WO2011097420A2 - Selection and characterization of dna aptamers with binding selectivity to campylobacter jejuni using whole-cell selex - Google Patents

Abstract

There is disclosed DNA aptamers demonstrating binding specificity to live Campylobacer jejuni cells and a method of using the DNA aptamers for capture, concentration, and detection of pathogens in simple and complex sample matrices, including but not limited to food and environmental samples.

Description

SELECTION AND CHARACTERIZATION OF DNA APTAMERS WITH BINDING SELECTIVITY TO CAMPYLOBACTER JEJUNI USING WHOLE-CELL

SELEX

The invention disclosed herein was made with government support from the Food Safety and Research Response Network funded through the United States Department of Agriculture grant number 2005-35212-15287. Accordingly, the U.S. Government has certain rights in this invention.

Field of the Invention

The present invention provides DNA aptamers demonstrating binding specificity to Campylobacter cells and a method of using these DNA aptamers to identify Campylobacer cells in food and other samples.

Background of the Invention

Campylobacter species are leading causes of acute and sporadic bacterial gastroenteritis worldwide. Campylobacters cause diarrhoeal illness about 2-7 times more frequently than do Salmonella spp., Shigella spp. or Escherichia coli 0157: H7, with C. jejuni, a zoonotic pathogen with wide host range, being responsible for the majority of these illnesses (14). C. jejuni infection may also trigger autoimmune neurological disorders such as Guillain-Barre' syndrome and Miller Fisher syndrome (24); less frequently, other complications can result (10). As few as 500 cells have been reported to cause clinical manifestations in humans (36). Contaminated foods (especially raw or partially cooked poultry and raw milk), untreated water, and seafood are common sources linked with infection (9).

Isolation of pathogenic Campylobacter cells from food and environmental samples is complicated, requiring precise atmosphere (microaerophilic) and specific temperature conditions to facilitate growth (14). In fact, the amount of time to confirm the presence of Campylobacters in foods and environmental samples using standard cultural methods frequently exceeds 4-5 days (23). Attempts have been made to reduce the time to detection and confirmation (16, 23), but in complex sample matrices with low levels of contamination, this has been difficult. Immunomagnetic separation has shown promise (17) in facilitating pathogen concentration and sample clean-up, but cross reactivity (15) and high cost of anti-Campylobacter antibodies remain a stumbling block.

The ability of single stranded nucleic acids such as aptamers that fold into unique and stable secondary structures has led to identification of rare nucleic, acid sequences with structures that not only bind specifically to selected targets such as proteins (2), cancer cells (12),. viruses (18), bacteria (4, 33), and parasites (32) but also discriminate between subtle molecular differences within the target These nucleic acid sequences or aptamers are selected from a large random sequence oligonucleotide (10¹³-10¹⁵ unique sequences) library by an iterative process of in vitro selection of sequences showing binding affinity, followed by PCR amplification in a method termed as Systemic Evolution of Ligands by Exponential enrichment (SELEX) (7, 31). Single-stranded nucleic acid aptamers represent a new generation of macromoleeules with applicability to the selective capture and subsequent detection of target molecules for development of sensitive, specific and rapid diagnostics (4, 33). The unique secondary structural elements formed by these single-stranded DNA oligomers can be. exploited, using multiple rounds of selection and sequence enrichment resulting in target-specific probes which can be labeled for visual detection or tethered to a. solid support for target capture and concentration. Due to their high affinity and specificity, aptamers have emerged as macromoleeules that rival antibodies in biodiagnostic and biotherapeutic applications. Aptamers have several characteristics that make them attractive for biodiagnostic assay development including smaller size, ease of synthesis and labeling, lack of immunogenicity, lower cost than antibodies and high target specificity (30).

First reported in 1.990,. SELEX has historically been applied to isolated and/ or purified protein and non-protein molecular targets (28) and for this type of SELEX, prior knowledge about the target molecules and specialized biochemical techniques are required for isolation and purification of the particular cell surface target. Moreover, selection against purified membrane-associated targets may not always yield functional aptamer candidates if the targets require the presence of the cell membrane or co-receptor(s) for folding into the stable native conformation (28) necessary for consistent presentation of structural epitopes during aptamer selection. Whole-cell SELEX (also called as complete- target SELEX) strategies (29, 34) could be employed to identify aptamers specific to multiple surface membrane targets in their native conformations and physiological environments, leading to candidate ligands with different levels of specificity (genus, species or strain) or even the ability to discriminate between different cellular states (3). For this invention, a whole-cell SELEX method was used for aptamer selection as an alternative to the more traditional SELEX approach applied to crude or purified

extracellular surface targets. Whole-cell SELEX or complete target SELEX is an approach for aptamer selection which has previously been applied to Mycobacterium tuberculosis (4), Rous sarcoma virus (26), Trypanosoma brucei (13) and Trypanosoma cruzi (32). Whole- cell SELEX has several advantages including the fact that it is not necessary to have prior knowledge of the target and that aptamers are selected against targets in their native conformation and physiological environment (3, 27). The whole-cell SELEX approach is also amenable to flow cytometry for both selection and binding affinity analyses (4, 29).

Summary Of The Invention

In the invention disclosed herein, whole-cell SELEX was employed to identify DNA aptamers specific to C. jejuni. These aptamers demonstrate a degree of highly specific binding affinity required for concentrating and detecting C. jejuni cells which is relevant to pure cultures, food or other samples.

An aspect of the invention is the identification of DNA aptamers that are specific for Campylobacter jejuni.

An aspect of the invention is DNA aptamers comprising sequences disclosed in this application. Another aspect of the. invention is DNA aptamers that have binding affinity for capture and detection of Campylobacter jejuni,

Another aspect of the invention is the use of one or more these DNA aptamers. to. capture or detect Campylobacter jejuni in a sample- Still another aspect of the invention is the use of one or more of these DNA aptamers to detect Campylobacter jejuni in a sample.

Yet another aspect of the invention is a method comprising the use of the DNA aptamer ONS-23 to detect Campylobacter jejuni in a sample.

Another aspect of the invention is a method comprising the use of the DNA aptamer 229 to detect Campylobacter jejuni in a. sample.

Still another aspect of the invention is a method to detect Campylobacter jejuni by combining a DNA aptamer based capture concentration step followed by quantitative real-time PCR (qPCR).

Brief Description Of The Figures

FIG. 1 is a schematic diagram of the whole-cell SELEX process used, to isolate DNA aptamers with high binding affinity for C. jejuni

FIG. 2 shows the binding affinity of selected aptamer candidates after 10 rounds of SELEX and 2 rounds of counter-SELEX compared with the aptamer pool selected after the 3^rd round of SELEX Aptamers ONS-20 and ONS-23 showed 28.58 % and. 31.44 % total fluorescent cells, respectively, in flow cytometric analysis while the aptamer pool from the 3^rd round of SELEX showed only 4.16 % total fluorescent cells.

FIG. 3A shows the correlation between aptamer ONS-23 concentration and total fluorescence intensity as a measure of target recognition. The percentage of fluorescent cells after incubation with 7.4 nM, 74 nM, 740 nM, 1.48 uM, 2,2 μΜ aptamer ONS-23 solution with 10⁸- 10⁹ C. jejuni (A9a) cells was 3.00 ± 0.99, 12.21 ± 2.43, 37.07 ± 6.1, 47.27 ± 5.58, 48.31 ± 8.22 respectively.

