ENHANCED MULTIPLEX FISH

Abstract

Subject of the present invention is a combination of nucleic acid molecules capable of hybridising with a target nucleic acid sequence. In order to overcome problems with the reproducibility of FISH assays and to decrease assay time, hairpin probes are used in combination with helper probes annealing adjacent to the target site of the hairpin probe.

Description

The present invention relates to the multiplexed usage of hairpin loops for fluorescent in-situ hybridisation and the enhancement of reproducibility, specificity, and speed of assay. A first aspect of the present invention is a combination of nucleic acid molecules capable of hybridising with a target nucleic acid sequence, wherein the combination comprises (a) at least one nucleic acid comprising a sequence capable of forming a hair pin loop (e.g. a molecular beacon), and (b) a second nucleic acid molecule, a third nucleic acid molecule, and optionally at least one further nucleic acid molecule being helper nucleic acids.

Rapid identification of pathogenic organisms in clinical samples is of ever increasing importance in order to reduce mortality, morbidity and cost of treating infectious diseases. The breakthrough in applying DNA-beacon technology to in-situ hybridisation applications (1) allows FISH-technology to compete with PCR systems and micro-array technology in terms of speed and surpass in cost efficiency. The objective of this invention was to find ways to solve the reproducibility problem FISH has been experiencing and further increase the speed of the assay time.

In order to increase the speed of an assay, the dynamics of the assays need to be analysed (2). In PCR-assays all components involved in the hybridisation are in homogeneous solution and follow 2nd order kinetics. Micro-arrays follow pseudo first-order rate, as the capturing oligonucleotides are fixed to the solid phase and the analytes are in solution (3). In FISH the respective roles are exchanged (i.e. the analyte is fixed to the solid phase, and the oligonucleotides are in solution), however, the configuration is similar from the kinetic point of view. The rate constants measured when probes were attached to a solid phase were as much as three orders of magnitude lower than those measured in solution (3). It therefore cannot be expected that the in-situ hybridisation kinetics can be brought to be in the same order of magnitude as in homogeneous solution.

The kinetic properties of hybridisation assays of the state of the art can be summarized as follows:

	Amplification	Micro-array
Assay	assays	assays	FISH
Probe	In solution	Solid phase with	In solution
		secondary structures
Analyte	In solution	In solution	deeply embedded in
			fixed RNA/protein
			macromolecules
Kinetics	Second order	Pseudo first-order	More comparable to
	rate	rate (3)	micro-array assembly
			Expectation is = to
			micro-array to pseudo-
			first order rate

Intrinsic problems of PCR lie in its sensitivity and proneness to inhibitors. In PCRs on clinical samples the DNA/RNA is extracted from very crude and extremely variable matrices that frequently harbour polymerase inhibiting components. Such inhibitors may generate undesirable false negative results. FISH does not require enzymes to generate a signal and is therefore not under such limitations.

Micro-array technology involves fixation of known sequences to a solid-phase support. When used for the hybridisation towards ribosomal RNA it must deal with the issue of accessibility of the target sequence within a large RNA molecule exhibiting secondary and tertiary structures. Fuchs et al have shown diligently, that regions in both the 16S and 23S rRNA are accessible to varying degrees (4, 5). This can range from an easily accessible (Fuchs score I) site to a completely inaccessible site (Fuchs score VI). The inaccessibility of regions limits the sites that can be chosen for species specificity. Equally, the inaccessible regions show the greatest variability and would be the most desirable targets for species specific probes. Moreover, trying to use an even partially inaccessible sequence introduces fluctuation in hybridisation results as a highly undesirable variable in the assay.

As FISH-probes also have to hybridise towards the complex structure of an intact ribosome, it also carries the same burden. Moreover, hybridising linear probes to accessible sites may also cause quenching due to interactions of the fluorophor with the protein/RNA complex. In such cases varying amounts of between only 1% and 20% of the total number of organisms present fluorescence. The interpretation of results with this variable requires extensive knowledge and reading experience. Other experimental variables such as the sample preparation and temperature fluctuation make FISH prone to generating false negative results. Diligent controls must be incorporated in order to get a reliable result. Care must be taken in the probe design so that secondary structures will not inhibit a probes access to a specific sequence. This is a challenge, as most species specific sequences lie in variable regions with poor accessibility (6). Additionally, if the temperature during the hybridisation and washing is not controlled precisely, no hybridisation will occur and a false negative may be generated. Initial enthusiasm in the use of FISH assays was soon replaced with frustration due to the erratic performance.

FISH may generate false positive results

• (a) by inadequate reading of auto fluorescence
• (b) by inadequate reading of particulate matter originating from the sample
• (c) when using linear probes, inadequate washing is the most frequent source of false positives
• (d) inadequate probe design may allow cross-reactivity with closely related organisms (7).

The sheer analytical sensitivity of amplification assays renders it prone to DNA/RNA contamination occurring during sample taking or in the lab, which in turn generates false positive results. False positives may be reduced by using complex closed systems.

For FISH technology to compete, its procedure and hybridisation conditions need to be stream-lined with respect to assay handling, kinetics and hybridisation procedure. Solutions must be found to ensure sensitivity and specificity as well as speed of energy transfer and hybridisation kinetics, thus eliminating the problems in FISH and significantly enhancing the performance.

Fuchs et al. showed the usage of helper oligonucleotides as an increase in signal from a weak 4-7% to 75% of an optimal signal using the standard hybridisation time of at least 90 min in 16S RNA of suspended E. coli cells (6). Fluorescing E. coli cells were detected by flow cytometry. The teachings of Fuchs et al are that helper-oligonucleotides may increase the signal when placed in the vicinity with respect to the secondary and tertiary structure, suggesting that by joint action of multiple adjacent helper oligonucleotides, every site on the rRNA can be opened for FISH. However, the teachings do not show conformity in the usage generating variable results. In some cases four adjacent helpers reduced the signal with respect the signal of two helpers.

Fuchs (6) described the different efficiency of a range of helpers, and found that the helpers adjacent to the probe were most efficient in this region. On the basis of these data, one would expect that the optimal position for helpers would vary from organism to organism according the respective differences in sequence and position of the target within the rRNA.

A signal limiting factor is the number of ribosomes present in an organism. This in turn depends on how an organism reacts to stressful conditions. It is well known in the art that under stressful conditions, the number of ribosomes is down-regulated, changing the signal strength in FISH from a full 4+ to a very weak signal (7).

U.S. Pat. No. 5,030,557 describes hybridisations experiments performed in solution employing isolated ribosomal RNA as target (8). Helper oligonucleotides are used to enhance the binding of labelled oligonucleotides to ribosomal RNA. However, this required an overnight incubation to achieve an enhanced signal. In addition, U.S. Pat. No. 5,030,557 call for a 50-200 fold higher concentration of each helper to achieve the improvement (8). Adding a further helper increased the signal by 20% and the further addition of a third helper only increased the signal by a further 7%. The data of U.S. Pat. No. 5,030,557 are summarized in FIG. 1.

In summary, rapid identification of pathogenic micro-organisms by hybridisation hampered by the following shortcomings

• • Microarray methods have been found to require long incubation times.
  • PCR methods are faster than microarray methods. PCR requires a polymerase which may be inhibited when exposed to a crude sample. Thus, clinical samples should be purified prior to PCR.
  • In-situ methods, such as FISH, may be hampered by accessibility of the target sequence in the cell to be identified. No uniform hybridisation conditions exist. Rather, in-situ methods require adaptation of hybridisation conditions in each new target sequence or/and organism. Experimental conditions of in-situ methods have to be controlled very carefully in order to avoid false negative or false positive results. Further, in-situ methods require long incubation times.

In the present invention, it was surprisingly found that a full 100% signal can be achieved in a FISH assay on cells fixed to a surface by a combination comprising a molecular beacon and at least two helper oligonucleotides in 8 minutes—irrespective of position within the rRNA and organism chosen. It was further surprising that the usage of the helpers together with the beacon as laid out in this invention produced a reproducible homogeneous staining of all organisms with full signal strength.

It was surprising that the said stringent design of beacon-helper arrays and assay conditions removed the problems FISH procedures had encountered.

It is the purpose of this invention to find universal rules for the combination of helper sequences in conjunction with molecular beacons for in-situ hybridisation and overcoming thermodynamic restrictions and heat transfer that hitherto have restricted hybridisation kinetics in FISH.

