ ID NO: 19) ATG ATG ATG TAT TGT AGT TAT GAA /iSp18/TAC ATC ATC ATT TGT CGC GGA TTT GCA ACT A Snap14RevNei (SEQ ID NO: 20) ATG ATG ATG TAT TGT AGT TAT GAA /iSp18/CAA TAC ATC ATC ATT TGT CGC GGA TTT GCA ACT A Snap16RevNei (SEQ ID NO: 21) ATG ATG ATG TAT TGT AGT TAT GAA /iSp18/TAC AAT ACA TCA TCA TTT GTC GCG GAT TTG CAA CTA

(133) TABLE-US-00023 TABLE 17 Rev primer type universal probe MFI Snap11revNei Univlabeled13 8 Snap11revNei Univlabeled13 6 Snap11revNei UnivLabeled 15 40 Snap11revNei UnivLabeled 15 43 Snap14RevNei Univlabeled13 3 Snap14RevNei Univlabeled13 3 Snap14RevNei UnivLabeled 15 3 Snap14RevNei UnivLabeled 15 4 Snap16RevNei Univlabeled13 3 Snap16RevNei Univlabeled13 1 Snap16RevNei UnivLabeled 15 2 Snap16RevNei UnivLabeled 15 2 NoSnaprevNei Univlabeled13 929 NoSnaprevNei Univlabeled13 1009 NoSnaprevNei UnivLabeled 15 862 NoSnaprevNei UnivLabeled 15 1399

(134) The goal of this study was to find a primer/probe pair such that the hairpin region of the primer would remain in the closed state in the presence of the universal labeled probe, but remain in the open state once a double stranded amplicon product was formed in the presence of the universal labeled probe. In order to ensure that the hairpin would remain in the open state after formation of the double stranded product, we chose a primer/probe pair such that the hairpin monomer was of a strong enough binding energy so as to remain in the closed state, but of a weak enough binding energy so as to remain in the open state in the presence of the double stranded product and universal labeled probe. Such a pair would have to near the point of open state in this study. The best pair was identified as the Snap11revNei/Univlabeled13 pair. This pair was chosen to be used in subsequent PCR reactions because the low MFI indicates that it is in the closed state, but if a longer universal labeled probe is used, some of the hairpins open, as indicated by the 40-43 MFIs. This indicates that the Snap11revNei/Univlabeled13 is closed, but it is near the point at which some would be open.

K. Example 11

(135) A dilution series of Neiseria Meningitidis DNA (ATCC 700532D-5) in a real-time quantitative PCR was performed in a closed tube. This experiment demonstrated the ability to perform quantitative real-time PCR in order to discriminate between varying input concentrations of template DNA. A PCR cocktail was prepared such that each 25 uL reaction contained:

(136) 8 mM MgCl.sub.2

(137) 1× Qiagen PCR buffer

(138) 5000 beads of each region

(139) 200 nM of primer

(140) 200 nM of universal reporter probe

(141) A sample of Neiseria Meningitidis DNA was amplified in real-time using sealed glass chambers and placed on a thermal cycler fitted with a slide griddle. These reactions were performed as in Example 11. The first sealed chamber contained 1 million copies of DNA, the second chamber contained 100,000 copies, and the third chamber contained 10,000 copies of N. Meningitidis DNA.

(142) Two bead sets were used in this experiment. One bead set (Set 2) was coupled to a probe (BeadTag Nei) that was complimentary to the tag region of the forward primer (Snap12fwdShrtNei). The other bead set (Set 1) was coupled to a probe (BeadTag antiList) that was not specific to hybridize to anything in the reaction. Set 1 was used to monitor the non-specific signal in the reaction and to act as a normalization and background subtract tool to account for differences in light intensity for each image taken.