FIG. 3B shows the data fitted to a non-interacting binding sites model y = Bmax*x/ [Kd + x], which yielded a dissociation constant {Kd value) of 292.8 ± 53.1 nM.

FIGS. 4A, 4B and 4C show the binding specificity for aptamer ONS-23 as percentage of total fluorescent cells determined for each described bacterial species.

FIG. 4A illustrates that aptamer ONS-23 showed minimal non-specific binding with B. cereus strain T (4.71 %).

FIG. 4B illustrates that aptamer ONS-23 shows binding with E. coli 0157:

H7 (1.26 %).

FIG. 4C illustrates that aptamer ONS-23 shows binding with L. monocytogenes ATCC191 15 (1.24 %).

FIG. 4D illustrates that aptamer ONS-23 shows binding with C. jejuni A9a (51.72%, highest binding affinity recorded in an assay).

FIGS. 5A, 5B, 5C and 5D show binding inclusivity for aptamer ONS-23. The percentages of fluorescent cells for different strains were determined using flow cytometery after labeling with aptamer ONS-23 as described herein.

FIG. 5A shows binding affinity for C. jejuni strain ATCC33560 (32.18 %).

FIG. 5B shows binding affinity for C. jejuni strain ATCC33291 (35.53 %).

FIG. 5C shows binding affinity for 2083 (33.67 %).

FIG. 5D shows binding affinity was slightly reduced for C. jejuni strain A14a (25.31 %) although well above what was observed for non-C. jejuni strains. FIG. 6 illustrates the secondary structure of aptamer ONS-23 using DNA Mfold. Structure consisted of the 4 base pair helix of the first hairpin loop, 3 base pair helix of the second hairpin loop, and 4 base pair helix of the third hairpin loop.

FIG. 7 shows Proteinase K digestion of C. jejuni prior to labeling with aptamer ONS-23. An approximate one-third reduction in the percentage of fluorescent cells was observed.

FIG. 8 shows binding analysis of selected biotinylated aptamers after 12 SELEX and 2 counter SELEX rounds.

FIG. 9 shows a standard curve showing the relationship between DNA extracted from C. jejuni cell concentrations subjected to qPCR.

FIG. 10 shows capture efficiency (% CE) of aptamer and antibody conjugated magnetic beads as applied to C. jejuni.

FIG. 1 1 shows capture efficiency (% CE) of aptamer conjugated magnetic beads as applied to serially diluted C. jejuni culture.

Detailed Description of the Invention

The details of one or more embodiments of the invention are set forth in the accompanying description below. Unless otherwise defined, all terms of art, notations and other scientific terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. Other features, objects, and advantages of the invention will be apparent from the description. In the specification, the singular forms also include the plural unless the context clearly dictates otherwise.

This invention relates to the identification and characterization of fluorescently labeled DNA aptamer sequences which can be used to capture and/or detect Campylobacter jejuni. Single stranded DNA molecules (aptarners) that adopt a sequence- defined unique secondary structure demonstrate a specific and. high affinity interaction with C, jejuni. These aptamers can be fluorescently labeled for use as molecular probes for detection and/or tethered to a solid support for use in capturing and concentrating low levels of C. jejuni from pure cultures or complex sample, matrices such as food or environmental samples. Aptamers can be biotinylated rather than fluorescently labeled

A whole-cell SELEX (Systematic Evolution of Ligands by Expotential Enrichment) method was used for DNA aptamer selection, as an alternative to. the more traditional SELEX approach applied to crude or purified extracellular surface targets. The whole-cell SELEX method used is outlined in Fig. 1. The whole-cell SELEX process consists of several iterations of aptamer enrichment by incubating a DNA. library with the target cell followed, by separation of bound aptamers from unbound aptamers using centrifugal washing. Candidate aptamer sequences are enriched by PCR amplification and the resulting pool subjected, to further rounds of SELEX. Counter-SELEX against pooled non-target bacterial cells is performed to increase the specificity of aptamer sequences. By manipulating the number and sequence of SELEX: and counter-SELEX iterations, aptamers with a high degree of target binding specificity can be produced.

The whole-cell SELEX approach was used to select DNA aptamers from large random sequence libraries demoiistrating functional binding specificity to C, jejuni. An 80-base combinatorial DNA aptamer library was: obtained from Integrated DNA Technologies (Coralville, IA), although libraries of varying length and using different constant region sequences could be used. Libraries may also he constructed of ssRNA. The. library sequences, location of random and. constant regions, fluorescent labels, and attachment, chemistry linkers are shown in Table 1.

Sequences from the DNA aptamer library were labeled with fluorescein (FAM) and biotin, but other fluorophore labels such as Cy5, BODIPY TMR-C₅ could be also used for labeling. The aptamer library was diluted in molecular grade water to an initial concentration of 5-15 μΜ. The. aptamer library was amplified by PCR targeting the constant regions at the 5' and 3' ends of the ssDNA strands. In an embodiment of the invention, the PCR was carried out using a solution containing 0.5-1.5X Go Taq^® Buffer (Promega Corp., Madison, WI), 0.1-0.3 mM GeneAmp^® dNTPs Mix (Applied Biosystems, Foster City, CA), 3-5U Go Taq^® DNA Polymerase (Promega), 300-600 nM FAM-Forward Constant. Region primer, and 300-600. nM Biotin- Reverse Constant Region primer as shown in Table 1. Any PCR protocol could theoretically be used for aptamer enrichment, and if ssRNA were used for library construction, RNA amplification strategies such as Sequence-Based Nucleic Acid Amplification (NASBA) might be used for aptamer enrichment The PCR was performed using a 3 step thermal protocol of initial denaruration at 93-95°C for 3-5 min followed by 15-30 cycles of 93-95°C for 30-90 sec, 45-70°C for 30- 60 sec, 70-72°C for 30-60 sec and final extension at 70-72°C for 7-10 min.

In an embodiment of the invention, the FAM-ssDNA moieties are separated from the immobilized biotin-labeled strands by alkaline denaturation for example, in 0.1- 0.2 M NaOH at room temperature for 5-7 min and then recovered by magnetic capture of the beads, using a Dynal MPC®-M magnetic particle concentrator (Dynal A.S, Oslo, Norway). Residual NaOH was removed using a Microcon® YM-30 filter device (Millipore, Biilerica, MA). Other methods known in the art can.be used to separate the ssDNA.