A first aspect of the present invention is a combination of nucleic acid molecules capable of hybridising with a target nucleic acid sequence, wherein the combination comprises

• (a) at least one first nucleic acid molecule comprising
  • (i) a sequence capable of hybridising with the target sequence,
  • (ii) two complementary sequences capable of forming a stem, and
  • (iii) a luminescent group and a quencher group, wherein the quencher group quenches the fluorescent group if the nucleic acid forms a stem-loop structure, and wherein the fluorescent group is capable of emitting a luminescence signal upon excitation if the oligonucleotide is hybridised with the target sequence,
• (b) a second nucleic acid molecule, a third nucleic acid molecule, and optionally at least one further nucleic acid molecule,
  wherein the second nucleic acid molecule, the third nucleic acid molecule, and the optional at least one further nucleic acid molecule hybridise with the target sequence at a sequence located 5′ or/and 3′ from the sequence to which the at least one first nucleic acid hybridises.

The at least one first nucleic acid of the present invention capable of forming a hybrid with a target nucleic acid sequence and capable of forming a stem-loop structure if no hybrid is formed with the target sequence is also referred herein as “beacon”, “molecular beacon”, “hairpin”, or “hairpin loop”, wherein the “open” form (no stem is formed) as well as the “closed” form (a stem is formed) is included. The open form includes a beacon not forming a hybrid with the target sequence and a beacon forming a hybrid with the target sequence.

In particular, the first nucleic acid molecule comprises a sequence capable of forming a hair-pin loop, e.g. a molecular beacon.

Sequence (i) of the first nucleic acid molecule is also termed herein as “probe sequence” or “probe sequence of the molecular beacon”.

If more than one first nucleic acid is present, the sequences to which the two or more first nucleic acids hybridise may be independently located directly adjacent to each other, or may be independently separated by a gap of at least one nucleotide, such as one, two, three, four, five or even more nucleotides. The sequences to which the two or more first nucleic acids hybridise may also be separated by a gap large enough that one or more helpers may hybridise with the sequence within the gap.

If more than one first nucleic acid is present, they may be directed against the same gene. In other words, if more than one first nucleic acid is present, the target sequences of the more than one first nucleic acid may be selected from sequences obtained from the same gene. Preferably, these sequences are non-overlapping. This allows the detection of individual genes without amplification.

If more than one first nucleic acid is present, they may be directed against the expression product mRNA of the same gene. In other words, if more than one first nucleic acid is present, the target sequences of the more than one first nucleic acid may be selected from sequences obtained from the mRNA expressed by the same gene. Preferably, these sequences are non-overlapping. This allows the detection of individual genes without amplification.

In the present invention, “located directly adjacent to each other” means that no gap is left if the nucleic acid molecules hybridise at adjacent positions on the target sequence.

The second nucleic acid, the third nucleic acid, and the at least one further nucleic acid are termed herein “helpers” or “helper nucleic acids” or “helper oligonucleotides”.

The cognate sequences of the helpers designed in this invention may be placed in close vicinity on the 5′ or/and 3′ end of the cognate sequence of the beacon. A multiplicity of helpers may be used, however full signal strength may be achieved with either two, three or four helpers. The combination of the present invention preferably comprises two, three, four, five, six, seven, eight or ten helper nucleic acids. Preferably, the combination of the present invention comprises two, three, four helper nucleic acids.

The nucleic acids of a combination of the present invention may hybridise with the target sequence at locations directly adjacent to each other, or may be independently separated by a gap of at least one nucleotide, such as one, two, three, four, five or even more nucleotides. For instance, at least two nucleic acid molecules may hybridise with the target sequence at locations separated from each other by a gap of at least one nucleotide, such as one, two, three, four, five or even more nucleotides.

More preferably, the combination of the present invention comprises four helper nucleic acids. In the most preferred configuration the cognate sequences of four helpers are located directly adjacent, without a gap next to the cognate sequence of the beacon and directly adjacent to each other, two to the 5′ flank and two to the 3′ end of the cognate sequence of the beacon. An Example is given in FIG. 3. In this design, the target sequences position and accessibility according to Fuchs may be disregarded.

The target sequence may be selected so that the sequences to which the at least one first, the second, the third and the optional at least one further nucleic acid molecules hybridise are non-overlapping sequences of the target sequence.

An exemplary configuration is described in FIG. 3. Helpers termed “1” and “2” extend from the 5′ end and helpers termed “3” and “4” extend from the 3′ end of the beacon's probe sequence forcing the stem-part of the beacon away from the ribosome and to function as a spacer. Helpers 2 and 4 are placed next to helpers 1 and 3 on the respective 5′ and 3′ ends equally without a gap. In order to achieve maximum synergism in hybridisation, all probe and helper sequences may carry the same thermodynamic properties with respect to the binding to cognate sequences. This stringent selection of oligonucleotides allows the orchestration of the mass hybridisation action covering the length of 100 bases (e.g. between 89 and 120) of the ribosomal RNA for the reproducible opening of ribosomal RNA with the fast kinetics and high specificity of small 20-mer (16-26-mer) oligonucleotides—all operating to the same said stringent conditions.

The sequence of the target sequence to which a nucleic acid of the present invention hybridises is termed herein as “cognate sequences” of the respective nucleic acid. For example, the cognate sequence of a first nucleic acid (i.e. a molecular beacon) is that sequence of the target sequence to which sequence (i), as indicated herein, hybridises. A hybrid of a nucleic acid molecules of the combination of the present invention with the target sequence is also referred herein as “hybrid with the cognate sequence” or as “cognate hybrid”.

The target nucleic acid sequence employed in the various embodiments of the present invention may be a nucleic acid sequence of a cell. The cell may be a eukaryotic cell or a prokaryotic cell. The cell may be any cell which can be present in a biological or clinical sample. In particular, the target nucleic acid sequence may be a nucleic acid sequence of a micro-organism, such as a micro-organism selected from bacteria, yeasts and moulds, in particular from Gram positive or/and Gram negative bacteria. Depending on the disease state certain pathogens most frequently are the causative agents and can thus be compiled into diagnostic groups. Addition or omission of certain pathogens may be required depending on regional epidemiology in order to reach the 95-percentile. The listing of Table 1 covers the requirements of Europe and most of North America. The micro-organism is preferably selected from the organisms listed in Table 1 and Table 4.

The cell employed in the present invention may be kept in suspension or/and suspension culture.

The target nucleic acid sequence may be a DNA sequence or/and a RNA sequence, in particular an rRNA sequence, such as a bacterial 16S rRNA or/and a bacterial 23S rRNA sequence. The target nucleic acid sequence may also be an mRNA sequence.

In particular, the two complementary sequences (ii) of the first nucleic acid molecule are flanking the sequence (i), i.e. the first sequence of (ii) is located at the 3′ end of the sequence (ii) and the second sequence of (ii) is located at the 5° end of the sequence (i).

The two complementary sequences of (ii) may independently have a length of 4 to 10 nucleotides, in particular 4, 5, 6, 7, 8, 9, 10 or even more nucleotides. Preferably, the two sequences of (ii) have the same length.

In the first nucleic acid molecule, the luminescent group may be attached at one of the two complementary sequences capable of forming a stem, whereas the quencher may be attached at the other of the two complementary sequences, so that the quencher essentially quenches the luminescence when a stem is formed, and that the luminescent can emit a luminescence signal when the hairpin is open.

Preferably, the luminescent group is independently attached at the 5′ end of the at least one first nucleic acid molecule, or at a position which is 1, 2, 3, 4, 5 or 6 nucleotides distant to the 5′ end. In this case, the quencher is independently attached at the other end not covered by the luminescent group, i.e. at the 3′ end, or at a position which is 1, 2, 3, 4, 5 or 6 nucleotides distant to the 3′ end.

It is also preferred that the luminescent group is independently attached at the 3′ end of the at least one first nucleic acid molecule, or at a position which is 1, 2, 3, 4, 5 or 6 nucleotides distant to the 3′ end. In this case, the quencher is independently attached at the other end not covered by the luminescent group, i.e. at the 5′ end, or at a position which is 1, 2, 3, 4, 5 or 6 nucleotides distant to the 5′ end.

The luminescent group may independently be coupled to the at least one first nucleic acid molecule by a linker. The quencher group may be independently coupled to the at least one first nucleic acid molecule by a linker. The skilled person knows suitable linkers. The linker may independently comprise at least one nucleotide.

The skilled person knows suitable luminescent group and quenchers. The luminescent group is preferably a fluorescent group. Suitable fluorescent groups may be independently selected from those readily commercially available absorbing from UV to the visible, to the IR light range and emitting with a Stokes shift enabling the physical separation of light due to excitation and emission. In the fluorescent group, autofluorescence may reduced via enhanced Stokes shift. Suitable fluorescent groups may independently be selected from FAM, Cy3, FITC and derivatives thereof.

