GB2359357A - FRET-based assay to detect RNA binding antimicrobials - Google Patents

Abstract

The invention provides a method for determining whether a test compound binds to a target RNA, the method comprising the steps of: (a) contacting the test compound with a pair of indicator molecules comprising an antimicrobial labelled with a donor group or an acceptor group and the target RNA labelled with a complementary acceptor or donor group, the pair being capable of binding to each other in an orientation that permits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer and/or quenching to take place; and (b) measuring the fluorescence of the target RNA and/or the antimicrobial in the presence of the test compound and comparing this value to the fluorescence of a standard.

Description

2359357 METHODS AND KITS FOR DISCOVERY OF RNA-BINDING ANTBUCROBIALS

FIELD OF THE ETION

The present invention relates to the specific interactions of low molecular weight compounds with RNA. More particularly, the present invention relates to compositions, methods and kits for identifying numicrobials and other compounds that Interfere with RNA-anthnicrobial interactions.

BACKGROUND OF THE INVENTION

In most biological systems, the fimction of RNA is often determined by the interactions between highly conserved RNA =es- In many circum:stances it is desirable to develop drags that bind RNA at sites of conserved structure to act as competitive inhibitors of the RNA function that is derived from various RNA interactions, such as those exemplified by RNARNA and RNA-protein interactions. These types of drugs have potential applications in a wide range of diseases including bacterial, viral, and fungal infectious.

1 - Use of fluoresce= to measure ligand binding to RNA 0 A critical step in the development of RNA-binding drugs is the development of simple and robust assays that are suitable for the high throughput screening of large compound 1 is libraries developed either by combinatorial synthesis traditional medicinal chemistry approaches, or from collections of natural produas.

There are many different types of assays that measure the binding of ligands to nur-lelc acids and utilize fluorescence resonance energy transfer (FRET) to generate a signal- FRET is caused by a change in the distance separating a fluorescent donor group from an interacting resonance energy acceptor, either another fluoropbore, a chromophore, or a quencher. Combinations of donor and acceptor moieties are known as "FRET pairs". Efficient FRET interactions require that the absorption and emission spectra of the dye pairs have a high degree of overlap. FRET is also a distance-dependent interaction which is dependent on the inverse sixth power of the intennolecular separation, maidng it a sensitive measurement of molecular distances (Stryer, 1978 and Selvin, 1995).

An improvement in the technology for measuring the ability of small molecules to bind to RNA is to utilize fluorescent reporters. Cuxrent methods all rely on the labeling. of either the nucleic acid or the ligand with a fluorescent tag and measuring changes in fluorescence emission spectrum after binding. For example, Royer (US Patent 5,445,935 (issued August 29, 1995)) described the use of polarization of the fluorescence emission from a Labeled macromolecule, such as a DNA or RNA oligonucleotide, to assess the bindinor of the labeled macromolecule to a second unlabeled macromolecule, such as a protein. Sinfilarly, (Metzger et al. (1997) have measured binding of unlabeled peptides derived from Tat to TAR RNA by measuxing quenching of the intrinsic fluorescence of the peptide after it is bound to RNA.

2 in another application of fluorescence polarization, Richardson and Scb (US Parent 4,257,774 (issued March 24, 1981)) reported a method for detecting compounds that interact with nucleic acids by inhibition of acridine orange binding to the nucleic acid which results in a change in fluorescence polarization. This method is of limited practical use because the binding of acridine is through intercalation at a wide variety of sites on double-helical structures, with the consequent result that the specificity of the assay is limited.

Wang & Rando (US Patent 5,593,835 (issued January 14, 1997) and Wang et al., 1997) discovered that the attachment of cc fluorescent moieties to an aminoglycoside antibiotic enables the subsequent binding Interaction of the antibiotic with an RNA molecule to be enhariced. They haveused this property to develop quantitative screening methods and kits for RNA binding compounds. In their method the fluorescently-labeled antibiotic is bound to a pre- selected region of the target RNA, thereby forming a complex which is less fluorescent than the unbound fluorescent antibiotic because of quenching of the fluorescent moiety due to its interaction with.the target RNA molecule. The complex is then mixed with a compound-to-be-ed, and the fluorescence of the antibiotic measured. The antibiotic becomes more fluorescent if the compound displaces the antibiotic in the complex and binds to the pre- selected region of the target RNA.

A general limitation to the use of a single fluorescent group on a reporter molecule is that this group has to interact directly with the RNA target in order to show alterations in its fluorescence emission speetrumThis severely limits the number of positions on the 3 reporter that can be modified and can also alter the nature of the binding of the reporter to the RNA.

It is an object of the invention to apply FREr methodologies to measure the formation of a complex between a fluorescently-labeled antimicrobial and fluorescently-labeled RNA target. One reason why this approach has not been undertaken previously is that studies have shown that of RNA-peptide complexes are in intermediate exchange, suggesting a high degree of conformational flexibility and dynamic exchange at the RNA-peptide interface (Paglisi et al., 1992; Aboul-ela et al.. 1995 Brodsky & Williarnson, 1997; Cai et aL, 1998, De Guzman cc al., 1998). These dynamic properties are, in theory, a severe hindrance to the development of FRET.