The labeled aptamers were incubated with C. jejuni and the aptamer bound cells were recovered. Partitioning of aptamer-bound complexes from unbound aptamer was achieved using a combination of centrifugation and fluorescence automated cell sorting. The partitioning is not limited to these methods. In an embodiment of the invention ten rounds of selection and two rounds of counter selection against a pooled mixture of unrelated bacteria were used to enrich the pool of functional aptamer sequences. More or fewer rounds of SELEX and counter-SELEX may be applied in aptamer selection,_: depending upon specificity requirements for use of the candidate aptamer,

In an embodiment of the invention, for enrichment of FAM-ssDNA. (aptamer) candidates, 10 rounds of SELEX were performed using C jejuni A9a cellst About 300-500 pmoles of aptamer pool was dissolved in 200-400 μΙ of binding buffer (0.01-0.05% Tween 20 in wash buffer), denatured by heating at 90-95°C for 8-12 min and renatured by flash cooling on ice for 8-12 min to allow intra-strand base pairing. The aptamer pool was incubated with 10⁶ - 10⁹ C, jejuni cells suspended in 50-100 μΐ wash, buffer for 40-60 min at room temperature with gentle rotation. Aptamer-bound cells were recovered by centrifugation at 1000-2000 x g for 7-10 min followed by 3-5 washings with 400-1.0Q0 μΐ binding buffer to remove unbound and non-specifically bound, aptamers. Cells were then reconstituted in a final volume of 100-200 ul using molecular grade water. Aptamer sequences bound to cells were directly enriched by PGR amplification using the FAM-Forward Constant Region primer and Biotin-Reverse Constant Region primer as described above. The FAM-labeled aptamer pool was separated by alkaline denaturation in preparation for the next round of SELEX.

After the 7^th and 10^th rounds of SELEX, aptamer-bound C. jejuni cells were sorted into different pools based, on fluorescence intensity using a Beckman Coulter MoFlo® modular flow cytometer (Beckman Coulter, Inc, Fullerton, CA). Specifically fluorescence based automated cell sorting of aptamer labeled cells was used for isolation and recovery of the top binding aptamers from the candidate pool. Multicolor flow cytometry in conjunction with cell sorting as a high-throughput, screening technique to separate target bound magnetic bead linked aptamers from non-functional bead linked aptamers was recently reported (35), but the real-time application of fluorescence-based automated cell sorting for separation of aptamer-labeled food, borne bacterial pathogens is unique to this study.

The binding affinity [expressed as % total fluorescent cells (n=200,000)] of the aptamers was determined using flow cytometry. The percentage of fluorescent cells for the different aptamer candidates ranged from 1.9-32% in binding assays using approximately 300 pmol of aptamer sequences with 10⁸-10⁹ Campylobacter cells (Table 2). As the concentration of FAM-aptamer was increased, there was. an increase in the total number of fluorescent cells, although the average fluorescence intensity per cell remained constant. Cells with the greatest fluorescence intensity (top 25%) were used for subsequent rounds of PCR-based enrichment of aptamer candidates.

Following multiple rounds of SELEX, counter SELEX was performed using non-Campylobacter genera, in which case the aptamer bound cells were recovered and discarded and the unbound aptamers were collected. To assure the specificity of aptamer candidates, two rounds of counter-SELEX were performed after the 10^th round of SELEX (Fig. 1). Briefly, the aptamer pool (300-500 p moles) suspended in 200-400 μΐ of binding buffer was incubated with the pooled counter-SELEX bacterial cocktail (non-C. jejuni strains described below) suspended in 50-100 μΐ wash buffer for 40-60 min at room temperature with moderate shaking. The aptamer-bound cells were recovered and discarded, while the unbound aptamers in the supernatant were collected for one more round of counter-SELEX.

Partitioning of aptamer-bound complexes from unbound aptamers was achieved using a combination of centrifugation and fluorescence automated cell sorting. In each selection round centrifugal washing was used to remove the loosely bound and non- bound aptamer sequences. After the 7^th and 10^th rounds of selection sorting of tightly bound aptamers was done by sorting out top fluorescent cells after aptamer labeling. Partitioning could be done by other means as well, such as using filtration devices to retain target- aptamer complex or using nitrocellulose membrane to immobilize the target-aptamer complex or using other solid affinity supports such as magnetic beads, affinity titer plates and agarose beads for target-aptamer complex immobilization.

An approximate 5-8 fold increase in binding affinity was observed for evolved aptamer sequences following 10 rounds of selection and two rounds of counter selection in comparison to the aptamer pool after the 3^rd round of SELEX (Fig. 2). Following the 10 rounds of SELEX and 2 rounds of counter-SELEX, the selected aptamer pool was amplified using PCR with the Forward Constant Region primer and Reverse Constant Region primer. The PCR product was electrophoresed on 1.25% agarose gel in IX modified TAE electrophoresis buffer and the amplicon band purified using an Amicon® Ultrafree®-DA centrifugal unit for DNA extraction from agarose (Millipore).

These aptamers were then cloned and the sequences determined. Seven unique aptamer sequences (Table 2) were identified. Three sequence motifs were prevalent among the selected aptamers sequences which divided them into three distinct families when analyzed using MEME server (data not shown). Motif 1 was expressed among all selected candidate aptamers while the other two motifs were not as prevalent. None of the aptamer candidates had all three motifs.

The highest binding affinity was demonstrated by aptamer ONS-23 (31.44%) while comparatively lower affinity was shown by aptamer sequence 22-21 (Table 2). On the basis of preliminary screening of selected aptamers, aptamer ONS-23 was selected for further characterization. C. jejuni A9a cells (10⁸-10⁹) were titrated with increasing concentrations of aptamer ONS-23 and analyzed by flow cytometry (Fig. 3A). Saturation was achieved at higher aptamer concentrations. The non-interacting binding sites model adequately described the binding relationship, yielding a dissociation constant (Kd value) of 292.8 ± 53.1 nM (Fig. 3B). The aptamer ONS-23 labeling of C. jejuni complex could be visualized using fluorescent microscopy (data not shown).

Biotinylated aptamer 229 was selected against Campylobacter jejuni (A9a) cells using whole cell-SELEX (Systematic Evolution of Ligands by Exponential enrichment) process in a similar manner as FAM- labeled aptamers. The biotinylated aptamer library for SELEX was generated using PCR amplification process. In brief, the unlabeled library was procured and amplified using unlabeled forward constant region primers and biotin labeled reverse constant region primers (Table 1). Biotin-labeled double stranded DNA was coupled with Streptavidin MagneSphere® Paramagnetic Particles (SA- PMPs) by incubating at room temperature with gentle rolling. The unlabeled ssDNA moieties were separated from the immobilized biotin-labeled strands by alkaline denaturation and then recovered by magnetic capture of the beads. The remaining biotin- ssDNA coupled magnetic beads were washed. A second alkaline denaturation was performed to recover the biotin-labeled ssDNA molecules which were washed an additional 3-4 times.

For enrichment of biotinylated-ssDNA (aptamer) candidates, multiple rounds of SELEX were performed. The aptamer pool was dissolved and renatured to allow intra-strand base pairing. The aptamer pool was incubated with 10⁵ - 10⁷ C. jejuni cells at room temperature. Aptamer-bound cells were recovered by cenlrifugation and washing to remove unbound and non-specifically bound aptamers. Aptamers bound to cells were directly enriched by PC amplification using the Forward Constant Region primer and Biotin-Reverse Constant Region primer as described for FAM labeled aptamers. The biotin- labeled aptamer pool was separated by alkaline denaturation in preparation for the next round of SELEX.

To assure the specificity of aptamer candidates, counter-SELEX was performed. The selected aptamer pool was incubated with the pooled counter-SELEX bacterial cocktail {Salmonella enterica 13076, Bacillus cereus 49063, Enterococcus faecalis 29212, E. coli 43895, Salmonella enterica ME 46, Listeria monocytogenes Scott A). The aptamer-bound cells were recovered and discarded, while the unbound aptamers in the supernatant were collected for further rounds of selection.