Luminescence, in particular fluorescence, may be determined by microscopy, flow cytometry or any other suitable method known in the art. In cells kept in suspension or suspension culture, luminescence, in particular fluorescence, may be determined by flow cytometry.

Hybridisation of the beacon of the present invention with a target sequence may take place under conditions where the loop will unfold in presence of a cognate sequence. A beacon with a closed stem will provide higher specificity and compensate for the decrease due to the increase in sequence length.

This goal is achieved by choosing a stem sequence with a negative AG even under hybridisation conditions, but substantially higher (less negative) than the loop sequence (cognate DNA/RNA hybrid), and preferably in the absence of Mg²⁺. Thus, the hybridisation with the target sequence may take place, when the stem is destabilized by the essentially Mg²⁺ free conditions.

“Substantially higher ΔG” means a difference of the respective ΔGs of is between about −15 and about −25 kcal/mol, preferably between about −17 and about −23 kcal/mol and even more preferable between about −19 and about 21 kcal/mol.

In order to achieve quenching of the luminescent group, both of which form part of the beacon, in those beacon molecules not hybridising with the target sequence, stem formation must be induced after the hybridisation reaction. This may for instance be achieved by a beacon having a ΔG<0, so the hairpin will form spontaneously. Further, stem formation may be introduced by washing with a Mg²⁺ containing buffer as described herein.

In particular, the hairpin loops are constructed in such a way that under standardised hybridisation conditions (e.g. under essentially Mg²⁺ free conditions) the stem is open so that possible sterical limitations do not hinder the hybridisation process. For instance, sterical limitations may be present when the target sequence is a rRNA sequence. If the effector is a fluorophor, the fluorophor will not be quenched by the close proximity of ribosomal proteins.

Suitable conditions for induction of stem formation after hybridisation include an Mg²⁺ containing buffer, for instance containing about 0.1 to about 20 mM Mg²⁺, about 1 to about 20 mM Mg²⁺, 5 to about 15 mM Mg', about 8 to about 12 mM Mg²⁺, about 1 mM to about 10 mM Mg²⁺, about 2.5 mM to about 7.5 mM Mg²⁺. Preferred is a concentration of about 5 mM Mg²⁺ or about 10 mM Mg²⁺. The buffer may have a pH>8, preferably of about 8.3. The pH may also be adjusted to about 7.5 to about 9 or about 8 to about 8.5.

Furthermore, the hair-pin loops function in their entirety and cannot be dissected. Stem and loop as nearest neighbour and stacking effect have a profound influence in their thermodynamic properties. Preferred nucleic acids of the present invention are described in Table 1, Table 3 and Table 4. They clearly show that the preferred stem sequence is independent from the ΔG, T_m, GC content or length of the sequence chosen to identify a species.

In the present invention, the thermodynamic specifications for the individual construction of nucleic acids employed in the combination of the present invention suitable for standardised conditions are set: The Gibbs energy (AG) for the formation of the nucleic acid may be designed in such a way that

• • The hairpin stem will form spontaneously (ΔG<0) in the absence of a cognate target sequence under hybridisation conditions.
  • The ΔG of the cognate hybrid is significantly lower (i.e. is more negative) than the ΔG of the hairpin stem.
  • The respective ΔG of the cognate sequence is lower than a mismatch or non-cognate sequence.
  • The T_m for the formation of the hair-pin loop has to be designed in such a way that the T_m of the hair-pin loop is lower than or essentially at the T_m of the hybrid.

In particular, the nucleic acids of the combination of the present invention independently hybridise with the target sequence with a more negative ΔG than the ΔG generated by the natural refolding of the target sequence, which preferably is a target mRNA or target DNA sequence.

It is preferred that the ΔG of the cognate hybrid (i.e. the hybrid of a helper or/and molecular beacon of the present invention with its target sequence) is in the range of about −15 and about −25 kcal/mol, preferably between about −17 and about −23 kcal/mol and even more preferable between about −19 and about 21 kcal/mol under hybridisation conditions. The ΔG of the cognate hybrid may independently be adjusted for the nucleic acid molecules of a combination as described herein.

It is also preferred that the ΔG of at least two cognate hybrids under hybridisation conditions do not vary more than 5 kcal/mol, preferably no more than 3 kcal/mol, more preferably no more than 2 kcal/mol and most preferably no more than 1 kcal/mol. In particular, the ΔG of the cognate hybrids under hybridisation conditions do not vary more than 5 kcal/mol, preferably no more than 3 kcal/mol, more preferably no more than 2 kcal/mol and most preferably no more than 1 kcal/mol.

The nucleic acid molecules of the combination may independently hybridise with a target sequence, preferably with a target rRNA sequence, with a combined AG in the range of −60 to −150 kcal/mol, −80 to −150 kcal/mol, or −100 to −120 kcal/mol. Surprisingly, it was found that, using the stringent gap-free configuration of 5 nucleic acids (including one molecular beacon), the increase in signal strength up to a universally strong signal was achieved not only for the one region in E. coli, but strong signal enhancement could be achieved for numerous regions of both 16S and 23S rRNA in a wide range of organisms with the same kinetics. It is preferred to combine labelled and unlabelled oligonucleotides that all carry the same thermo-dynamic characteristics in such a way that they hybridise under identical conditions in all organisms with a combined and standardised ΔG=−60 to −150 kcal/mol without loss of single base discrimination capability.

The criteria for the selection of a probe assembly could thus be determined to be driven by sequence specificity first and secondly by the free energy (ΔG) generated upon hybridisation, disregarding T_m as the hitherto driving thermodynamic parameter used in the art. As all helpers and beacons may be designed to have very similar characteristics, it was not only possible to have matched helpers together with a beacon, but also to generate multiple examples of said groupings, all working under identical conditions and binding to both 16S and 23S rRNA with closely similar kinetics. Effectively the free hybridisation energy of a 100mer generated may be used while maintaining the discriminatory specificity of for example short 18-26-mer oligonucleotides thus favoring the hybrid binding with a strong signal over the re-formation of the native ribosomal structure. Table 4 compiles the beacons designed together with their respective helpers together with the thermodynamic properties and the scoring according to Fuchs et al. (6).

Occasionally cognate sequences may form spontaneous hairpin loops, where one arm only needs to be supplemented to achieve the beacon formation. If the target sequence is a rRNA sequence, this, however renders the effector, e.g. the fluorophor, in very close proximity to potentially quenching proteins of the ribosome. In a preferred configuration the stem is extended. In order to conform with said thermodynamic specifications as described herein even with an extended stem a method was devised to keep both the T_m and ΔG within the specifications. According to the present invention, this can be achieved by the introduction of at least one non-matched nucleotide or nucleotide analogue. In the present invention, introduction of at least one non-matched nucleotide may be enhanced by the introduction of an additional nucleotide or nucleotide analogue, so that the two complementary sequences have a different length, and the stem becomes “bended” (see for example position 36 in SEQ ID NO:1), or/and may be achieved by a replacement of a matching nucleotide or nucleotide analogue by a non-matching nucleotide or nucleotide analogue (see for example position 5 in SEQ ID NO: 7). Thus, in the present invention, the “complementary sequences capable of forming a stem” may also include at least one non-matched nucleotide, preferably 1, 2, 3, 4 or 5 non-matched nucleotides.

As can be seen from Table 2 none of the sequences disclosed here could be devised as PNA-beacons due to the said limitations in the construction of PNA-oligonucleotides. The major limitation being in the oligonucleotide length required to have both sufficient specificity and a stem length sufficient to ensure the re-folding of the loop when not hybridised. It is therefore necessary to devise DNA-beacons that are able to hybridise with sufficient affinity and speed to enable the in-situ identification of micro-organisms.

The beacon of the present invention is preferably not a PNA beacon. The backbone of the beacon is preferably a nucleic acid backbone, in particular DNA. The beacon may comprise a nucleic acid analogue such as a deoxyribonucleotide analogue or a ribonucleotide analogue in the nucleic acid portion or/and in the linker if a linker is present. This analogue is preferably a nucleotide analogue modified at the sugar moiety, the base or/and the phosphate groups. The nucleotide analogue is preferably not a PNA building block.

Following the said 95-percentile in clinical samples, pathogens can be grouped into disease related groups. Probes towards these organisms must work simultaneously under the said conditions, especially if all probes are to be utilised on one chip. The chip application calls for a stringent standardisation of both the cognate and stem characteristics. If a combination of more than one probe is employed, i.e. at least two probes, all probes have to be designed to work on the same slide/chip simultaneously.

The molecular beacon of the combination of the present invention may be selected from the beacons of Table 1, Table 3, and Table 4. The combination of the present invention may comprise one, two, three or even more beacons as described herein, which may be selected from the beacons of Table 1, Table 3 and Table 4. If more than one beacon is present in the combination of the present invention, the beacons may have the same or different cognate sequences. It is preferred that the cognate sequences of individual beacons are different.