2. RNA Targets for drug discovery Although RNA is often referred to as being single stranded and unstructured, most biologically active RNA molecules actually have a number of intramolecular bindings and contacts that create a wide variety of structures and folds. In RNA structures, the secondary structure is energetically the largest contributor to the ov=aft three- dimensional fold- A primary element of secondary structure in large RNA molecules is the RNA double helix built by Watson-Crick base pairings between two regions of the RNA polynueleotide- Ihe helical elements in RNA are typicaBy interrupted by bulges and internal loops. In addition to disruptions of the helical structures, biologically active RNA molecules typically contain specialized loop sequences that create stable bends in RNA. Associations between single stranded regions as well as those between single stranded regions and double helices lead to 4 t structural elements creating tertiary structures. Many ternary structural elements in RNA fom recurrent motifs, such as upseudoknots" created by the interactions of pairs of loop structures. Additional tertiary structure elements such as base triples are also commonly found in Lirge RNA structures- 3. RNA targets in ribosomal RNA Many antibiotics function by ifflubiting protein synthesis, and it has become increasingly clew that many do so by acting at the level ofribosornal RNA (rRNA). The 16S rRNA of the small, 30S rihosomal subunit and the 23S rRNA of the large, SOS ribosornal subunit are both large RNAs for which th= are highly refined secondary structure models.

The rRNA binding sites of many different types of antibiotics have been mapped by chemical and enzymatic probing approaches. nese antibiotic binding sites are localized to various subregions on the 16S and 23S rRNAs, as exemplified by those identified for the Escherichia cAi rRNAs (FIGS. 1 and 2). These sites include, but are not limited to, the 16S rRNA A site (FIGS- 5 and 13), the 16S rRNA spectinomycin binding site (FIGS. 12 and 16), the 23S rRNA LI (or E site) TIGS. 10 and 14), and the 23S rkNA GTPase center (FIGS. 11 and 15).

Examples of antibiotics targeted to theze sites include, but are not limited to> binding of the 16S rRNA A site by members of the aminoglycoside class, binding of the 23S rRNA Ll site (the E site) by the oxazolidinone class, and binding of the 23 S rRNA GTPase center by the thiazole class- 4. RNA rnimics of antibiotic binding sites Y Targeting drugs against large RNAs such as the 16S rRNA (> 1,400 nucleotides) and 23S rRNA (> 2,700 nucleotides) can be difficult in part due to the size of the RNAs, which can hinder drug development assays. For instance, it can be difficult to produce a suitable quantity and quality of large RNA molecules for assays, and the large size of RNAs can make them refractory to the physical or chemical manipWations of assays. Studies on RNA structure have shown that large RNAs are often composed of subdomains whichliave the ability to fold autonomously. Based on subdomains, it is possible to generate small fi-agments of RNA that are often able to fold into structures that mimic binding sites found in the entire, larger RNA. Model RNAs that fold into the correct structures have been 10 demonstrated to bind molecules with similar aTinities and specificities to those of the original RNA sequences. These small RNAs are useful for studying RNA binding interactions, since their small size permits synthesis on a large scale either by chemical methods or by transcription from DNA templates.

RNA model sequences include nucleic acid structures derived from parental ribosomal RNA that are capable of binding to a ligand (such as an aminoglycoside) as in the original RNA structure. These model sequences often include a stabilizing sequence that provides the model RNA with a conformation that permits ligand binding that is substantially identical to the parental RNA ligand binding pattern. For example, a small model RNA sequence used for investigating the binding of an aminoelycoside on Escilexichia mh 16S rRNA has bceu described by Purohit and Stem (1994. and US Patent 5,712,096 (issued 27 Jan., 1998). The use of small model RNAs based on subdomains from large rRNAs will facilitate the development of RNA-binding drugs.

6 SUMMARY OF THE INVENTION

The invention provides a method for determining whether a test compound binds to a target RNA, the method comprising the steps of. (a) contacting the test compound with a pair of indicator molecules comprising an antimicrobial labelled with a donor group or an acceptor group and the target RNA labelled with a complementary acceptor or donor group, the pair beffig capable of binding to each other in an orientation that permits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer andfor quenching to take place; and (b) measuring the fluorescence of the target RNA andfor 1he antimicrobial in the presence of the test compound and comparing this value to the fluore=nce of a standard.

In preferred embodiments, the standard comprises the indicator pair in the presence or absence of test compound, the fluorescently-labelled target RNA in the presence or absence of test compound, or fluorescentlylabelled antimicrobial in the presence or absence of test compound. It will be appreciated that the fluorescence of the standard may have been determined before performing the method, or may be determined during or after the method has been performed. It may be an absolute standard.

The method may also be used in the identification of compounds that bind to the target RNA from within a plurality of test compounds. such as in screening methods. The method may, therefore, involve the initial step of providing a plurality of test compounds, which may include compounds not already known to bind to the target RNA sequence.

7 In a typical embodiment, therefore, the invention provides a method of screening, for compounds that bind to a target RNA, comprising the steps of (a) contacting a test compound with an indicator complex, the indicator complex comprising a tluorescently-labeled antimicrobial bound to a fluorescently labeled target RNA in an orientation that permits the fluorescent groups present on each molecule to come into sufficient proximity to permit fluorescent resonance energy transfer to take place; and (b) measuring the fluorescence of the target RNA and the antimicrobial in the presence of the test compound and comparing this value to the fluorescence of a standard In preferred embodiments of the methods of the invention, the antimicrobial is selected from the ancirobW classes aminoglycoside, cyclic peptide, macrolide, tetracycline, oxazolidinone, thiazole, protein, glycoprotein, alkyloid, nuclease, and N o, cosidase.

lly Typically, the antimicrobial binds the target RNA with a M of between 1X1012 and 1xl C M, and the target RNA is between 5 and about 750 nucleotides in length.

is In other embodiments, the target RNA is derived from bacterial or viral eukaryotic RNA, and may be chemically modified.