(143) TABLE-US-00024 Snap11revNei (SEQ ID NO: 22) ATG ATG ATG TAT TGT AGT TAT GAA /iSp18/TAC ATC ATC ATT TGT CGC GGA TTT GCA ACT A BeadTag Nei (SEQ ID NO: 23) /5AmMC12/GAT TGA TAT TTG AAT GTT TGT TTG /3InvdT/ Snap12fwdShrtNei (SEQ ID NO: 24) CAA ACA AAC ATT CAA ATA TCA ATC /iSp18/AAT GTT TGT TTG GCT GCG GTA GGT GGT TCA A Univlabeled13 (SEQ ID NO: 25) AAT ACA TCA TCA T/3Cy3/ BeadTag antiList (SEQ ID NO: 26) /5AmMC12/GTT TGT ATT TAG ATG AAT AGA AAG /3InvdT/

(144) The data for each bead set for each cycle is given below. The average MFI for each bead Set 1 for each time point in all 3 reactions was 3931 MFI. This average value was used to create a normalization factor by dividing the non-specific bead set (Set 1) by 3931 MFI. Each raw data point was divided by this normalization factor that was specific to each time point. After normalization, the specific bead set for detecting Neiseria Meningitidis (Set 2) normalized MFI was subtracted by Set 1 normalized MFI. This calculation resulted in a net normalized MFI for Set 2 for each time point. The data are given in the table below.

(145) TABLE-US-00025 TABLE 18 Normal- Normal- Bead Raw ization Net ized Net Normal- Cycle Set Median Factor MFI MFI MFI ized 1 million copies  0 1 3757 0.96 127 3931 133 2 3884 4064 12 1 3120 0.79 −76  3931 −96  2 3044 3836 18 1 3124 0.79 158 3931 199 2 3282 4130 24 1 3009 0.77 563 3931 736 2 3572 4667 30 1 2863 0.73 601 3931 825 2 3464 4757 100,000 copies  0 1 3931 1.00 −15  3931 −15  2 3916 3916  6 1 4120 1.05  18 3931  17 2 4138 3949 12 1 4403 1.12  58 3931  52 2 4461 3983 18 1 4431 1.13 154 3931 137 2 4585 4068 24 1 4396 1.12 579 3931 518 2 4975 4449 30 1 4083 1.04 790 3931 761 2 4873 4692 36 1 4175 1.06 787 3931 741 2 4962 4673 10,000 copies  0 1 4220 1.07 136 3931 127 2 4356 4058  6 1 4417 1.12 244 3931 217 2 4661 4149 12 1 4819 1.23 210 3931 171 2 5029 4103 18 1 4671 1.19 144 3931 121 2 4815 4053 24 1 4671 1.19 144 3931 121 2 4815 4053 30 1 3326 0.85 521 3931 616 2 3847 4547 36 1 3162 0.80 699 3931 869 2 3861 4801

(146) A graph of this data (FIG. 11) shows a clear distinction between each of the input concentrations of N. Meningitidis which allows for quantitation.

L. Example 12

(147) The following results demonstrate the ability to multiplex hairpin-forming primers for the detection of pathogens. A 3-plex meningitis assay was designed to detect Neisseria Meningitidis, Listeria Monocytogenes, and Haemophilus Influenzae. Three primer sets were multiplexed in the same reaction. Genomic DNA from separate bacteria species were placed in individual reactions to demonstrate the specificity of the assay.

(148) The following primer and probe sequences were ordered from IDT and used.