If more than one beacon is present in the combination of the present invention, the ΔG difference of the individual beacons of the hybrid of the sequences of (ii) or/and the hybrid of the sequence of (i) with a target sequence may be at the maximum about 4 kcal/mol, preferably at the maximum about 3 kcal/mol, more preferably at the maximum about 2 kcal/mol, and most preferably at the maximum about 1 kcal/mol with respect to the cognate sequence.

The second nucleic acid, the third nucleic acid, and the at least one further nucleic acid may independently contain a label that can be distinguished from the luminescent group of the at least one first nucleic acid. The second nucleic acid, the third nucleic acid, and the at least one further nucleic acid preferably do not contain luminescent group. The second nucleic acid, the third nucleic acid, and the at least one further nucleic acid preferably do not contain a quencher.

The design of the helper nucleic acid molecules may be performed according to the stringent thermodynamic design as laid out in EP 07 818 883.6 (1) which is included herein by reference. The cognate sequence of the labelled beacon and the helpers may all carry the same thermodynamic characteristics and thus may operate synergistically. The synergy of action due to the precision of design generates the difference in the hybridisation kinetics.

The sequence of a helper nucleic acid capable of hybridising with the target sequence may be designed on the basis of its complementary target sequence (cognate sequence), wherein the sequence of the helper preferably has no mismatch with reference to the target sequence. Having designed a molecular beacon, the skilled person can select cognate sequences for the helper nucleic acids from sequences adjacent to the cognate sequence of the molecular beacon. Suitable sequences may be obtained from public databases. As described herein, preferred molecular beacons may be selected from Table 1, Table 3 and Table 4. In this case, the cognate sequences of the helper nucleic acids may be selected from database sequences of the respective organism adjacent to the cognate sequence of the beacons described in Table 1, Table 3 and Table 4. The cognate sequences of the helper nucleic acids may also be selected from the sequences described in Table 1, Table 3 and Table 4.

The sequences indicated in Table 1, Table 3, and Table 4 as “helper sequences” or “helper” may also be employed for the design of a molecular beacon. In this case, the N-terminal and C-terminal complementary sequences (ii) capable of forming a stem or/and other components described herein have to be added. The sequences indicated in Table 1, Table 3, and Table 4 as “beacon sequences” may also be employed for the design of a helper nucleic acid. In this case, the stem sequences have to be eliminated. For example, Table 4 describes combinations of five nucleic acids of the present inventions, wherein the sequence of one specific nucleic acid is termed “beacon sequence”. It is contemplated that any combination of Table 4 is within the scope of the present invention wherein one or more sequences of a combination of Table 4 are selected for design of a molecular beacon, and the remaining sequences are employed as helper sequences. If applicable, stem sequences or/and other components described herein are eliminated or added.

The combinations of hair-pin loops and helper nucleic acids described in Table 4 are preferred. Table 4 describes individual combinations of hair-pin loops and helper nucleic acids, wherein the cognate sequences of the hair-pin loop and the helper sequences are localized on the target sequence of a micro-organism. Specific embodiments of the present invention refer to combinations described in Table 4 comprising a hair-pin loop and one, two, three or four helper nucleic acids. The combinations described in Table 4 can be designated by the name of the hair-pin loop. A preferred combination may be selected from combinations represented by B-Achxyl, B-Acinbaum-IV, B-Acibact-2, B-Baccer-II, B-BacPrev, B-Bcc, B-Ctherm, Citfreu-WIII, B-Clodiff, B-Cloper-II, B-Clospp, Corspp, SB-Corspp, EcoShi, B-EHEC-II, B-Entbac-II, SB-EntSak-I, SB-EntSak-II, Eubiae, Entcoc III, B-Entcoc-II, B-Entalis-2, B-Entium-II, B-E. coli III, B-Haeinf, SB-InqLum, Klepne-5, B-Kleboxy-II, SB-Klepne-6, B-Klepne-4, B-Limo-II, SB-Mycavi-A, SB-Mycavi-B, B-Neigon, B-Neimeng, SB-Panapi, SB-PansppA, SB-PansppB, B-propacn, B-propacn, B-Protmir, B-Protvul, SB-Psaer-E, B-Psaer D, SB-RalsppA, SB-SB-RalsppC, Stalug, B-Sal 1686, B-Sermarc-II, B-Shig-II, B-Shig-III, Sb-Shispp-4, B-Staphspp-2, B-Staur-3, Stalug, B-Stemal-2, B-Straga-3, B-Strepne-2, B-Strepne-3, B-Strpyo-D, B-Strept-III, B-Yers-III, and B-Yers-II. It is more preferred to select a group of combinations from combinations represented by B-Achxyl, B-Acinbaum-IV, B-Acibact-2, B-Baccer-II, B-BacPrev, B-Bcc, B-Ctherm, Citfreu-WIII, B-Clodiff, B-Cloper-II, B-Clospp, Corspp, SB-Corspp, EcoShi, B-EHEC-II, B-Entbac-II, SB-EntSak-I, SB-EntSak-II, Eubiae, Entcoc III, B-Entcoc-II, B-Entalis-2, B-Entium-II, B-E. coli III, B-Haeinf, SB-InqLum, Klepne-5, B-Kleboxy-II, SB-Klepne-6, B-Klepne-4, B-Limo-II, SB-Mycavi-A, SB-Mycavi-B, B-Neigon, B-Neimeng, SB-Panapi, SB-PansppA, SB-PansppB, B-propacn, B-propacn, B-Protmir, B-Protvul, SB-Psaer-E, B-Psaer D, SB-RalsppA, SB-RalsppB, SB-RalsppC, Stalug, B-Sal 1686, B-Sermarc-II, B-Shig-II, B-Shig-III, Sb-Shispp-4, B-Staphspp-2, B-Staur-3, Stalug, B-Stemal-2, B-Straga-3, B-Strepne-2, B-Strepne-3, B-Strpyo-D, B-Strept-III, B-Yers-III, and B-Yers-II. The group may comprise at least 2, at least 5, at least 10, at least 15, at least 20, at least 30, at least 40, at least 50, at least 60, or even all of the combinations described in Table 4. The group may comprise at the maximum 60, at the maximum 50, at the maximum 40 at the maximum 30 at the maximum 20, at the maximum 10, or at the maximum 5 of the combinations described in Table 4. It is contemplated that specific embodiments of the present invention refer to groups having the minimum number or/and the maximum number of combinations as indicated herein, wherein any combination may be selected from Table 4. For example, specific embodiments of the present invention refer to groups comprising two, three, four, five, six, seven, eight, nine, or ten combinations selected from Table 4.

Preferred groups of combinations of the present invention refer to diagnostic groups. Preferred groups of combinations are selected from combinations suitable for identifying organisms in blood culture (BC) of Gram negative organisms, as for instance indicated in Table 4. Other preferred groups of combinations are selected from combinations suitable for identifying organisms in blood culture of Gram positive organisms, as for instance indicated in Table 4. Other preferred groups of combinations are selected from combinations suitable for identifying organisms capable of causing pneumonia, as for instance indicated in Table 4. Other preferred groups of combinations are selected from combinations suitable for identifying organisms associated with cystic fibrosis, as for instance indicated in Table 4. Other preferred groups of combinations are selected from combinations suitable for identifying organisms found in stool, as for instance indicated in Table 4.

It is contemplated that a combination selected from Table 4 may be a combination wherein one or more sequences of the combination are selected for design of a hair-pin loop, and the remaining sequences are employed as helper sequences, as described herein. In other words, not only the sequence indicated in Table 4 as probe sequence (complementary to the target sequence), but also a sequence indicated in Table 4 as helper sequence may be employed for the design of a hairpin loop.

The helper nucleic acid of the present invention is preferably not a PNA. The backbone of the helper is preferably a nucleic acid backbone, in particular DNA. The helper nucleic acid may comprise a nucleic acid analogue such as a deoxyribonucleotide analogue or a ribonucleotide analogue in the nucleic acid portion or/and in the linker if a linker is present. This analogue is preferably a nucleotide analogue modified at the sugar moiety, the base or/and the phosphate groups. The nucleotide analogue is preferably not a PNA building block.

The second nucleic acid, the third nucleic acid, and the at least one further nucleic acid preferably do not contain a mismatch in the sequence capable of hybridising with the target sequence. The second nucleic acid, the third nucleic acid, and the at least one further nucleic acid may independently comprise at least one nucleotide which does not hybridise with the target sequence, preferably independently located at the 3′ or/and the 5′ terminus of the nucleic acid molecule.