The selected aptamer pool was subjected to cloning and sequencing to identify aptamer candidates. The flow cytometric analysis of aptamer bound cells was performed to analyze the mean fluorescence intensity and percentage of fluorescent cells occurring as a consequence of aptamer binding. A total of eleven sequences were analyzed. Aptamer sequence 229 was of these (5'-/5Biosg/ GCA AGA TCT CCG AGA TAT CGT GCT GGG GGG TGG TTT GTT TGG GTC GGT TGT TTT GGT TGG GCT GCA GGT AAT ACG TAT ACT -3' (SEQ ID NO: 20)) with 21.62 % cell fluorescent.

The aptamers identified can be used to. identify, capture, concentrate, and/or detect die presence of Campylobacter cells in a variety of sample matrices deluding those which are relatively pure and uniform in composition (such as waters) to complex sample, matrices such as foods, feces, or environmental samples. For example, in ligand-specific capture and direct detection approaches, biotinylated aptamers would be conjugated to a solid support (such as streptavi din-coated magnetic particles or nitrocellulose membranes) for C. jejuni capture followed by detection using molecular amplification of target DNA. In the 2-site binding /sandwich assay format, C. jejuni would be sandwiched between two ligands, one immobilized to a solid support used for capture and the other conjugated to a. suitable receptor molecule which is used for detection. Any combination of ligands can be. used (e.g., two different aptamers, one aptamer and one antibody, one aptamer and a phage- based ligand, etc.); there are virtually an endless number of combinations in this regard. For instance, fluorescent detection assays could be developed using flourophore-conjugated reporter ligands. Likewise, ligand-linked immobilized sorbent assays could be developed, in microtiter plate format. Another interesting option would be capture using the sandwich approach with indirect detection of the target by applying PCR using primers targeting a. constant region of the detector aptamer. Additionally, fluorescently labeled DNA aptamers could be used in the direct and indirect detection of C. jejuni using various fluorescence based assays including flow cytometric analysis, fluorescence based automated sorting of specific cell types, aptamers-linked immobilized sorbents assay (ALISA), calometric analysis, dot blot assays, biosensors, fluorescent microscopy, and quantitative real-time PCR. Biotinylated aptamers can also be used.

A kit according to the invention would be envisioned to contain one or more the aptamers of SEQ ID NOs: 8 to 14 in solution or tethered to a solid support (non limiting examples of supports are magnetic beads, microliter plates and nylon membranes). This could be sold as a stand-alone reagent for user-specified applications. In addition, the invention could be tailored to specific assay formats such as those described in the paragraph above but with inclusion of specialized reagents. For example, immobilized aptamers could be combined with nucleic acid extraction and amplification reagents to produce a kit for PCR and reverse-transcription PCR-based detection of C. jejuni. When used in combination with other ligands (phage receptor ligands, antibodies),, a kit containing labeled and/or immobilized aptamers in addition to the other ligands would provide all reagents necessary for assay completion.

Kits may comprise components, which may be individually packaged or placed in a container, such as a. tube, bottle, vial, syringe, or other suitable container means. Individual components may also be provided in a kit in concentrated amounts; in some embodiments, a component is provided individually in the same concentration as it would be in a solution with other components. Concentrations of components may be provided as 1x, 2, 5x, 10x, or 20x or more.

It should be noted that, as used in this specification and the appended claims, the singular forms "a," "an," and "the" include plural, referents unless the content clearly dictates otherwise. Thus, for example, reference to a composition containing "a compound" includes a mixture of two or more compounds. It should also be noted that the term "or" is generally employed in its sense including "and/or" unless, the content clearly dictates otherwise.

It is to be understood that other than in any operating examples, or where otherwise indicated, all numbers expressing, for example, quantities of ingredients used in the specification and claims are to be understood as being modified in all. instances by the term "about"* Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are approximations that may vary depending upon the desired properties to be obtained by the present invention. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.

Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard variation found in their respective testing measurements.

Also, it should be understood that any numerical range recited herein is intended to include all sub-ranges subsumed therein. For example, a range of "1 to 10" is intended to include all sub-ranges between (and including) the recited minimum value of 1 and the recited maximum value of 10, that is, having a minimum value equal to or greater than 1 and a maximum value of equal to or less than 10.

All publications and patent applications in this specification are indicative of the level of ordinary skill in the. art to which this invention pertains.

The invention has been described, with reference to various specific and preferred embodiments and techniques. However, it should be understood that many variations and modifications may be. made while remaining within the spirit and scope of the invention.

The invention is further understood by reference to the following Examples, which are intended to be purely exemplary of the invention. The present invention is not limited in scope by the exemplified embodiments, which are intended as illustrations of single aspects of the invention only. Any methods that are functionally equivalent to those described in the Examples are within the scope of the invention. Various modifications of the. invention in addition to those described herein , will become apparent to those skilled in the art from the foregoing description. Such modifications tall within the scope of the appended claims.

Example 1

Microbial Strains. Culture Conditions And Preparation Of Cells

C. jejuni strain A9a, a naturally-occurring strain isolated from a poultry processing plant was used as the target for whole-cell SELEX. This strain was chosen because of the high prevalence of contamination of raw poultry with C. jejuni, and the consistent association between human campylobacteriosis and poultry products (14). Moreover, as a naturally occurring isolate, this strain was assumed to present the cell surface signature typical of field strains. C. jejuni cultures of different zoonotic origin were used for inclusivity studies and included C. jejuni ATCC33560 (bovine feces), C. jejuni 2083 (cattle), C. jejuni ATCC33291 (human feces) and C. jejuni A14a (poultry processing plant) (all non-ATCC cultures provided courtesy of Dr. Lynn Joens, University of Arizona, Tucson, AZ). All C. jejuni strains were cultivated in 10 ml BBL™ brucella broth (Becton, Dickinson and Co., Sparks, MD) under a micro-aerophilic environment generated using the BBL™ CampyPak™ Plus Microaerophilic System (Becton, Dickinson) in a BBL™ GasPak™ jar by incubation at 42°C for 48 h. The cells were observed using Leica DM LB2 bright field microscope with the oil immersion objective (Vashaw Scientific Inc., Norcross, GA) to confirm typical comma and spiral morphology. Cells were harvested by centrifugation, washed 3 times in wash buffer (IX Dulbecco's PBS (pH 7.1) with calcium chloride and magnesium chloride (Invitrogen Corp., Carlsbad, California)) and finally suspended in 100 μΐ of wash buffer prior to use in experiments.

Other bacterial strains used in this study (for counter-SELEX and exclusivity studies) included the following: Pseudomonas fluorescens (ATCC13525), P. aeruginosa (ATCC23993), Shigella flexneri (ATCC12022), E. coli 0157: H7, Bacillus cereus (ATCC- 49063), Staphylococcus aureus (ATCC23235), B. cereus (strain T), Listeria monocytogenes (ATCC191 15), L. monocytogenes Scott A, Salmonella enterica subsp. Enterica

(ATCC4931), E. coli (ATCC33625), S sonnei (ATCC25931), Streptococcus gallolyticus (ATCC9809), Enterococcus faecium (ATCC19434), E. faecalis (ATCC51299), S. enterica serovar. Enteritidis (ME 46), Salmonella enterica serovar. Typhimurium (human isolate), all grown in 10 ml BBL™ BHI broth; and Lactobacillus plantarum, Leuconostoc mesenteroides (LA 0268-USDA), and Pediococcus pentosaceus (LA 0076-USDA grown overnight at 37°C in 10 ml de Man, Rogosa and Sharpe (MRS) broth. One ml culture of each bacterium was pooled, centrifuged, washed three times in wash buffer and finally suspended in 100 μΐ wash buffer for use in counter-SELEX as described below.