In a particularly preferred embodiment, the target RNA is bacterial 165 rRNA or 23S rRNA or is a fragment of 5-750, 10-450, 15-150, or 20-50 nucleotides of 16S rRNA or 23S rRNA that binds to an antimicrobial.

In other preferred embodiments, the target RNA and the antimicrobial are fluorescently labelled by covalent attachment of a fluorescent group. For instance, the target 8 i RNA may be fluorescently labelled at the 3' or S' end of a strand within the target RNA. or within the chain of the target RNA.

It also may be preferred in some instances that the antimicrobial or the target RNA molecule is adhered to a solid 5UPPort.

In the methods of the invention, it also is preferred that either (i) the donor is auached to the target RNA, and the acceptor is attached to the crobial, or (ii) the donor is attached to the anfumicrobial, and the acceptor is attached to the target RNA - The invention also includes a method for determining the presence in a biological sample of a compound that binds to a target RNA molecule, comprising (a) contacting the sample with a pair of indicator molecules con4xising an antimi ial labelled with a donor group or an acceptor group and the target RNA labelled with a complementary acceptor or donor group, the pair being capable of binding to each other in an orientation that permits the donor group to come mto sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer andlor quenching to take place; and (b) measuring the fluorescence of the target RNA and the antimicrobial as an indication of binding. Preferably in this method, said biological sample comprises a tissue or fluid from a mammal, a plant extract, or prokaryotic exu-,ta.

In other preferred embodiments, the acceptor is able to quench the fluorescence of the donor after binding of the target RNA and the antimicrobial.

In certain preferred mients of the invention. only quenching of the donor due to the proximity of the aczeptor in the antimicrobiA complex;3 measured. In certain embodiments of The invention, the target RNA carries a chromophore or fluorophore that 9 4 t quenches tile fluores=ce of the fluorescent group on the antimicrobial after binding of the two moleculesIn other embodiments of the invention, the antimicrobial carries a cbromophore or fluorophore that quenches the fluorescence of the fluorescent group on the target RNA after binding of the two molecules In some methods according to the invention, the target RNA, the antimicrobial, and the test compound me mixed, and the fluorescence of the mixture is compared to standards.

In other methods, the test compound is first mixed with the labelled RNA in order to form a complex in the absence of the labelled antimicrobial, and the antimicrobial is then added.

Alternatively, a complex is pre-formed between the labelled RNA and the labelled antimicrobial before addition of the test compound The invention also encompasses a Idt for determining whether a test compound binds to a target RNA, the Idt comprising (a) a target RNA labelled with a donor group or an acceptor group and (b) an antimicrobial labelled with a complementary acceptor or donor group, wherein the antimicrobial and the target RNA are capable of binding to each other in an orientation that permits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer andfor quenching.

As used herein, "antbfficrobiaI" refers to an agent that inhibits the growth (i.e. by %, 10 %, 50 %, or even up to 100 %, as determined by measuring optical density of cells during log phase growth) andlor metabolism of a microorganism or Idlls a microorganism, including a prokaryotic andfor a eukaryotic cell, such as yeast. andlor a viras. Anthnicrobials useful in the invention can thus be virtually any of those that may bind to RNA in such a manner so as. to reduce or prevent metabolism andlor growth of the microorganism containing the RNA, and include but are not limited to antimicrobials from the classes amino,c,,lycosides, peptides, cyclic peptides, macrolides, lincomycins, tetracyclines, chloramphenicols, cycloheximides, oxazolidinones, thiazoles, proteins, glycoproteins, alkyloids, nucleases, and N-glycosidases.

As used herein, "taxget RNA" refers to the fluorescently labelled RNA that binds the fluorescently labelled antimicrobial. The target RNA c-m constitute a complete RNA that may mclude, one or more n-bosornal proteins and that is capable of binding an antimicrobial, such as a complete 16S ribosomal RNA or a complete 23S ribosomal RNA. Alternatively, the target RNA can be comprised of a fragment or subregion of the entire 16S or 23S rRNA that may include one or more ribosomal proteins and that binds to an antimicrobial.

Rlmal RNAs useful as targets in the invention include those from microorganirns, such as cubactena and yeast, as many anturacrobials have been demonstrated. to bind to both 16S rRNA (FIG. 1) and 23S rRNA (FIG2). Ribosornal RNAs are highly conserved in their sequences, secondary and tertiary structure, as are the antimicrobial binding fragments of rkNAs (see FIGS. 5 and 12), and thus prokaryotic and eukaryotic rRNAs of lower organism are useful according to the invention.

As used herein, the term "fragrnent" refers to a RNA that is structurally siniflar to a portion of a larger RNA, wherein the fragment is capable of binding molecules in the same manner as the entire, larger RNA.