The nucleic acids of the combination according to the present invention are in particular suitable for in situ hybridisation, more particular for FISH. The hybridisation may take place within the cell as described herein, in particular within a micro-organism as described herein. The nucleic acids of the combination may be designed for hybridisation under stringent hybridisation conditions.

Stringent hybridisation conditions, as used herein, preferably comprises hybridisation at 52° C. (±0.2° C.) for up to 30 min, up to 20 min, up to 15 min or up to 10 min, preferably for about 10 minutes, under high salt and preferably under conditions essentially free of divalent cations, in particular under essentially Mg²⁺ free conditions (e.g. 900 mM NaCl, 20 mM Tris/HCl pH 8.3, 0.01% w/w SDS, 1 mM EDTA, 20% v/v formamide), and washing in essentially ethanolic, low salt and room temperature for about 30 to about 90 seconds or about 45 to about 75 seconds, preferably about 60 seconds. Preferably, washing is performed under high Mg²⁺ conditions, for instance in 50% ethanol, 215 mM NaCl, 5 mM MgCl₂, 50 mM Tris/HCl pH 8.3.

In the present invention, hybridisation may be performed in the presence of SDS, for instance about 0.005% w/w to 0.015% w/w or about 0.01% w/w SDS. Hybridisation may also be performed in the presence of formamide, for instance about 15% v/v to about 25% v/v formamide, preferably about 20° A) v/v formamide. During hybridisation, an agent capable of complexing divalent cations, such as EDTA, may be present in a concentration of about 0.2 mM to about 2 mM, or about 0.5 mM to about 1.5 mM. Preferred is an EDTA concentration of about 1 mM.

Room temperature, as used herein, preferably refers to a temperature in the range of about 18° C. to about 24° C. or about 19° C. to about 22° C., such as about 18° C., about 19° C., about 20° C., about 21° C., about 22° C., about 23° C., or about 24° C.

“Essentially ethanolic conditions” as used herein, preferably refer to an ethanol concentration of 0 to 90% v/v, 40 to 90% v/v, 50 to 90% v/v, 60 to 90% v/v, for instance in the range of 40 to 60% v/v, preferably about 50% v/v.

During hybridisation or/and washing, pH may be independently be adjusted to >8, about 7.5 to about 9, or about 8 to about 8.5, preferably to about 8.3.

As used herein, low salt conditions include a total salt concentration of about 50 mM to about 400 mM, about 100 mM to about 300 mM, or about 150 to about 250 mM. Preferred is a concentration of about 200 mM, such as 215 mM. High salt, as used herein, includes a total salt concentration of about 700 mM to about 1100 mM, about 800 mM to about 1000 mM, or about 850 mM to 950 mM. Preferred is a concentration of about 900 mM, such as 915 mM. “Total salt concentration”, as used herein means the concentration of salts of monovalent cations.

It is preferred that in the combination of the present invention the individual nucleic acids function uniformly. “Functioning uniformly” means that successful hybridisation can be achieved with different nucleic acids probes of the present invention under the same hybridisation conditions, for instance under standardised hybridisation conditions. In other words, uniformly functioning nucleic acids of the present invention do not require individual optimisation of the hybridisation conditions.

The combination of nucleic acid molecules as described herein may be provided in one or more compositions, optionally together with the required hybridisation reagents. It is preferred that the combination is provided in one composition.

In the nucleic acids of the combination of the present invention, the AG values of individual nucleic acids with respect to its respective cognate sequence may differ at the maximum by about 10 kcal/mol, preferably at the maximum of about 6 kcal/mol, more preferably at the maximum of about 3 kcal/mol. In particular, if more than one beacon is present in the combination of the present invention, the AG values of individual beacon stems with respect to its respective cognate sequence may differ about 8 kcal/mol, preferably at the maximum by about 5 kcal/mol, more preferably at the maximum of about 3 kcal/mol.

The nucleic acid molecules of the combination of the present invention may independently be oligonucleotides. The sequences of the nucleic acid molecules capable of hybridising with the target sequence independently may have a length in the range of 16 to 26 nucleotides, in particular about 20 nucleotides. For instance, at least one sequence of the nucleic acid molecules hybridising with the target sequence may have a length in the range of 16 to 26 nucleotides, in particular about 20 nucleotides.

The art teaches that helper sequences should be applied in large surplus concentrations. Surprisingly it was found that the working concentration of the helpers and beacons required in the said configuration may be essentially equimolar. Moreover, this design removed the restrictions due to the inaccessibility of rRNA regions and allowed a free choice of unique sequences. Surprisingly, it was possible to generate a uniform 100% signal after only 8 minutes irrespective of the position beacons were hybridising towards. The nucleic acid molecules of the combination may provided in a composition in essentially equimolar concentrations. In the present invention, “essentially equimolar concentrations” means that the concentrations of at least two nucleic acid molecules in the composition may differ by 15 percent by weight at the maximum, 10 percent by weight at the maximum, or 5 percent by weight at the maximum.

Yet another aspect of the present invention is a kit or chip comprising a combination of nucleic acid molecules as described herein, optionally together with the required hybridisation reagents. Preferably, the chip or kit contains one or more combinations of nucleic acid molecules as described herein in separate compositions, for instance one, two, three, four, five, six, seven, eight, nine, ten or even more combinations. Eight separate combinations in a kit or on a chip are preferred. List of groupings and resulting kits for the detection, enumeration and identification of the listed organisms is compiled in Table 1.

A further aspect of the invention is that utilizing combinations according to this invention, active expression products of genes may be detected on mRNA-level, for example by aligning more than one of hair-pin loop pairs along a specific sequence without prior amplification. Highly expressed sequences of genes coding for antibiotic resistance, toxin production or indeed oncogenes may be detected with the same speed and specificity as in the identification of micro-organisms.

The combination, kit or/and chip of the present invention may be used for the identification of a cell as described herein, in particular of a micro-organism as described herein. The combination or/and kit of the present invention preferably is for diagnostic use. More preferably, the combination of the present invention is for diagnosis of the presence of a cell as described herein, in particular of a micro-organism as described herein.

The combination or/and kit of the present invention may be used for the determination of antibiotic resistance.

The combination or/and kit of the present invention may be used for the determination of toxin production, for instance of a cell or/and micro-organism as described herein.

The combination or/and kit of the present invention may be used for the determination of oncogene expression, for instance in a cell or/and micro-organism as described herein.

The combination, kit or/and chip of the present invention may be used for the manufacture of a pharmaceutical composition of the diagnosis of the presence of a cell as described herein, in particular of a micro-organism as described herein.

The combination, kit or/and chip of the present invention may be used for the manufacture of a pharmaceutical composition for the diagnosis of pathological characters within a cell as described herein.

The combination can be applied to assays designed to be performed in tubes, microtitre plates, filtered microtitre wells, slides and chips. The detection can be made with fluorescence, time resolved fluorescence, with a plurality of fluorophores.

In the preferred embodiment for FISH the assay is performed on glass slides designed to hold and separate several samples.

Yet another aspect of the present invention is a method of identifying a cell in a sample, comprising the steps

• • (a) providing a sample,
  • (b) contacting the sample of (a) with the combination of nucleic acid molecules according to the present invention under conditions allowing hybridisation of the oligonucleotides with the target sequences in the cell, and
  • (c) determining the luminescence of the luminescent group of the first nucleic acid molecule.
  • wherein the luminescence of the first oligonucleotide indicates the presence of the target sequence.

The presence of the target sequence indicates the presence of the cell or/and a group of cells, in particular if the target sequence is specific for the cell or/and the group of cells.

The cell may be a cell as described herein, for instance a prokaryotic or a eukaryotic cell. In particular, the cell may be a micro-organism as described herein.

The sample may be any sample of biological origin, such as a clinical or food sample, suspected of comprising a nucleic acid to be detected by the hair-pin loop. The sample may be a sample comprising a cell, in particular a micro-organism, such as a bacterium, yeast or/and a mold, in particular a Gram positive or/and a Gram negative bacterium. The general procedure for the assay is identical with a minor deviation in the pre-treatment of Gram negative and Gram positive organisms (see for instance Example 3).

In the method of the present invention step (b) and (c) may be performed in situ, in particular by FISH.

In step (b), the sample may be fixed on a surface. Step (b) may comprise stringent hybridisation conditions, as described herein.

In step (b), contacting the sample of (a) with the combination of nucleic acid molecules may be performed for up to about 30 min, for up to about 20 min, for up to about 15 min, or for up to about 10 min.

The hybridisation buffer employed in step (b) preferably contains essentially no divalent cations, in particular, the hybridisation buffer employed in step (b) preferably is essentially free of magnesium.