SELEX Process

The whole-cell SELEX process is outlined in Figure 1. An 80-base combinatorial DNA aptamer library was obtained from Integrated DNA Technologies (Coralville, IA). The library sequences, location of random and constant regions, fluorescent labels, and attachment chemistry linkers are shown in Table 1.

Labeling of DNA library

To label with fluorescein (FAM) and biotin, the diluted aptamer library (10 μΜ initial concentration) was amplified in 50 μΐ PCR reactions containing IX Go Taq^® Buffer (Promega Corp., Madison, WI), 0.2 mM GeneAmp^® dNTPs Mix (Applied Biosystems, Foster City, CA), 5U Go Taq^® DNA Polymerase (Promega), 500 nM FAM- Forward Constant Region primer, and 500 nM Biotin- Reverse Constant Region primer (Table 1). The PCR was performed in a DNA Engine (PTC-200) Peltier Thermal Cycler- 200 (MJ Research/ Bio-Rad Laboratories, Hercules, CA) using a 3 step thermal protocol of initial denaturation at 95°C for 5 min followed by 30 cycles of 95°C for 1 min, 55°C for 1 min, 72°C for 1 min and final extension at 72°C for 10 min.

Separation of the FAM Labeled Single Stranded DNA (FAM-ssD A)

Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) (Promega) were washed 3 times in 0.5X SSC buffer and coupled with the FAM and biotin labeled double stranded DNA library by incubating at room temperature for 30 min with gentle rolling. The library-coupled magnetic beads were washed 3 times in 0.1X SSC buffer. The FAM-ssDNA moieties were separated from the immobilized biotin-labeled strands by alkaline denaturation in 0.15 M NaOH at room temperature for 5-6 min and then recovered by magnetic capture of the beads using a Dynal MPC®-M magnetic particle concentrator (Dynal A.S, Oslo, Norway). Residual NaOH was removed using a Microcon® YM-30 filter device (Millipore, Billerica, MA).

Example 2 SELEX

For enrichment of FAM-ssDNA (aptamer) candidates, a total of 10 rounds of SELEX were performed using C. jejuni A9a cells. About 300 pmoles (-1.8 ^χ 10¹⁴ sequences) of aptamer pool was dissolved in 400 μΐ of binding buffer (0.05% Tween 20 in wash buffer), denatured by heating at 95 °C for 10 min and renatured by flash cooling on ice for 10 min to allow intra-strand base pairing. The aptamer pool was incubated with lO⁸ - 10⁹ C. jejuni cells suspended in 100 μΐ wash buffer for 45 min at room temperature with gentle rotation. Aptamer-bound cells were recovered by centrifugation at 1500 x g for 10 min followed by 3 washings with 500 μΐ binding buffer to remove unbound and non-specifically bound aptamers. Cells were then reconstituted in a final volume of 200 μΐ using molecular grade water. Aptamer sequences bound to cells were directly enriched by PCR amplification using the FAM-Forward Constant Region primer and Biotin-Reverse Constant Region primer as described above. The FAM-labeled aptamer pool was separated by alkaline denaturation in preparation for the next round of SELEX.

Cell Sorting

After the 7^th and 10^th rounds of SELEX, aptamer-bound C. jejuni cells were sorted into different pools based on fluorescence intensity using a Beckman Coulter MoFlo® modular flow cytometer (Beckman Coulter, Inc, Fullerton, CA). Cells with the greatest fluorescence intensity (top 25%) were used for subsequent rounds of PCR-based enrichment of aptamer candidates. Counter-SELEX

To assure the specificity of aptamer candidates, two rounds of counter- SELEX were performed after the 10^th round of SELEX (Fig. 1). Briefly, the aptamer pool (300 p moles) suspended in 400 μΐ of binding buffer was incubated with the pooled counter-SELEX bacterial cocktail (non-C. jejuni strains described in Example 1) suspended in 100 μΐ wash buffer for 45 min at room temperature with moderate shaking. The aptamer- bound cells were recovered and discarded, while the unbound aptamers in the supernatant were collected for one more round of counter-SELEX.

Example 3

Identification of C. jejuni Specific Aptamers

Following 10 rounds of SELEX and 2 rounds of counter-SELEX, the selected aptamer pool was amplified using PCR with the Forward Constant Region primer and Reverse Constant Region primer. The PCR product was electrophoresed on 1.25% agarose gel in IX modified TAE electrophoresis buffer and the amplicon band purified using an Amicon® Ultrafree®-DA centrifugal unit for DNA extraction from agarose (Millipore).

Cloning

The purified aptamer pool was treated with DNA Polymerase I ( lenow fragment) (Invitrogen) for 20 min on ice to produce blunt-ended aptamer sequences which were then ligated into the pCR®-Blunt vector using T4 DNA ligase provided in the Zero Blunt® PCR cloning kit (Invitrogen). The ligated vectors were transformed into One Shot® ToplO chemically competent E. coli cells (Invitrogen) and 30-50 μΐ of cells were plated on high salt Luria-Bertani (LB) agar plates with kanamycin (50 μg/ ml) and incubated at 37°C for 20-24 h. Individual colonies of the transformed cells were propagated in 5 ml high salt LB broth with kanamycin (50 μg/ ml) for 16 h at 37°C. The cells were harvested by centrifugation and plasmid DNA was extracted using the QIAprep® Spin plasmid Miniprep Kit (Qiagen Inc., Valencia, CA). The size of the amplified product was confirmed by PCR and visualized using 2% agarose gel electrophoresis. Transformants with an amplicon band size of 81 bases were selected for sequencing.

Sequencing

Sequencing of plasmid DNA of the selected transformants was done using a GenomeLab™ methods development kit (Beckman Coulter, Inc, Fullerton, CA) for dye terminator cycle sequencing. Plasmid DNA (approximately 75 ng) was pre-heated at 96°C for 1 min and sequencing reactions (10 μΐ total volumes) were performed for dNTP (I) chemistry using 5.5 μΐ premix (Beckman Coulter) and 0.16 μΜ M-13 reverse primer (Invitrogen). Thirty cycles consisting of 96°C for 20 sec, 50°C for 20 sec and 60°C for 4 min using a DNA Engine (PTC-200) thermal cycler were performed for all sequencing reactions. Reactions were stopped by mixing freshly prepared stop solution, ethanol precipitated and resuspensed in Sample Loading Solution (Beckman Coulter) as per instructions provided with the sequencing kit. The sequencing was performed using the LFR-1 program for 85 min and sequences were analyzed using the CEQ-8000™ /GenomeLab™ series genetic analysis system (Beckman Coulter). Some of the plasmid DNA was also sequenced by Davis Sequencing, Inc. (Davis, CA).