As used herein, the term "antimicrobial binding site" refers to a site on a RNA that is capable of binding an antimicrobial molecule. Antimicrobial binding sites on the 16S rRNA include but are not limited to those on the 16S A site, the 16S spectinomycin site, and sites capable of bg pactamycin and edeine, as shown in FIG. 1. Antimicrobial binding sites on the 23S rRNA include but are not limited to ihose 23S GTPase center/LI 1 binding site, the Ll (E site) binding site, the viomycin binding site, the vernamycin B binding site, and the site bound by the MLS group of antibiotics, as shown in FIG. 2.

As used herein, the term "donor" refi-,rs to a fluorophore which absorbs at a first wavelength and emits at a second, longer wavelength. The term "acceptor" refers to a fluorophore, chromophore or quencher with an absorption spectrum which overlaps the donor's emission spectrum and is able to absorb some or most of the eniked energy from the donor when it is near the donor group (typically between 1-10Onm). If the acceptor is a fluorophore capable of exhibiting FRET, it then re-emits at a third, still longer wavelength; if it is a chromophore or quencher, then it releases the energy absorbed from the donor without emitting a photon. Although the acceptor's absorption spectruin overlaps the donor's emission spectrum when the two groups are in proximity, this need not be the case for the spectra of the molecules when free in solution. Acceptors thus include fluorophores, chromophores or quenchers that, following attachment to either the RNA target molecule or to the antimicrobial, show alterations in absorption spectrum which permit the group to exhibit either FRET or quenching when placed in proximity to the donor through the binding interactions of two molecules.

AS used herein, references to "fluorescence" or "fluorescent groups" or "fluorophores" include luminescence and luminescent groups, respectively.

12 1 f As used herein, the term "quenebing" refers to the transfer of energy from donor to acceptor which is associated with a reduction of the intensity of the fluorescence exhibited by the donor Standard nucleotide abbreviaiions are used herein: A is a nucleotide comprising an adenine base; G is a nueleotide comprising a guanine base; C is a nucleotide comprising a cytosine base, and U is a nucleotide comprising a uracil base; R is a nucleotide comprising a purine base (i. e- A or G), Y is a nucleotide comprising a pyrimidine base (Le- C or U); and N is any nucleotide- Each occurrence of R, Y or N in a sequence may be the same or different. As used herein the term nucleotide may refer to a deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Preferably, the compounds of the present invention are RNA.

Further features and advantages of the invention will become more fifily apparent in the following description of the embodiments and drawings thereof, and from the claims.

is BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a secondary structure model of 16S rkNA with numerous antibiotic binding sites indicated.

FIG. 2A shows a secondary structure model of the 5' half of 23S rRNA with numerous antibiotic binding sites indicated.

13 FIG. 2B shows a secondary strucúwe model of the 3' half of 23S rRNA with numerous antibiotic binding sites indicated.

FIG. 3 shows the structures of several anilnoglyosides.

FIG- 4 shows the structures of several oxazolidinones.

FIG. 5 shows the identification of a model sequence for the 16S rRNA A site.

FIG. 6 shows the results of binding paramomycin-TAMRA to DABCYL-A site RNA.

FIG. 7 shows the results of binding pararnomycin-TA to DABCYL-A site RNA as measured in a fluorescent plate reader.

FIG. 8 shows the Inhibition of binding of paramomycin-TAMRA to DABM-A site RNA by neomycin.

FIG. 9 shows the inhibition of binding of paramomyein-TA to DABM-A site RNA by paramomycin.

FIG. 10 shows the identification of a model sequence for the 23S rRNA LI binding site (the E site).

is FIG- 11 shows the identification of a model sequence for the 23S rRNA GTPase center, the site of action of the thiazole antibiotics.

FIG. 12 shows shows the identification of a model sequence for the 16S rRNA spectinomycin binding site.

FIG. 13 Representative 16S rRNA sequences for the ribosomal A site, including the diverse organisms Bacillus subtilis, Borrelia burgdorferi, ylobacter sputorum, Mycophunw hyop"umontae, aostndium inwcuun4 Haernophijus influenZac. MycoplaSMa genitalium.

14 FIG- 14 Representative 23S rRNA sequences for the L1 binding site including the dive= organism B4d11us subtilis Borrelia burgdorferi, Helicobacterpylori, Mycoplas= genitalium, Mycobacte.-ium leprae and Haemophilu3 znfluemae.

FIG. 15 Representative 23S rRNA nces for the L1 1 binding site including the diverse orgamsms BmIlus subrilts, Borrefla burgdorfen, Helzcobacterpylori, Mycoplasn= genrtaLt=4 Mycobacterium Leprae and Haemophilus tnfiuenzae- FIG. 16. Representative 16S rRNA sequences for helix 34 the S5 protein binding site at which speetnomycin binds. The diverse organisms Hus subritis, BorreHa burgdoilkd, Canpylobacter spworm, Mycop hyopnmwniae, C7oum imocmm, Haemophilms influenzae and Mywpl=nw genitalium are shown.

is DESCRIPTION

The invention pertains to a simple and robust solution-based assay designed to detect compounds that compete for RNA-binding with an antumerobial.

The use of an appropriately positioned donor group on one molecule and acceptor group on a second molecule leads to significantly improved sensitiviry and speciticity in the assay and distinguishes this assay from previous approaches involving the use of only a single fluorescent group placed on either the target RNA or the antimicrobial. These findings have been exploited to develop the present invention, which includes quantimtive screening methods and Jdts for identifying RNA-binding compounds. The invention is described in detail below.