In step (b), the nucleic acids of the combination may be applied in essentially equimolar concentrations.

Step (b) of the method of the present invention may comprise

• • (1) contacting at least one nucleic acid of any of the present invention or a combination of nucleic acids of the present invention with the biological sample,
  • (2) hybridising the nucleic acid or the combination of nucleic acids of (1) with the sample under conditions where the stem will open in the presence of a cognate sequence, e.g. hybridising with a buffer which is essentially free of divalent cations, in particular essentially free of Mg²⁺ and
  • (3) hybridising the nucleic acid or the combination of nucleic acid of (1) with the sample under conditions where the stem of the nucleic is open, e.g. hybridising with a buffer which is essentially free of divalent cations, in particular essentially free of Mg', and
  • (4) inducing conditions which allow for stem formation in those nucleic acid molecules of (1) not forming a hybrid with the sample, e.g. washing with a magnesium containing buffer, for instance at pH>8 or/and at room temperature.

Any hybridisation protocol comprising application of an essentially Mg²⁺ free solution and a Mg²⁺ containing solution as indicated above may be applied. “Essentially free of divalent cations” refers to divalent cations in a concentration of less than 1 mM, preferably less than 0.1 mM, more preferably less than 0.05 mM, most preferably less than 0.01 mM. “Essentially free of Mg²⁺” refers to a Mg²⁺ concentration of less than 1 mM, preferably less than 0.1 mM, more preferably less than 0.05 mM, most preferably less than 0.01 mM. In addition, the removal of divalent ions may be ensured by the addition of a complexing agent, such as EDTA, present in a concentration of about 0.2 mM to 2 mM, or 0.5 mM to 1.5 mM. Preferred is an EDTA concentration of about 1 mM.

The magnesium containing buffer employed in step (b) may contain about 0.1 mM to about 20 mM Mg²⁺, about 1 mM to about 20 mM Mg²⁺, about 1 mM to about 10 mM Mg²⁺, about 2.5 mM to about 7.5 mM Mg²⁺. Preferred is a concentration of about 5 mM Mg²⁺.

At the end of the hybridisation all non-bound beacons need to be returned and secured in the hair-pin loop formation. According to the thermodynamic parameters the refolding should take place spontaneously at room temperature. It was found that this could only be ensured in the presence of bi-valent metal ions. Moreover, the specificity of the assay depended upon the concentration of mono-valent salt in the stop-buffer.

Thus the refolding can be achieved by briefly dipping the slide first into an ethanol bath and then into a stop-buffer bath containing mono-valent salt to support dissociation of weakly bound beacons and divalent salts that support hair-pin loop formation and at a temperature that favours the hair-pin loop formation. In a preferred configuration the ethanol and salt baths are combined and may contain 0-90% v/v ethanol, 10 mM to 1M mono-valent salt, 0.1-20 mM bi-valent salt and buffered between pH 7 and pH 9. In the most preferred configuration the stop-buffer contains 50% v/v ethanol, 215 mM NaCl, 5 mM MgCl₂ and 20 mM Tris/HCl pH 8.3.

For instance, the following protocol may be used: Aliquots of clinical samples are applied to defined fields on the slides. Preferably a defined quantity of 10 μl is applied and dried.

• 1. The samples are the heat fixed to the slides.
• 2. Gram positive organisms are subjected to a Lysozyme/Lysostaphin digestion following well published specifications. In a preferred embodiment the digestion is run for 2 to 7 minutes at between 28 and 60° C. in a humidified chamber. The most preferred digestion is performed by adding digesting enzymes onto each required field of the slide, directly while being on the (52° C.) hotplate and left until dryness.
• 3. Pores are then formed for instance by immersing the slide in pure methanol or pure (at least 96%) ethanol for several minutes. In a preferred embodiment the methanol or ethanol is ice cold and the immersion time is between 2 and 10 minutes. In a more preferred embodiment the slides are immersed for 4 to 6 minutes in ethanol. In the most preferred embodiment the slides are immersed in 96% industrial methylated spirits (IMS) ethanol (or equivalently denatured ethanol) for 5 minutes at room temperature.
• 4. The slide is the dried on a hot-plate, for instance at 52° C.
• 5. The nucleic acids (one or more beacons, at least two helpers) are dissolved in a hybridisation buffer (which may be essentially free of Mg²⁺) and then applied to each field of the slide while on the slide warmer.
• 6. The slide is placed in a hybridisation chamber, humidified with hybridisation buffer. In a preferred embodiment the slide is covered with a hydrophobic cover slip and placed on a covered slide warmer at 52° C. for about 10 minutes.
• 7. The slide is then washed with a magnesium containing buffer, for instance at pH>8 or/and at room temperature. The buffer main contain about 0.1 to about 20 mM Mg²⁺, in particular about 1 to about 10 mM Mg²⁺, more particular about 2.5 to 7.5 mMMg²⁺, even more particular about 5 mM Mg²⁺.
• 8. The slide is then dried and may be mounted with mounting fluid and can be read under an epifluorescence microscope at a total magnification of for instance 400×, 600×, or 1000×.

Should other vessels be used for the hybridisation, the detection may be via flow-cytometry or automated fluorescence reader well known in the art.

Also employed in the method of the present invention can be a kit or chip as described herein.

Yet another embodiment of the present invention relates to chip applications of the beacons of the present invention. For chip applications the beacons need to be covalently attached to a carrier surface. To facilitate this, the 3′-terminal base of the designed beacons may be either biotinylated or linked via a hetero-bifunctional reagent to an enzyme using methods well known in the art of protein and nucleic acid chemistry. Biotinylated beacons may then be added to Streptavidin coated chips as can be obtained freely from commercial sources (19). In this application the respective biotinylated hairpin loops can be attached to plurality of distinct fields of one chip, for instance at least 10, at least 50, at least 100, at least 200, or at least 500 fields, or at the maximum 500, at the maximum 400 or at the maximum 300 fields. Total RNA can be extracted from samples using commercially available kits (20) and can be applied to the chip under hybridising conditions as described herein. After hybridisation the chip can be briefly washed with a magnesium containing buffer, as described herein, for instance at pH>8. Fluorescence on a field marks the presence of specific target sequence, for instance a specific RNA indicating the presence of a respective organism in the sample.

In order to open hybridisation assays to large scale routine applications it is necessary to analyse a plurality of samples sequentially on one reusable chip. The design of the chip must allow large scale production, efficient quality control and long shelf live.

To perform such an assay a large plurality of sequences with identical characteristics (e.g. Table 1, Table 3 or/and Table 4) have been developed, which may be applied to defined positions on the detecting device (chip) respectively.

In a typical assay, total RNA is extracted from a sample utilising extraction procedure and kits readily available on the market and placed on the chip under said hybridisation conditions. After the hybridisation the chip is washed with said stop buffer at room temperature, and is read as is well known in the art. At the end of the cycle all hybridised RNA is washed off with DNA and RNA free hybridisation buffer at about 62° C. The temperature is then dropped to about 52° C. to equilibrate for the next hybridisation cycle.

The invention is further illustrated by the following examples and figures.

LEGENDS

Table 1 describes beacon sequences of the present invention. Abbreviations: R&G: a red or/and a green fluorescent dye may be attached to the beacon, such as Cy3 or FITC or a derivative thereof.

Table 2 describes that PNA beacons are not suitable in the present invention. Calculations were performed with the sequences of Table 1 assuming the beacon to be a PNA beacon. In contrast to DNA beacons, all of the following five criteria have to be fulfilled: GC content <60%, <3 bases selfcomplementary, 4 purines in a row, length of maximal 18, inverse sequence palindromes or repeats or hairpins. “Yes” (“No”) in Table 2 indicates that the criterion is fulfilled (not fulfilled). The column “Final” indicates if a PNA beacon is suitable in the present invention (“Yes”) or not (“No”). “No” in final indicates that one of the five criteria is not met. “Yes” would indicate that all criteria are met. All sequences of Table 2 are judged to be “No”. Thus, no one of the sequences of Table 1 would be suitable in a PNA beacon.

Table 3: List of beacon probes that work under identical conditions as in Table 1 and possess very similar physicochemical conditions.

Table 4: Individual combinations of hair-pin loops and helper nucleic acids, wherein the cognate sequences of the beacon and the helper sequences are localized on the target sequence of a micro-organism (“target organism”). In the hair-pin loop sequence, the sequence complementary to the cognate sequence is underlined. “rRNA” refers to localisation of the target sequence in 16S or 23S rRNA, if applicable. “Alignment with E. coli” refers to the position of the corresponding sequence in E. coli 16S or 23S RNA, respectively. “Fuchs score” refers to the score (brightness class) defined in Fuchs et al. (4). The columns “active beacons in kits” indicate preferred groups of combinations. Preferred groups of combinations refer to groups of combinations suitable for identifying organisms in blood culture (BC) of Gram negative organisms, organisms in blood culture of Gram positive organisms, organisms causing pneumonia, organisms associated with cystic fibrosis, and organisms found in stool. Members of these “diagnostic groups” are indicated by “1” in the respective columns.