(149) TABLE-US-00026 Primer Set 1: SIF4fwdList-t88 (SEQ ID NO: 27) TTA CTT CAC TTT CTA TTT ACA ATC /iSp18/AAG TGA AGT AAA TTG CGA AAT TTG GTA CAG C SIF13RCrevList (SEQ ID NO: 28) ATG ATG ATG TAT TGT AGT TAT GAA /iSp18/TAC ATC ATC ATC TGA TTG CGC CGA AGT TTA CAT TC Primer Set 2: SIFprobeFwdHaem-t86 (SEQ ID NO: 29) CTA ATT ACT AAC ATC ACT AAC AAT /iSp18/GTT AGT AAT TAG TTG TTT ATA ACA ACG AAG GGA CTA ACG T SIFrevHaem (SEQ ID NO: 30) ATG ATG ATG TAT TGT AGT TAT GAA /iSp18/TAC ATC ATC ATG ATT GCG TAA TGC ACC GTG TT Primer Set 3: Snap12fwdShrtNei (SEQ ID NO: 31) CAA ACA AAC ATT CAA ATA TCA ATC /iSp18/AAT GTT TGT TTG GCT GCG GTA GGT GGT TCA A Snap11revNei (SEQ ID NO: 32) ATG ATG ATG TAT TGT AGT TAT GAA /iSp18/TAC ATC ATC ATT TGT CGC GGA TTT GCA ACT A Probes coupled to Beads: Bead Set 27/Specific for N. meningitidis fwd. primer: (SEQ ID NO: 33) /5AmMC12/GAT TGA TAT TTG AAT GTT TGT TTG /3InvdT/ Bead Set 62/Specific for L. Monocytogenes fwd. primer: (SEQ ID NO: 34) GAT TGT AAA TAG AAA GTG AAG TAA /3AmM/ Bead Set 67/Specific for H. Influenzae fwd. primer: (SEQ ID NO: 35) ATT GTT AGT GAT GTT AGT AAT TAG /3AmM/ Universal Labeled Probe: 13Uni- (SEQ ID NO: 36) AAT ACA TCA TCA T/3Cy3Sp/

(150) The following volumes in μL were used in each PCR cocktail:

(151) TABLE-US-00027 TABLE 19 1x Material volume 10x Buffer 5 H20 35.1 Primer set 1 (10 μM) 1 Primer set 2 (10 μM) 1 Primer set 3 (10 μM) 1 Each Template 1 dntps (10 mM) 1 Polymerase (50 U/μL) 0.2 MgCl2 (50 mM) 6 Bead Set 1 (5000 beads/μL) 0.5 Bead Set 2 (5000 beads/μL) 0.5 Bead Set 3 (5000 beads/μL) 0.5 U13 (100 μM) 0.2 TOTAL 53

(152) PCR Materials: (Roche) Apta Taq delta exo DNA pol., Glycerol free, 50U/ul—Sample 2, 5KU(100 ul); (Roche PN:13409500) PCR Buffer without MgCl2, 10× concentration; (Invitrogen PN:18427-088) 10 mM dNTP Mix.

(153) Thermal Cycling Parameters: 97° C. for 4 min; then 35 cycles of: (97° C. for 30 sec, 62° C. for 30 sec); then 72° C. for 7 min.

(154) Each bead set was previously prepared using Luminex MagPlex-C Magnetic Microspheres by coupling their respective probe sequences using Luminex recommended EDC coupling procedures.

(155) The following genomic DNA samples were obtained from American Type Culture Collection (ATCC):

(156) TABLE-US-00028 TABLE 20 Item Number Description Lot Number 700532D-5 DR Neisseria meningitidis; Strain FAM18 7385221 BAA-679D-5 DR Listeria monocytogenes; Strain EGDe 57878064 51907D FZ Haemophilus influenzae 2662083

(157) After the PCR reaction, samples were heated to 95° C. for 2 minutes and placed at room temperature for 8 minutes prior to analyzing on a Luminex 200 analyzer. 100 bead events per bead set were collected and a Median Fluorescence Intensity (MFI) value was derived for each bead set in each reaction. The following MFI values were obtained for each sample:

(158) TABLE-US-00029 TABLE 21 Input Genomic DNA Bead Set 27 Bead Set 62 Bead Set 67 Sample 1 H. Influenza 7 10 67 Sample 2 L. Monocytogenes 6 87 3 Sample 3 N. Meningitidis 73 13.5 0 Sample 4 No Template 2 9.5 0

(159) These results demonstrate the multiplex ability of hairpin primers.