All references below are incorporated herein in their entirety.

THE ANTMCROBIAL An antimicrobial useful according to the invention is capable of binding to the target RNA. Several antimicrobials function by inhibiting protein synthesis, and have been demonstrated to inhibit a variety of steps in translation by binding to etbacterial n-bosomal RNA (rRNA) (Spabn and Prescott, 1996, J. M61. Med- 74:423). Many antibiotic binding sites on rRNAs have been identified by mutational and structural probing analyses (Spahn and Prescou, 1996, supra). These binding sites are exemplified by, but not limited to, those shown for 165 rRNA in PIG. 1 and 235 rRNA in FIG. 2. The binding of antibiotics is not limited to binding of rRNA, as anzibiotics have been found to bind to other RNAs, including but not ffiffited to transfer RNA (tRNA) (see Table 7), the MVA RRE transcriptional activator region (Zapp er al., 1993, Cell 74:969), self-splicing group I intron RNA (von Absen et aL, 1991, Nature 353: 268) and hammerhead ri-bozymes (Stage et al., 1995, RNA 1:95).Antimicrobials usefid in the invention can thus be virtually any of those that may bind to RNA, and inclu& but are not limited to antimicrobials from the classes aminoglycosides, peptides, cyclic peptides, macrolides, lincomycins, tetracyclines, chloramphenicols, cycloheximides, oxazolidinones, thiazoles, proteins, glycoproteins, aliffioids, nucleases, and N-glycosidases. Representative antimicrobials of these classes include but are not limited to those listed in Tables 1-4, 7, and 8, as well as the aminoglycosides pictured in FIG. 3 and the oxazolidinones pictured in FIG4. The antimicrobial may bind at a particular site of interest in the target RNA, and preferably forms a one-to-one complex with the target RNA, 16 1 r except for catalytic antimicrobials. The affinity with which the antimicrobial binds the target RNA may range in values of M of between 1X10,12 and IX10.4 M.

THE TARGET RNA A "target RNA" useful according to the invention includes an RNA of interest which can be approly labeled (i.e., as desen-bed herein so as to provide PRE as fluoresence or quenching) and to which a suitable antimicrobial can be bound. IZI1bosomal RNAs usefal as targets in the invenzion include those from microorganisms, such as cabacteria (exemplified by Escherichia. coli, Bacillus subtilis, Borrelia burgdorferi, Campylobacter 10 sputorum, Mycop hyopneumonlae, Clostridium innocuum, Raemophilus influenzac, Mycoplasma genitalium, Helicobactor pylori, Mycobacterium leprae), y=t, actinomyces, and streptomyces, as many antibiotics have been demonstrated to bind to both 16S rRNA (FIG. 1) and 23S rRNA (FIG. 2) (Spahn and Prescott, 1996, supra). Targets may also include other RNAs identified as having antibiotic binding sites Examples of such RNAs include, but are not limited to, the self-splicing group 1 introns (von Alisen et al., 1991, suPra), the hammerhead n-bozyme derived from the Avocado Sunblotch Viroid (Stage et al, 1995, supra), the nbozyme derived from the human Hepatitis Delta Virus (Rogers et al., 1996, J. Mol. Biol. 259:916), and the HIV RNA (Zapp et al., 1993, supra). In addition, RNAs that have been sel=ed for their ability to bind antimicrobials, using techniques such 20 as in vitro evolution and selection of RNAs, may be u"M targets.

Within the target 16S and 23S rRNAs, particular subregions of the rRNAs have been identified as the sites for which several antibiotics bind (Spahn and Prescott, 1996, supra). 17 1 These rRNA subregions can serve as model target sequences that are representative of the sequences widiin the context of the entire rRNA. Such rRNA subregions include but are not limited to the 16S rRNA A site, the spectinomycin site in 16S rRNA, the Ll binding site (the E site) in 23S rRNA, and the the GTPase: center in 23S rRNA. An example of an effective model rRNA ence has been described for an arninoglycoside anti-biotic binding site on Escherichia coli 16S rRNA by Purohit and Stem (1994, and US Patent 5,712,096 (issued 27 Jan., 1998). IIiis RNA model sequence includes a nucleic acid structure derived from the parental rRNA that is capable of binding to an aminoglycoside ligand (as in the parental structure) and a stabg sequence that provides the model RNA with a conformation that permits ligand binding that issubstantially identical to the parenW RNA ligand binding pattern.

A target site usdul in the invention may include the antimicrobial target site or a nucleic acid structure which mimics the antimicrobial binding site in the native RNA. Preferably the mimic adopts a conformation substantially identical to the antimicrobial binding site in the nadve RNA and exhibits a ligand binding pattern substantially identical to that site bound in the native RNA - The RNA targets of the present invention may comprise a single molecule, for example a single stranded RNA. Altematively, the RNA targets of the present invention may comprise two or more, preferably two, amealed molecules, for example two single stranded RNA molecules annealed to one another.

is A linker canserve to stabilize the RNA target. The linker may be a nucleotide (RNA or DNA) sequence capable of forming a duplex comprising Watson-Crick base pairs, a cross linked sequence, andlor a sequence capable of forming a secondmy structure such as a loop.