Preliminary Binding Screening and Predicted Structure of Aptamer Candidates

The unique aptamer sequence insert in plasmid DNA, identified by automated fluorescence sequencing, were amplified in the PCR reactions using the FAM- Forward Constant Region primer and Biotin-Reverse Constant Region primer. The FAM- labeled aptamer sequences were separated using alkaline denaturation. Preliminary binding assays using 300 pmol FAM-labeled candidate aptamers were performed on 10⁸- 10⁹ intact cells of C. jejuni strain A9a and analyzed using flow cytometry. In addition, the structural folding (secondary structure) of aptamer sequences, displaying binding affinity to C. jejuni was predicted using the online software DNA Mfold version 3.2 (mfold.bioinfo.rpi.edu/cgi_'- bin/dna-forml .cgi) (37). Common sequence motifs were identified using the online. MEME server (meme.sdsc.edu), which identifies motifs in groups of related DNA sequences using statistical modeling techniques (1).

Further Characterization of ONS-23

Aptamer ONS-23 was selected for further binding characterization because of its high binding affinity to C. jejuni during the preliminary screening. Highly purified (by ion exchange, high performance liquid chromatography) aptamer ONS-23 (with 5'FAM) obtained from Integrated DNA Technologies, Inc. was used in these studies.

Determination of Equilibrium Dissociation Constant

Varying concentrations of ONS-23 (74 pM, 740 pM, 7.4 nM, 74 nM, 740 nM, 1.48 μΜ, 2.2 μΜ) were prepared in binding buffer and incubated, with 10⁸ -10⁹ washed C. jejuni A9a cells at room temperature for 45 min with moderate shaking. Aptamer-bound cells were centrifuged at 1500 x g and washed with 500 μl of binding buffer. Binding assays for each concentration were performed in three, independent trials and analyzed using flow cytometry.. The equilibrium dissociation constant (K_d) was calculated by fitting the average total, per cent fluorescent bacterial cells (y) due to binding with FAM-labeled aptamer ONS-23 as a function, of the concentration of aptamer (x) using a non-interacting binding sites model in SigmaPlot (Jandel, San Rafel, CA).

Microscopic Confirmation of Aptamer ONS-23 labeling to C jejuni

Microscopic confirmation of ONS-23 binding to C. jejuni A9a cells was done using an Olympus BX51 microscope (100X objectives with 1.3 NA oil immersions) (Olympus America Inc., Center Valley, PA) with FITC-specific Chroma filter (Chroma Technology Corp., Rockingham, VT). The images were recorded using a Hamamatsu (ORCA-ER) digital camera (Hamamatsu Corporation, Bridgewater, NJ) with Metamorph molecular device imaging system (Molecular Devices, Sunnyvale, CA).

Confirmation of Aptamer ONS-23 Binding Inclusivity and Exclusivity.

Assays to evaluate the binding affinity of aptamer ONS-23 with other C. jejuni strains as well as to unrelated bacterial species were undertaken. In these experiments, 10⁸ -10⁹ bacterial cells and 1.48 μΜ aptamer ONS-23 were mixed in solution at 25°C for 45 min with moderate agitation to facilitate aptamer binding. Cells were centrifuged at 1500 x g and washed with 500 μΐ of binding buffer to separate unbound from bound aptamers prior to analysis using flow cytometry. Binding exclusivity studies were done using B. cereus strain T, E. coli 0157:H7 and L. monocytogenes (ATCC191 15).

Aptamer ONS-23 Binds Selectively With Multiple C, Jejuni Strains Of Different

Zoonotic Origins

To assess the sub-species effect of aptamer ONS-23 binding, assays were performed with C. jejuni strains ATCC-33291 (human), A14a (poultry processing plant), 2083 (cattle), ATCC-33560 (bovine). The percentage of fluorescent cells (n=200,000) following binding with all four strains ranged from 25-36%. The binding affinity was most similar for strain ATCC-33560 (Fig. 5A), ATCC-33291 (Fig. 5B), and 2083 (Fig. 5C) and somewhat decreased for strain A14a (Fig. 5D).

Molecular Confirmation of Aptamer ONS-23 Selectivity toC jejuni in a Mixed Cell

Suspension

The selective affinity of aptamer ONS-23 for C. jejuni in a mixed bacterial

8 9

population (10 -10 cells each) comprised of C. jejuni A9a, B. cereus strain T, E. coli 0157:H7 and L. monocytogenes (ATCC191 15) was also assessed. After exposure of aptamer ONS-23 with the mixed cell population, approximately 10⁵ cells with highest fluorescence intensity were collected by cell sorting. Total genomic DNA from sorted cells was extracted using a NucleoSpin^® Food genomic DNA extraction kit (Macherey-Nagel, Diiren, Germany) as per manufacture's instructions. DNA was amplified in a PCR reaction with primers targeting a 176 bp region of hippuricase gene, a C. jejuni species-specific target (22). The 20 μΐ PCR reaction contained IX Go Taq® PCR buffer, 0.8 mM dNTP mix, 400 nM Primer mix containing 10 μΜ each of forward primer Hip la and reverse primer Hip 2b (Table 1), 0.65 U Go Taq® DNA Polymerase. Amplification was performed using DNA Engine (PTC-200) thermal cycler with cycle time/ temperature combinations of 95°C for 5 min followed by 35 cycles of 95°C for 30 sec, 50°C for 30 sec and 72°C for 1 min followed by final extension at 72°C for 7 min. As a positive control, C. jejuni (NCTC11168) DNA was amplified. The PCR product was analyzed by 1.5% agarose gel electrophoresis and bands were visualized following ethidium bromide staining

Counter-SELEX Maintains Aptamer Specificity During Whole-Cell SELEX

Counter-SELEX was performed against a cocktail of non-target bacterial strains which are commonly found in foods, or which are common targets in food borne pathogen detection assays. To assess the effectiveness of counter-SELEX for aptamer ONS-23, separate binding assays using B. cereus Strain T, E. coli 0157: H7 and L. monocytogenes ATCC-191 15 we performed; all three of these strains were included in the pooled bacterial cocktail for counter-SELEX. There were no appreciable fluorescently labeled cell counts (n^:::200,000) associated with binding of aptamer ONS-23 for any one of these non-target microorganisms as compared to signals obtained for C. jejuni strain A9a (Fig. 4A, 4B, 4C, 4D).

ONS-23 Binds with Specific Cell Surface Targets of C. jejuni

A reduction of aptamer ONS-23 binding was observed for Proteinase K treated cells (9.94 % fluorescent cells) compared with untreated cells (26.14 % fluorescent cells) suggesting a proteinous nature for cell surface targets being recognized by ONS-23 (Fig.7). Prediction of Unique Secondary Structure of Aptamer ONS-23

The unique 3 dimensional structural folding of aptamer ONS-23 at 37°C was predicted using DNA Mfold (version 3.2)(37) (Fig. 6). With a minimum free energy of - 6.36 kcal/ mol, the structure of aptamer ONS-23 consisted of an external loop of 30 bases with three closing helices. The first hairpin loop was located between the closing base pair G17-C40 with a 4 base pair helix. The second hairpin loop was located between the closing pair at T56-A61 with a 3 base pair helix. A third hairpin loop with a 4 base pair helix was located between the closing base pair at T69-A73. The first two hairpin loops were partially located in the random region, while the third hairpin loop was located in the constant region of the DNA aptamer library.