(160) The portions of the primer sets that are target specific to the different bacterial species were obtained from the following publicly available references:

(161) Neisseria Meningitidis:

(162) Corless, C. E., Guiver, M., Borrow, R., Edwards-Jones, V., Fox, A. J., and Kaczmarski, E. 2001. Simultaneous Detection of Neisseria Meningitidis, Haemophilus Influenzae, and Streptococcus Pneumoniae in Suspected Cases of Meningitis and Septicemia Using Real-Time PCR. Journal of Clinical Microbiology. 39: 1553-1558.

(163) Listeria monocytogenes:

(164) Johnson, w., Tyler, S., Ewan, E., Ashton, F., Wang, G. and Rozee, K. 1992. Detection of Genes Coding for Listeriolysin and Listeria monocytogenes Antigen A (LmaA) in Listeria spp. by the Polymerase Chain Reaction. Microbial Pathogenesis 12; 79-86.

(165) Bohnert, M., Dilasser, F., Dalet, C. Mengaud, J. and Cossart, P. 1992. Use of Specific Oligonucleotides for Direct Enumeration of Listeria monocytogenes in Food Samples by Colony Hybridization and Rapid Detection by PCR. Res. Microbiol. 143; 271-280.

(166) Haemophilus Influenzae:

(167) Maaroufi, Y., Bruyne, J., Heymans, C., and Crokaert, F. 2007. Real-Time PCR for Determining Capsular Serotypes of Haemophilus Influenzae. Journal of Clinical Microbiology. 45: 2305-2308.

(168) All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the methods described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