Target RNA sequences for use in ihe present invention can therefore be RNA sequences typically between 10 and about 750 nucleotides in length, or model RNA fl., g. en preferably between about 20 and about 150 nucleotides. Target RNA sequences can be comprised of either chemically synthesised or etically transcribed RNA. The RNA can be a single RNA capable of folding to form a wco structure present in the original RNA target. Alternatively, the target sequences can be assembled from a number of short oligribonucleotides that have been hybridized together and are capable of creating the RNA stru=t of interest present in the original RNA structure- Discontinuities in the target RNA sequence such as single stranded regions or helical Junctions that are not involved m antimicrobial recognition can also be connected by short, single- stranded regions of RNA, tetraloops or other non-nucleotide linkers. Double ded target RNA sequences, constructed frorn short oligoribonueleotides can be further stabilized in regions that are not involved in anthnicrobial recognition by the eon of the helix beyond its normal length.

The integrity of the RNA folding, and the stability of the folded structure can be increased by including the ribosomal protein that is associated with the region in the intact ribosome Examples of the use of pairs of oligonucleotides which, after annealing, are able to mimic a folded RNA target =u=e are given in Kalu et aL (WO92102228 and US Patent 5.821,046 (issued Oct. 13, 1998)) and Karn et al. (WO92105195 and US Patent 5,786,145 (issued Jul 28, 1998)). A synthetic analogue of a n-bozyme formed by the annealing of a pair 19 of oligonueleotides is described in Slim et al., (1991) and Grasby et al., (1993). An example of the use of three oligomicleoildes, which after annealing, are able to mimic a folded RNA target strue= is the TW6 mimic of the Rev binding site on RRE RNA (Iwai et al., 1992; W092/05195).

The target RNA may be a nann-al or- synthetic RNA.

Since oligoribonucleotides are sensitive to cleavage by cellular ribonucleases, as well as to alkaline or acid conditions, it may be preferable to use as the RNA target molecule a chemically modified molecule that m=cs'rhe action of the RNA binding sequence but is more stable. Other modifications may also be desirable to provide groups for immobilizing the RNA target oligonucleotide on solid supports by covalent or non- covalent attachments.

The RNA target ohgonuelcotide may be a naty occurring oligonucleotide, or may be a structurally relaied variant of such an oligonucleotide having modified bases andlor sugars andlor linkages. The terms TNA target" or "RNA target oligonucleotides" or 'RNA oligonucleotides" as used herein are intended to cover all such variants.

Modifications, which may be made either into the binding site per se or to a part of the RNA target oligonucleotide that does not inhibit binding of the antimicrobial, may includ:, but are not limited to the followiner "s:

Z:1 a) Backbone modifications:

(i) phosphorothicates (single S substituents or any combination of two or more with the remainder as 0 (Stein et aL, 1988; Cossrick, 1990 #28; Cartithers, 1989 #27) (R) methylphosphonates (Miller et al., 1980); (iii) phosphoramidates; (Agrawal et al., 1988; Mag & Eugels, 1988); 1 (!v) phosphotriesters (Miller et aL, 1982); and (v) phosphorus-fme linkages (e.g. carbamare, acetamidate, acetate), (Gait et al., 1974); b) Sugar modifications: (i) 2'-deoxynueleosides (R= R); (ii) 2'-0-methylated nucleosides (R = 0Me; (Sproat et aL, 1989)); (iii) 2'-fluoro-2'deoxynucleosides (R = F; (Schmidt et al., 1992)); and (!v) 2'-0-aUVIated nucleosides (Sproat et al., 1991); c) Base modifications (for a review see Gait et al., 1998):

(i) pdine derivatives substituted in the 5-position (c.g. methyl, bromo, fluOrO etc... or replacing a carbonyl group by an amino group, (Piceirffii et AL, 1990); and (ii) purine derivatives lacking specific nitrogen atoms (c-g. 7-deaza- adenine, hypoxanthine, or functiongised in the 8-position (e.g. 8-azido adenine, 8- bromo, adenine), or additional fimcdonalities (e.g. 2, 6-diaminopurine (Lamin et aL, 1991)); d) Oligonucleotides covalendy linked to reactive ftmctional groups (c-g. psoralens, (Lee et aL, 1988); phenanthrolines, (Sun et aL, 1988); mustards, (VIassov et aL, 1988)); c) irreversible cross-linking agents with or without the need for co- reagents) (i) acridine (intercalating agents, (H6lene et al., 1985)); (ii) thiol derivatives (reversible disulphide formation with proteins, (Connolly & Newman, 1989)); (iii) aldehydes (Schiff s base formation); (iv) azido, bromo groups (UV cross-linking); and 21 (v) ellipticenes (photolytic cross-linking, (Perrouault er al., 1990); f) oligonucleotides containing haptens or other binding groups; g) fluorescent moieties or other non-radioactive labels (TuscW et al., 1994); and h) combination of two or more modifications selected from a to g- Regions of the target RNA selected for binding to the antimicrobial include, but are not limited to, sequences bound by an RNA-binding protein and sequences with specific secondary structures formed by bulges, internal loops and junctions etc.