FIG. 1: Comparison of hybridisation data derived from U.S. Pat. No. 5,030,557 (“conventional probe”) and hybridisation data of the present invention. The data of Tables I, IIa, IIb, and IIc of U.S. Pat. No. 5,030,557 have been averaged. (1) Probe alone according to U.S. Pat. No. 5,030,557. (2) Probe and one helper according to U.S. Pat. No. 5,030,557. (3) Probe and two helpers according to U.S. Pat. No. 5,030,557. (4) Probe and three helpers according to U.S. Pat. No. 5,030,557. (5) Probe (molecular beacon) and four helper nucleic acids according to the present invention. “12 min” and “overnight” indicate hybridisation periods. “Overnight improvement” indicates the % improvement by hybridisation of overnight incubation compared with 12 min hybridisation. “% hybridisation” indicates the percentage of hybridisation sites in a sample which are occupied by a hybridisation probe.

FIG. 2: Kinetics of hybridisation. (1) E. coli molecular beacon with helper, (2) E. coli without helper, (3) B-Straga-3 molecular beacon (see Table 4) with helper, (4) B-Straga-3 without helper. Fluorescence is given in relative units.

FIG. 3: Scheme describing the alignment of a molecular beacon and four helper oligonucleotides to a rRNA sequence.

EXAMPLE 1

Effect of Helpers

Comparison of the effects of state of the art FIG. 1 summarizes the effect of helper oligonucleotides upon probe hybridisation, as described in U.S. Pat. No. 5,030,557 (see bars (1) to (4) in FIG. 1). The data have been obtained from Tables I, IIa, IIb and IIc of U.S. Pat. No. 5,030,557. Averages have been calculated.

U.S. Pat. No. 5,030,557 teach the use of helper oligonucleotides to enhance the binding of labelled oligonucleotides to isolated ribosomal RNA. Linear probes of 18 to 24 nucleotides in length have been employed. Helpers had a length from 23 to 58 nucleotides. However, this required an overnight incubation to achieve an enhanced signal. In addition, U.S. Pat. No. 5,030,557 call for a 50-200 fold higher concentration of each helper to achieve the improvement. Adding a second helper increased the signal by 20% and the further addition of a third helper only increased the signal by a further 7% (see “overnight” bars in FIG. 1).

In in-situ hybridisation in a micro-organism with a combination of a molecular beacon and four helper nucleic acids according to the present invention, hybridisation reaches about 100% after 12 min (see bars (5) in FIG. 1). Taking into account that in-situ hybridisation generally needs longer hybridisation periods than hybridisation taking place in solution, a hybridisation period of only 12 min with a combination of the present invention compared with overnight hybridisation as described in U.S. Pat. No. 5,030,557 is a strong improvement with respect to state of the art combinations of probes and helpers.

EXAMPLE 2

Kinetics of In-Situ Hybridisation

Molecular beacons of the present invention (E. coli molecular beacon, B-Straga-3, see Table 4) are tested in the absence and presence of four helper nucleic acids in in-situ hybridisation with E. coli and Streptococcus, respectively, fixated on a slide. The beacon B-Straga-3 comprises a sequence hybridising with a target sequence located in 16S rRNA of Streptococcus agalactiae.

10 μl aliquots of a respective bacterial suspension were placed onto each field of a slide and dried to render 10⁵ cells per field. The further in-situ hybridisation assay was performed as described in the invention with one exception. Field 1 received the hybridisation mix at time=0; field 2 after 2 min.; field 3 after 4 min.; field 4 after 6 min.; field 5 after 8 min.; field 6 after 10 min.; field 7 after 11.5 min.; and field 8 before dipping into the stop solution.

As can be seen in FIG. 2, the hybridisation of an unaided E. coli beacon is weak and thus reversible and the re-annealing of rRNA is preferred over the hybridisation with the beacon. The speed of hybridisation as shown in FIG. 2 is due to the stringent design of beacons together with respective helpers.

EXAMPLE 3

A typical hybridisation procedure for the assay is identical for all beacons with a minor deviation in the pre-treatment of Gram negative and Gram positive organisms, as indicated in the Table below.

Step	Gram negative applications	Gram positive applications
1	Apply 10 μl sample to each	Apply 10 μl sample to each
	designated field of a slide	designated field of a slide
2	Dry on hot plate 52° C.	Dry on hot plate 52° C.
3		On the hot plate add 10 μl
		lysis-mix (3.4) and dry (takes 4 min)
4	In a coplin jar, immerse	In a coplin jar, immerse the slide
	the slide in IMS for 7 min.	in IMS for 3 min. and dry
	and dry on hot plate 52° C.	on hot plate 52° C.
5	Remove from hot plate and add 10 μl ready to use hybridization
	mix to each field
6	Place the hybridization cover over the slide and incubate at 52° C.
	in an oven (2.5) for 10 minutes
7	In a coplin jar, immerse the slide in Stop-Mix (3.2) for 1 min.
8	Briefly dip in IMS and dry on hot plate 52° C.
9	Immediately place a small drop of mounting media on each field
	and cover with cover slip
10	Read with fluorescence microscope

The reading can be performed visually or with the aid of automated reading devices with a fluorescence microscope. As is well known in the art, in-situ hybridisation can be easily adapted to flow cytometry by performing the said steps in a micro titre plate and reading via a flow-cytometer. The obvious advantage lies in the ease of automation.