REFERENCES

(169) The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference. U.S. Pat. No. 4,284,412 U.S. Pat. No. 4,498,766 U.S. Pat. No. 4,659,774 U.S. Pat. No. 4,661,913 U.S. Pat. No. 4,682,195 U.S. Pat. No. 4,683,202 U.S. Pat. No. 4,714,682 U.S. Pat. No. 4,767,206 U.S. Pat. No. 4,774,189 U.S. Pat. No. 4,816,571 U.S. Pat. No. 4,857,451 U.S. Pat. No. 4,883,750 U.S. Pat. No. 4,942,124 U.S. Pat. No. 4,959,463 U.S. Pat. No. 4,989,977 U.S. Pat. No. 5,137,806 U.S. Pat. No. 5,141,813 U.S. Pat. No. 5,160,974 U.S. Pat. No. 5,264,566 U.S. Pat. No. 5,428,148 U.S. Pat. No. 5,478,722 U.S. Pat. No. 5,525,494 U.S. Pat. No. 5,539,082 U.S. Pat. No. 5,554,744 U.S. Pat. No. 5,574,146 U.S. Pat. No. 5,595,890 U.S. Pat. No. 5,602,244 U.S. Pat. No. 5,639,611 U.S. Pat. No. 5,645,897 U.S. Pat. No. 5,654,413 U.S. Pat. No. 5,705,629 U.S. Pat. No. 5,714,331 U.S. Pat. No. 5,719,262 U.S. Pat. No. 5,736,330 U.S. Pat. No. 5,736,336 U.S. Pat. No. 5,766,855 U.S. Pat. No. 5,773,571 U.S. Pat. No. 5,786,461 U.S. Pat. No. 5,837,832 U.S. Pat. No. 5,837,860 U.S. Pat. No. 5,840,873 U.S. Pat. No. 5,843,640 U.S. Pat. No. 5,843,650 U.S. Pat. No. 5,843,651 U.S. Pat. No. 5,846,708 U.S. Pat. No. 5,846,709 U.S. Pat. No. 5,846,717 U.S. Pat. No. 5,846,726 U.S. Pat. No. 5,846,729 U.S. Pat. No. 5,846,783 U.S. Pat. No. 5,849,487 U.S. Pat. No. 5,849,497 U.S. Pat. No. 5,849,546 U.S. Pat. No. 5,849,547 U.S. Pat. No. 5,853,990 U.S. Pat. No. 5,853,992 U.S. Pat. No. 5,853,993 U.S. Pat. No. 5,856,092 U.S. Pat. No. 5,858,652 U.S. Pat. No. 5,861,244 U.S. Pat. No. 5,863,732 U.S. Pat. No. 5,863,753 U.S. Pat. No. 5,866,331 U.S. Pat. No. 5,866,366 U.S. Pat. No. 5,882,864 U.S. Pat. No. 5,891,625 U.S. Pat. No. 5,905,024 U.S. Pat. No. 5,908,845 U.S. Pat. No. 5,910,407 U.S. Pat. No. 5,912,124 U.S. Pat. No. 5,912,145 U.S. Pat. No. 5,912,148 U.S. Pat. No. 5,916,776 U.S. Pat. No. 5,916,779 U.S. Pat. No. 5,919,630 U.S. Pat. No. 5,922,574 U.S. Pat. No. 5,925,517 U.S. Pat. No. 5,928,862 U.S. Pat. No. 5,928,869 U.S. Pat. No. 5,928,905 U.S. Pat. No. 5,928,906 U.S. Pat. No. 5,929,227 U.S. Pat. No. 5,932,413 U.S. Pat. No. 5,932,451 U.S. Pat. No. 5,935,791 U.S. Pat. No. 5,935,825 U.S. Pat. No. 5,939,291 U.S. Pat. No. 5,942,391 U.S. Pat. No. 5,981,180 U.S. Pat. No. 6,057,107 U.S. Pat. No. 6,103,463 U.S. Pat. No. 6,287,778 U.S. Pat. No. 6,322,971 U.S. Pat. No. 7,226,737 U.S. Pat. No. 7,226,737 U.S. Pub. Appln. 2005/0191625 Egholm et al., Nature, 365(6446):566-568, 1993. EP Appln. 266,032 EP Appln. 320,308 EP Appln. 329,822 Fodor et al., Biochemistry, 30(33):8102-8108, 1991. Froehler et al., Nucleic Acids Res., 14(13):5399-5407, 1986. Frohman, In: PCR Protocols: A Guide To Methods And Applications, Academic Press, N.Y., 1990. GB Appln. 2 202 328 Holmstrom et al., Anal. Biochem. 209:278-283, 1993. Koshkin and Dunford, J. Biol. Chem., 273(11):6046-6049, 1998a. Koshkin and Wengel, J. Org. Chem., 63(8):2778-2781, 1998b. Kwoh et al., Proc. Natl. Acad. Sci. USA, 86:1173, 1989. Mueller et al., Current Protocols in Mol. Biol.; 15:5,1993. Newton et al., Nucl. Acids Res. 21:1155-1162, 1993. Ohara et al., Proc. Natl. Acad. Sci. USA, 86:5673-5677, 1989. PCT Appln. WO 00/47766 PCT Appln. WO 88/10315 PCT Appln. WO 89/06700 PCT Appln. WO 90/07641 PCT Appln. WO 92/20702 PCT Appln. WO 93/17126 PCT Appln. WO 9731256 PCT Appln. WO05087789 PCT Appln. WO07/085087 PCT Appln. PCT/EP/01219 PCT Appln. PCT/US87/00880 PCT Appln. PCT/US89/01025 Pease et al., Proc. Natl. Acad. Sci. USA, 91:5022-5026, 1994. Rasmussen et al., Anal. Biochem, 198:138-142, 1991. Running et al., BioTechniques 8:276-277, 1990. Santalucia et al., Biochemistry; 38:3468-3477, 1999. Wahlestedt et al., Proc. Natl. Acad. Sci. USA, 97(10):5633-5638, 2000. Walker et al., Nucleic Acids Res. 20(7):1691-1696, 1992.