Target 16S and 235 rRNAs are shown in FIGS. 1 ands 2, respectively- The sequence (5'-CCGUCACACCUUCGGGUGAAGUCGG -Y) used for the 16S A site binding studies was derived from 16S rRNA as depicted in FIG. 9. Examples for target RNA sequences that could be derived for the LI binding site (the E site) in 23S rRNA (FIGS. 10 and 14), theGTPase center in 23S rRNA (FIGS11 and 15), and the spectinomycin site in 16S rRNA (FIGS- 12 and 16) are represented in the indicated figures- is FLUORESCENT LARELING Tbe target RNA and the antunicrobial may be fluorescently labeled for use according to the invention by any suitable method, preferably by covalent attachment of a fluorescent group. The labels may be any fluorescent label or fluorophore that does not interfere with the ability of the ant=crobial to interact with the target RNA and is able to show quenching andlor fluorescence resonance energy transfer with the corresponding label on the target RNA.

22 1 The target RNA may be fluorescently labeled at any suitable position. For instance, the fluorescent group or quenching group is placed on or adjacent to the 5' end of the target RNA. Alternatively, the fluorescent or quenching group is placed on or adjacent to the S' end of one of a pair of oligomcleotides forming an RNA duplex, or the S' end of one of the 5 component oligonucleotides in RNA structure created by the am of three or more RNA oligm=leotides. In other instances, the fluorescent group may be placed on or adjacent to the 3' end of one of the synthetic RNA molecules. Fluorescent dyes can be introduced specifically ax the 3' end of transcribed RNA by oxidation with peri followed by coupling with the dye-hydrazide- The fluorescent group also may be placed within the chain of the synthMc RNA molecules. fior instance by incorporation of a fluorescent nuclootide derivative, modification of a nucleotide or substitution of a nucleotide by a fluorescent molecule. For example, tet=edlylrhodamine (TA) can be introduced into synthetic RNA by incorporating the modified deoxy-undine phosphoramidite (5'Dimethoxytntyloxy-S-[N-((tet=ethyl15 odaminyl)-aminohexyl)-3-acryimido)2'-deoxy-uridine-3'-[(2-cyanoethyl)-(N, N-diisoprop yl)l-phosphoramidite)Fluorescein may be incorporated in an analogous way with: YDimethoxytrityloxy-S-[N-((3',6'-dipivaloylfluoresceinyl)-andnohexyl)-3aer yimidol-2'-de oxy-uridine-3'-[(2-cyauoethyl)-(N,N-dhsopropyl)]phosphoramidite. The DABCYL group may also be incorporated using 5'-Dimetboxytrityloxy-S-[N-((4- (dimethybmino)azob.-nzme)20 ohexyl)-3-acryimidol-2'-deoxy-uddine-3'-[(2eyanoethyl)-(N,N-dfisopropyl)]-phospb- oramidite. More generally, a free amino group may be reacted with the active ester of any 23 dye; such an amino group may be introduced by the inclusion of the modified uridine 5'-Dimethox1-5-1N-(tifluoroacetylamirLohexyl)-3- acrylimido]-2'-deoxy-urid ine,3'- [(2--r-yanoethyl)-(N,N-dilsopropyl)]-phosphoramidite. The incorporation of a single deoxy-undine often does not significantly perturb RNA structure and the modification at the 5 position of the base allows for normal base-pairing.

It is also possible to include more than one fluorescent label on a synthetic RNA target molecule without departing from the scope the invention- For instance, a target RNA molecule is labelled with 2 fluorescent groups. with one group placed adjacent to the 5' end of the target RNA sequence and a second fluorescent group placed adjacent to the 3' end, of the target RNA sece. In other embodixnents, two or more fluorescent groups are placed adjacent to the 5' and/or 3' ends of the target RNA molecule andlor at int sites in the RNA target sequences. Multiply labelled target RNAs can be used to increase the intensity of the signals detected in the assay.

Antimicrobial molecules that bind to RNA contain functional groups that render them amenable to derivatization by fluorescent dyes. Ile antimicrobials contain primary and secondary amines, hydroxyl, nitro and carbonyl groups. Methods that can be used to make fluorescent antimicrobial ligands are described below.

A number of chemical reactions can be applied to the fluoret labelling of amines including but not limited to the following, where the fluorescent dye is conjugated to the indicated reactive group:

EURC GICOUP. R=Cfion Amine dye-isothiocyanates Thiourea.

24 Amine dye-succinimidyl ester Carboxamide Amine dye-sulfonyl chloride Sulphonamide Amine dye-aldehyde Alkylamine Acrobials containing amine groups that are appropriate for the introduction of fluorescent dyes include but are not limited to those listed in Table 1.

A number of chemical reactions can be applied to the fluorescent labelling of ketone groups including but not limited to the following, where the fluorescent dye is conjugated to the indicated reactive group:

Eunc Reaction Product Ketone dye-hydrazides Hydrazones Ketone dye-semicarbazides Hydrazones Ketone dye-=bohydrazides Hydrazones Ketone de-amines Alkylamine Antimicrobials containing ketone groups that are appropriate for the introduction of fluorescent dyes include but are not limited to those listed in Table 2.

A number of chemical reactions can be applied to the fluorescent labelling of aldehyde groups including but not lirnited to the following, where the fluorescent dye is conjugated to the indicated reactive group:

&nctional -C)Zon Reacti Product Aldehyde dye-hydrazides Hydrazones Aldehyde dye-semicarbazides Hydrazones Aldebyde dye-carbohydrazides Hydrazones Aldehyde dye-amines Alkylamine Andmicrobials containing 2dehyde groups that are appropriate for the introduction of fluorescent dyes include but are not limited to those listed in Table 3-

Dehydrobutyrene and dehydroalanine moieties have characteristic reactions that can be utilized to introduce fluorophores, as illustrated but not limited to the following, where the fluorescent dye is conjugated to the indicated reactive group:

Rea.cliou Bmduct Dehydrobutyrine dye-sulphydryl Methyl lanthionine Dehydroalanine dye-sulphydryl Lanthionine Andinicrobials containing aldehyde groups that are appropriate for the introduction of fluorescent dyes include but are not limited to those listed in Table 4.