REFERENCES

• (1) EP 07 818 883.6
• (2) M. S. Shchepinov, S. C. Case-Green and E. M. Southern, Appl Environ Microbiol. 2007 January; 73(1): 73-82. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays
• (3) Michael M. A. Sekar, Will Bloch and Pamela M. St John, Nucleic Acids Research 2005 33(1):366-375; Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres
• (4) BERNHARD M. FUCHS, KAZUAKI SYUTSUBO, WOLFGANG LUDWIG, AND RUDOLF AMANN, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, AEM.67.2.961-968.2001, In Situ Accessibility of Escherichia coli 23S rRNA to Fluorescently Labeled Oligonucleotide Probes
• (5) BERNHARD MAXIMILIAN FUCHS, GUNTER WALLNER, WOLFGANG BEISKER, INES SCHWIPPL, WOLFGANG LUDWIG, AND RUDOLF AMANN1, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, December 1998, p. 4973-4982 Flow Cytometric Analysis of the In Situ Accessibility of Escherichia coli 16S rRNA for Fluorescently Labeled Oligonucleotide Probes
• (6) BERNHARD M. FUCHS, FRANK OLIVER GLÖCKNER, JÖRG WULF, AND RUDOLF AMANN, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, August 2000, p. 3603-3607, Unlabeled Helper Oligonucleotides Increase the In Situ Accessibility to 16S rRNA of Fluorescently Labeled Oligonucleotide Probes
• (7) RUDOLF I. AMANN, WOLFGANG LUDWIG, AND KARL-HEINZ SCHLEIFER, MICROBIOLOGICAL REVIEWS, March 1995, p. 143-169, Phylogenetic Identification and In Situ Detection of Individual, Microbial Cells without Cultivation
• (8) U.S. Pat. No. 5,030,557: Means and Methods for enhancing nucleic acid hybridisation. Inventors: Hogan J J and Milliman C L.
• (9) WO 1992014841 19920903, NOVEL LANTHANIDE CHELATE-CONJUGATED OLIGONUCLEOTIDES.
  Subject of the present invention are also the following embodiments:
• Item 1. A combination of nucleic acid molecules capable of hybridising with a target nucleic acid sequence, wherein the combination comprises
  • (a) at least one first nucleic acid molecule comprising
    • (i) a sequence capable of hybridising with the target sequence,
    • (ii) two complementary sequences capable of forming a stem, and
    • (iii) a luminescent group and a quencher group, wherein the quencher group quenches the fluorescent group if the nucleic acid forms a stem-loop structure, and wherein the fluorescent group is capable of emitting a luminescence signal upon excitation if the oligonucleotide is hybridised with the target sequence,
  • (b) a second nucleic acid molecule, a third nucleic acid molecule, and optionally at least one further nucleic acid molecule,
  • wherein the second nucleic acid molecule, the third nucleic acid molecule, and the optional at least one further nucleic acid molecule hybridise with the target sequence at a sequence located 5′ or/and 3′ from the sequence to which the first nucleic acid hybridises.
• Item 2. The combination according to item 1, wherein the sequences to which the at least one first, the second, the third and the optional at least one further nucleic acid molecules hybridise are non-overlapping sequences of the target sequence.
• Item 3. The combination according to item 1 or 2, wherein the nucleic acids are suitable for in situ hybridisation, in particular for FISH.
• Item 4. The combination according to any of the items 1 to 3, wherein the hybridisation takes place within a cell.
• Item 5. The combination according to any of the preceding items, wherein the target nucleic acid sequence is selected from DNA sequences and RNA sequences.
• Item 6. The combination according to item 5, wherein the target nucleic acid sequence is a rRNA sequence.
• Item 7. The combination according to item 5, wherein the target nucleic sequence is a mRNA sequence.
• Item 8. The combination according to any of the preceding items, wherein the luminescent group is independently attached at the 5′ end or the 3′ end of the first nucleic acid, and the quencher is attached at the other end not covered by the luminescent group
• Item 9. The combination according to any of the preceding items, wherein the first nucleic acid molecule comprises a sequence capable of forming a hair-pin loop, e.g. a molecular beacon.
• Item 10. The combination according to any of the items 1 to 8, wherein the nucleic acid molecules hybridise with the target sequence at locations directly adjacent to each other.
• Item 11. The combination according to any of the items 1 to 8, wherein at least two nucleic acid molecules hybridise with the target sequence at locations separated from each other by a gap of at least one nucleotide.
• Item 12. The combination according to any of the preceding items, wherein at least one sequence of the nucleic acid molecules hybridising with the target sequence has a length in the range of 16 to 26 nucleotides.
• Item 13. The combination according to any of the preceding items, wherein the nucleic acid molecules of the combination are provided in a composition in essentially equimolar concentrations.
• Item 14. The combination according to any of the preceding items, wherein the nucleic acid molecules of the combination independently hybridise with the target sequence with a ΔG in the range of −15 to −25 kcal/mol.
• Item 15. The combination according to any of the preceding items, wherein the nucleic acids of the combination independently hybridise with the target sequence with a combined ΔG in the range of −60 to −150 kcal/mol, −80 to −150 kcal/mol, or −100 to −120 kcal/mol.
• Item 16. The combination according to any of the preceding items, wherein the nucleic acids of the combination independently hybridise with the target sequence with a more negative ΔG than the ΔG generated by the natural refolding of the target sequence.
• Item 17. The combination according to any of the preceding items for diagnostic use.
• Item 18. The combination according to any of the preceding items for diagnosis of the presence of a cell.
• Item 19. The combination according to any of the preceding items for the determination of antibiotic resistance.
• Item 20. The combination according to any of the preceding items for the determination of toxin production.
• Item 21. The combination according to any of the preceding items for the determination of oncogene expression.
• Item 22. Kit or chip comprising the combination of any of the preceding items.
• Item 23. A method of identifying a cell in a sample, comprising the steps
  • (a) providing a sample,
  • (b) contacting the sample of (a) with the combination of nucleic acid molecules of any of the items 1 to 16 under conditions allowing hybridisation of the oligonucleotides with the target sequences in the cell, and
  • (c) determining the luminescence of the luminescent group of the first nucleic acid molecule.
  • wherein the fluorescence of the first oligonucleotide indicates the presence of the target sequence.
• Item 24. The method according to item 23, wherein the sample is selected from biological samples, in particular clinical samples.
• Item 25. The method according to item 23 or 24, wherein step (b) and (c) are performed in situ, in particular by FISH.
• Item 26. The method according to any of the items 23 to 25, wherein in step (b), the sample is fixated on a surface.
• Item 27. The method according to any of the items 23 to 26, wherein step (b) comprises stringent hybridisation conditions.
• Item 28. The method according to any of the items 23 to 27, wherein contacting the sample of (a) with the combination of nucleic acid molecules is performed for up to about 30 min.
• Item 29. The method according to any of the items 23 to 28, wherein the hybridisation buffer employed in step (b) does not contain divalent cations.
• Item 30. Use of a combination of any of the items 1 to 21 or a kit or chip of item 22 for the identification of a cell.
• Item 31. Use of a combination of any of the items 1 to 21 or a kit or chip of item 22 for the manufacture of a pharmaceutical composition for the diagnosis of the presence of a cell.

Claims

1. A combination of nucleic acid molecules capable of hybridizing with a target nucleic acid sequence, wherein the combination comprises

(a) at least one first nucleic acid molecule comprising (i) a sequence capable of hybridizing with the target sequence, (ii) two complementary sequences capable of forming a stem, and (iii) a luminescent group and a quencher group, wherein the quencher group quenches the fluorescent group if the nucleic acid forms a stem-loop structure, and wherein the fluorescent group is capable of emitting a luminescence signal upon excitation if the oligonucleotide is hybridized with the target sequence,

(b) a second nucleic acid molecule, a third nucleic acid molecule, and optionally at least one further nucleic acid molecule, wherein the second nucleic acid molecule, the third nucleic acid molecule, and the optional at least one further nucleic acid molecule hybridize with the target sequence at a sequence located 5′ or/and 3′ from the sequence to which the first nucleic acid hybridizes.

2. The combination according to claim 1, wherein the nucleic acids are suitable for in situ hybridization.

3. The combination according to claim 1, wherein the target nucleic acid sequence is selected from DNA sequences and RNA sequences.

4. The combination according to claim 1, wherein the nucleic acid molecules hybridize with the target sequence at locations directly adjacent to each other, or wherein at least two nucleic acid molecules hybridize with the target sequence at locations separated from each other by a gap of at least one nucleotide.

5. The combination according to claim 1, wherein at least one sequence of the nucleic acid molecules hybridizing with the target sequence has a length in the range of 16 to 26 nucleotides.

6. The combination according to claim 1, wherein the nucleic acid molecules of the combination independently hybridize with the target sequence

(i) with a t×G in the range of −15 to −25 kcal/mol,

(ii) with a combined AG in the range of −60 to −150 kcal/mol, −8 to −150 kcal/mol, or −100 to −120 kcal/mol, or/and

(iii) with a more negative AG than the AG generated by the natural refolding of the target sequence.

7. (canceled)

8. (canceled)

9. Kit or chip comprising the combination of claim 1 in one container and instruction of how to use the combination in another.

10. A method of identifying a cell, diagnosing the presence of a cell and/or a target sequence in a cell in a sample, comprising

(a) providing a sample,

(b) contacting the sample of (a) with the combination of nucleic acid molecules of claim 1 under conditions allowing hybridization of the oligonucleotides with the target sequences in the cell, and

(c) determining the luminescence of the luminescent group of the first nucleic acid molecule,

wherein the fluorescence of the first oligonucleotide indicates the presence of the target sequence.

11. The method according to claim 10, wherein the sample is selected from biological samples including clinical samples.

12. The method according to claim 10, wherein (b) and (c) are performed in situ.

13. The method according to claim 10, wherein the hybridization buffer employed in step (b) does not contain divalent cations.

14. The method of claim 10, wherein in (b) the composition provided is part of a kit or is on a chip.

15. The combination of claim 1, wherein the combination is contained in of a pharmaceutical composition for diagnosing presence of a cell.

16. The combination according to claim 2, wherein fluorescence in-situ hybridization (FISH) is employed.

17. The combination according to claim 3, wherein the target nucleic acid sequence is a rRNA sequence or a mRNA sequence.

18. The combination according to claim 5, wherein the nucleic acid molecules of the combination independently hybridize with the target sequence

a. with a t×G in the range of −15 to −25 kcal/mol,

b. with a combined AG in the range of −60 to −150 kcal/mol, −8 to −150 kcal/mol, or −100 to −120 kcal/mol, or/and

c. with a more negative AG than the AG generated by the natural refolding of the target sequence.

19. The method of claim 10, wherein said target sequence is associated with antibiotic resistance, toxin production, or/and oncogene expression.

20. The method according to claim 12, wherein (b) and (c) are performed by fluorescence in-situ hybridization (FISH).

21. The combination of nucleic acid molecules according to claim 1, wherein the sequence in (a) (i) hybridizes with the target sequence, the two complimentary sequences in (a) (ii) form a stem and the fluorescent group in (a) (iii) emits a luminescence signal upon excitation if the oligonucleotide is hybridized with the target sequence.

22. The combination of claim 1, wherein the combination comprises in (b) said at least one further nucleic acid molecule and said further nucleic acid molecule hybridizes with the target sequence at said sequence located 5′ or/and 3′ from the sequence to which the first nucleic acid hybridizes.