Flow Cytometric Analysis of Aptamer Binding Affinity

All binding affinity assays using FAM-labeled aptamers were analyzed by flow cytometry using FACSCalibur flow cytometer (BD Biosciences, San Jose, CA). The mean fluorescence intensity and percentage of fluorescent cells (n = 200,000) due to aptamer binding was determined. Data from the FACSCalibur was analyzed using BD CellQuest™ Pro software (BD Biosciences). Histogram overlays were created with BD CellQuest™ Pro and Microsoft Office Excel 2003.

Example 4

Selection of Biotin labeled Aptamers

Preparation of biotinylated single stranded DNA Library: Biotinylated aptamer 229 was selected against Campylobacter jejuni (A9a) cells using whole cell- SELEX (Systematic Evolution of Ligands by Exponential enrichment) process in a similar manner as FAM- labeled aptamers. The biotinylated aptamer library for SELEX was generated using PCR amplification process. In brief, the unlabeled library was procured and amplified using unlabeled forward constant region primers and biotin labeled reverse constant region primers (Table 1). Biotin-labeled double stranded DNA was coupled with Streptavidin MagneSphere® Paramagnetic Particles (SA-PMPs) (Promega) by incubating at room temperature for 30-45 min with gentle rolling. The library-coupled magnetic beads were washed 3 times in 0.1X SSC buffer. The unlabeled ssDNA moieties were separated from the immobilized biotin-labeled strands by alkaline denaturation in 0.1-0.2 M NaOH at room temperature for 4-10 min and then recovered by magnetic capture of the beads using a Dynal MPC^®-M magnetic particle concentrator (Dynal A.S, Oslo, Norway). The remaining biotin-ssDNA coupled magnetic beads were washed thrice in IX Tris-EDTA. A second alkaline denaturation was performed in tightly packed microcentrifuge tubes using ammonium hydroxide (28% ammonia in water) (Sigma Aldrich) at 70-90°C to recover the biotin-labeled ssDNA molecules which were washed an additional 3-4 times using molecular grade water and concentrated using a Microcon^® YM-30 filter device (Millipore, Billerica, MA).

SELEX and Counter SELEX Process: For enrichment of biotinylated- ssDNA (aptamer) candidates, a total of 12 rounds of SELEX were performed. Approximately 250-500 pmoles of the aptamer pool was dissolved in 200-400 μΐ of 0.025% Tween 20-PBS (binding buffer), denatured by heating at 80-95°C for 7-10 min and renatured by flash cooling on ice for 7-10 min to allow intra-strand base pairing. The aptamer pool was incubated with 10 - 10 C. jejuni cells for 45 min at room temperature with gentle rotation. Aptamer-bound cells were recovered by centrifugation at 1500 x g for 7-10 min followed by washing 2-3 times in 500-1000 μΐ binding buffer to remove unbound and non-specifically bound aptamers. Cells were then reconstituted in a final volume of 100-200 μΐ using molecular grade water. Aptamers bound to cells were directly enriched by PCR amplification using the Forward Constant Region primer and Biotin-Reverse Constant Region primer as described for FAM labeled aptamers. The biotin-labeled aptamer pool was separated by alkaline denaturation in preparation for the next round of SELEX.

To assure the specificity of aptamer candidates, two rounds of counter- SELEX were performed. Briefly, the selected aptamer pool was incubated with the pooled counter-SELEX bacterial cocktail (Salmonella enterica 13076, Bacillus cereus 49063, Enterococcus faecalis 29212, E. coli 43895, Salmonella enterica ME 46, Listeria monocytogenes Scott A ) in binding buffer for 45 min at room temperature with moderate shaking. The aptamer-bound cells were recovered and discarded, while the unbound aptamers in the supernatant were collected for further rounds of selection.

Identification of Aptamer 229: The selected aptamer pool after 12 rounds of SELEX and 2 rounds of counter SELEX was subjected to cloning and sequencing to identify aptamer candidates. All binding affinity assays of selected biotin-labeled aptamers were performed by flow cytometry using a FACSCalibur flow cytometer (BD Biosciences, San Jose, CA). Briefly 200-500 p mol of individual biotinylated aptamer were mixed with 10^5" 10⁷ C. jejuni cells for 45-60 min using a roller. After mixing, biotinylated aptamer bound cells were washed and treated with FITC conjugate. The flow cytometric analysis of aptamer bound cells was performed to analyze the mean fluorescence intensity and percentage of fluorescent cells (n ^::: 200, 000) occurring as a consequence of aptamer binding. A total of eleven sequences were analyzed and aptamer sequence 229 (5'-/5Biosg/ GCA AGA TCT CCG AGA TAT CGT GCT GGG GGG TGG TTT GTT TGG GTC GGT TGT TTT GGT TGG GCT GCA GGT AAT ACG TAT ACT -3' (SEQ ID NO: 20)) with 21.62 % cell fluorescent was selected for further characterization.

Characterization of Aptamer 229

Bacterial strains. Campylobacter jejuni (A9a) was grown in Brucella broth and incubated under microaerophilic conditions achieved using the GasPakTM EZ Campy Container System (Bexton, Dickinson and Co, Sparks, MD) for 48 h at 42°C. The pure culture was centrifuged, washed and diluted IX in phosphate buffered saline (PBS, pH 7.0) and cell concentrations were determined by plating serial dilutions on Campy Cefex Agar (Hardy Diagnostics, Santa Maria, CA, USA). Salmonella enterica subsp. enterica (ATCC 13076), Bacillus cereus (ATCC 9789), Shigella sonnei (ATCC 25931), and E. coli 0157:H7 (ATCC 43895) were used in studies to assess the specificity of aptamer 229.

Preparation of ligand-bound magnetic beads. Aptamer 229 is 81 nucleotides in length, consisting of constant regions at the 5' and 3' ends (corresponding to the constant region of the parent library), flanked by the target-specific region. The aptamer was denatured at 95 °C and conjugated to streptavidin-coated magnetic beads (Promega, Madison, WI) at a concentration of 0.1 nmol aptamer per 50

beads in IX PBS Tween (PBST) buffer for 30 min at room temperature. Biotinylated polyclonal Campylobacter antibody was obtained from Thermo Scientific (Rockford, IL, USA) and conjugated to streptavidin-coated magnetic beads (7 μg antibody per 50

beads) as described above.

Capture of C. jejuni. In initial studies using small sample volumes, a fresh C. jejuni A9a culture was 10-fold serially diluted in PBST to yield concentrations ranging from 10² to 10⁷ CFU/ml. One milliliter of each 10², 10³, 10⁵ and 10⁷ CFU/ml C. jejuni was mixed with a suspension of four other food borne pathogens (S. enterica, B. cereus, S. sonnei, and E. coli 0157:H7 which were held at a concentration of 10³ CFU/ml. A 250 μί aliquot of this cocktail was mixed with 50 μ£ of aptamer-conjugated magnetic beads (or antibody conjugated magnetic beads) followed by incubation for 45 min at room temperature with rotation. After incubation, the C. jejuni bound beads were captured using a magnetic separation stand (Promega, San Luis Obispo, CA USA) and washed 3 times with IX PBS buffer at room temperature. Scale-up studies were done using the same general protocol but 300 μί of aptamer-bead complex (0.6 nmol aptamer/300 beads) was

applied to 10 ml buffer system containing 10², 10³, 10⁴, 10⁵and 10⁶ CFU/10 ml of pure C. jejuni culture.

Quantitative real-time PCR. DNA was extracted from recovered beads using the MasterPure™ DNA Purification kit (Epicentre, Madison, WI) in accordance with manufacturer instructions. Detection of C. jejuni was done using a Taqman™ quantitative real-time PCR (qPCR) protocol targeting a 126 bp region of gfyA gene. The primers (Forward 5'- TAA TGT TCA GCC TAA TTC AGG TTC TC-3' (SEQ ID NO: 27); Reverse 5'- GAA GAA CTT ACT TTT GCA CCA TGA GT -3' (SEQ ID NO: 28)) and the TaqMan probe (5756-FAM/AAT CAA AGC CGC ATA AAC ACC TTG ATT AGC (SEQ ID NO:29)/TAMRA_l/-3') were used for DNA amplification (Jensen et al, 2005). The qPCR was carried out in the SmartCyler PCR system (Cephid, CA, USA). A 25 μί PCR reaction volume containing 1 x PCR Buffer, 5 mM MgCl₂, (Invitrogen Life Technologies, CA, USA), 0.4 mM dNTPMix (Applied Biosystems, CA, USA), 300 nM forward primer, 300 nM reverse primer, 200 nM Taqman probe, 1.75 U Platinum Taq DNA Polymerase (Invitrogen Life Technologies, CA, USA) and 2.5 μί of C. jejuni DNA were used. The two-step temperature protocol used in real-time PCR was as follows: after initial denaturation of 95°C for 120 sec, annealing was performed for 40 cycles of 95°C for 20 sec and 60°C for 30 sec.

Data Analysis. Percent capture efficiency (% CE) of the bead-bound aptamers (or antibodies) was estimated as the ratio of CFU equivalents per reaction by qPCR to the total CFU in the sample processed for magnetic bead capture Statistical comparisons between % CE at each inoculum level were done by one-way analysis of variance (ANOVA) followed by Duncan's multiple-range test using the Statistical Analysis System (SAS vr. 9.2, Cary, North Carolina) (p <0.01).

Selection of biotin labeled aptamers

Aptamers selected after 12 rounds of SELEX and two rounds of counter SELEX was analyzed using flow cytometry. A total of eleven aptamer sequences were analyzed and showed approximately 1- 22 % fluorescent cells (n= 200, 000 cell counted) on labeling with the aptamers (Figure 8). Total fluorescent cells on flow cytometric analysis were 8.04% for Aptamer 254, 18.51% for Aptamer 186, 21.62% for Aptamer 229, 6.5% for Aptamer 157, 4.83% for Aptamer 153, 6.0% for Aptamer 71, 5.95% for Aptamer 74, 5.14 % for Aptamer 162, 1.93% for Aptamer 70, 10.1 1% for Aptamer 232 and 0.81 for Aptamer 136 (Figure 8). Aptamer 229 with highest number of per cent fluorescent cells was further characterized using real-time PCR based analysis preceded by aptamer 229- magnetic bead complex based capture assays.

Characterization of Aptamer 229 using real-time PCR based analysis qPCR Standard Curve. To make the standard curve, C. jejuni cells were 10-fold serially diluted to concentrations ranging from 10¹ to 10⁸ CFU/ml. The DNA was extracted from each dilution and subjected to qPCR. The term "CFU equivalents" was used in the standard curve to describe the relationship between initial cell number (before DNA extraction) and C_T value. The qPCR standard curve demonstrated log linear detection in the range of 10¹- 10⁸ CFU equivalents C. jejuni cells per reaction, with a lower limit of detection of 10¹ CFU equivalents (Fig. 9).

Experiments in small volumes of mixed culture: When qPCR was preceded by aptamer capture followed by qPCR, the assay detection limit was 10² C. jejuni cells in 300

buffer. Percent CE (capture efficiency) for aptamer 229 was <5% at inoculum levels of 10 CFU/300 μί and increased to 10-13% at levels of 10 C. jejuni cells in 300 μί PBST buffer. Overall, the aptamer capture assay was more efficient than was the corresponding IMS-qPCR assay, for which capture efficiency never exceeded 2% (which occurred at 10⁷ CFU/300

) and the lower limit of assay detection was one log higher, i.e. 10³ CFU/300 μί. Beads without either ligand demonstrated some non-specific binding at inoculum levels >10⁵ CFU/300 μί (Fig. 10).

Capture efficiency (% CE) of aptamer and antibody-conjugated magnetic beads as applied to serially diluted C. jejuni culture suspended in 300 μί of a bacterial cocktail containing 10³ CFU each of four representative food borne pathogens. * Results are expressed as mean (n=3) ±S.D with Duncan's multiple range test used to determine statistical significance (p < 0.01) when comparing aptamer, IMS, and control beads.

Scale-up Experiments: When aptamer-bound magnetic beads were used to capture C. jejuni diluted in 10 ml volumes of PBST, the limit of detection of the combined aptamer capture-qPCR assay was 10² cells per 10 ml. Again, capture efficiency improved with decreasing cell concentration, with a low of <1% and a high of 4-7% at 10² C. jejuni cells in 10 ml PBST. Non-specific binding of non-conjugated beads was apparent at high target cell concentration but substantially reduced at low target cell number (<10³ CFU/10 ml) (Fig. 1 1).

Capture efficiency (% CE) of aptamer conjugated magnetic beads as applied to serially diluted C. jejuni culture suspended in 10 ml PBST. * Results are expressed as mean (n=3) ±S.D with Duncan's multiple range test was used to determine statistical significance (p < 0.01) when comparing aptamer and control beads.

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Claims

What is claimed is:

1. An aptamer that binds to a live Campylobacter jejuni cell and the aptamer comprises the nucleic acid sequence selected from SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: l l, SEQ ID NO: 12, SEQ ID NO:13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO : 16, SEQ ID NO : 17, SEQ ID NO : 18, SEQ ID NO : 19, SEQ ID NO :20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24 and SEQ ID NO:25.

2. An aptamer according to claim 1 that binds to a live Campylobacter jejuni cell and the aptamer comprises the nucleic acid sequence selected from SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: l l, SEQ ID NO: 12, SEQ ID NO: 13, and SEQ ID NO: 14.

3. An aptamer according to claim 1 that binds to a live Campylobacter jejuni cell and the aptamer comprises the nucleic acid sequence selected from SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24 and SEQ ID NO:25.

4. The aptamer according to anyone of claim 1 to 3, wherein the aptamer binds to a cell membrane protein of the Campylobacter jejuni cell.

5. An aptamer comprising the nucleic acid sequence selected from SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO: l l , SEQ ID NO: 12, SEQ ID NO: 13, and SEQ ID NO: 14.

6. An aptamer comprising the nucleic acid sequence selected from SEQ ID NO:15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24 and SEQ ID NO:25.

7. A method of binding a nucleic acid molecule comprising the nucleic acid sequence selected from SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: l l, SEQ ID NO: 12, SEQ ID NO: 13, and SEQ ID NO:14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24 and SEQ ID NO:25 to a live Campylobacter jejuni cell comprising combining the nucleic acid molecule and the live Campylobacter jejuni cell for a time and under conditions effective to allow the nucleic acid molecule to bind to the Campylobacter jejuni cell.

8. The method according to claim 7, further comprising means to detect the Campylobacter jejuni cell.

9. A kit comprising an aptamer of claim 5 or 6, and written material describing a method for its use.