Useful fluorophores (in addition to those listed in Tables 5 and 6) include, but are not limited to: Texas Red7m (TR), Lissaminem rhodamiue B, Oregon Green' 488 (2',7'-difluorofluoresecin), carboxyrhodol and carboxyrhodamine, Oregon Green' 500, 6-JOE (6-carboxy-4',5'-ffichloro-2',7'-dimethyoxyfluorescein, Cosin F3S (6-=obxymethylthio-2',4', 5',7'-tetrabromo-trifluorofluorescein), cascade blu6' (CB), aniinomethylcoumarin (AMC), pyrenes, dansyl chloride (5dimethyImiinonaphthalene-lsulfonyl chloride) and other napththalenes, PyMPO, ITC (1(3-isothiocyanatophenyl) 2-yI)pyridinium bromide).

DONORIACCEPTOR PAIRING 26 Contact between the pair of indicator molecules may occur in solution (c- g-, a ten tube, dish or well of a microtitre plate) or, alternatively, either the antimicrobial molecule or the target RNA molecule may be adhered to a solid support (eg. an affinity gel, matrix, or colum) by covalent or non-covalent linkages using methods known in the art. The support bound target RNA or antimicrobial molecule is then mixed with a solution containing the od= compound of the indicator pair.

When the antimicrobial and RNA target are mixed, they can form a complex which brings the donor and acceptor groups into proximity. The 'fluorescenw" of, or light emitted ftom, the complex formed between the antimicrobial molecule and the target RNA is altered by fluorescence resonance energy transfer (FRET)- "FRM is a distance- dependent interaction beween the electronic exited states of two dye molecules in which excitation is tr L.;f=ed from a donor molecule to an aemptor molecule. FRET is dependent on the inverse sixth power of the intermolecular separation, making it usefal over distances comparable to the dimensions of biological macromolecules and obtainable in the complexes formed between the antimicrobial molecules and target RNA molecules in the method of this invention. In most embodiments, the donor and acceptor dyes for FRET are different, in which case FRET can be detected. by the appearance of sensitized fluorescence of the acceptor andlor by quenching of donor fluorescence. When the donor and acceptor are the same, FRET is detected by the resulting fluorescence depolarization.

The donor group may be attached to either the target RNA or to the antimicrobial.

When the donor is; atrached to the target RNA, the complementary acceptor is attached to the 27 2Titbmicrobial; conversely, when the donor is Rtmebed to the antimicrobial, the complementaIY acceptor is amched to the tarc., pt RNA- The donor and acceptor groups may independently be selected from suitable fluorescent groups, chromophores and quenching groups. Donors and acceptors useful according to the invenflon include but are not limited to: 5-FAM (also called 5-=boxyfluorescein; also called Spiro(isobenzofuran-1(3H), T- (9H)Xanthene)-5 carboxylic acid,3,6'-dihydroxy-3-oxe-6-carboxyfiuorescein); 5-Hexachloro- Fluorescein ([4,7,2',4',5',7'-hexachloro-(3',6'-dipivaloyl-fiuoresceinyl) -6carboxylic acid 1); 6 Hexachloro-Fluorescein ([4,7,2,4',5',7'-hexachloro-(3,6'- dipivaloylfluoresceinyl)-5- carboxylic acid]); 5-Tetrachloro--Fluoresecin ([4,7,2',7-tetra chIoro-(3',6'-dipivaloylfiuoresceinyl)-5-carboxylic acid]); 6-Tetrachloro, -Fluorescein (14,7,2',7'-tetmchloro-(3',6'-dipivaloylfiuoresceinyl)-6-carboxylic acid]); 5-TA (5-carboxytetramethylrhodamine; Xanthyam, 9-(2,4-dicarboxyphenyl)-3,6- bis(dimethyl- amino); 6-TA (6-carboxytetramethylrhodamine; Xanthylium, 9-(2,5- dicarboxyphenyl) -3, 6-bis(dimethylaraino)-1 EDANS (5((2-aminwthyl) amino)naphthalene-ISulfonic acid); 1,5-IAEDANS (5((((2-lodoaceryl)amino)ethyl) amino)naphthalene-l-sulfonic acid); DARCYL (4-((4-(dimethyIamino)phenyl) azo)benzoic acid) CyS (Indodicarbocyanine-5) Cy3 (Indo-dicarbocyanine-3); and BODIPY FL (2,6-di-bromo-4,4-difluoro-5,7- dimethyl- ra^ja,4a-diaza-s-indacenf--3-propriorxic acid), as well as suitable derivatives thereof.

According to some methods of the invention, the RNA target molecule has been specifically labelled by a donorlacceptor that is different from the acceptorldonor that is present on the antimicrobial. Preferred combinations of donors and acceptors are listed as, 28 4 but not limited to, the donorlacceptor pairs shown in Tables 5 and 6 (which includes values for R, -the distance at which 50% of excited donors are deactivated by FRET).

Reference herein to "fluorescence" or "fluorescent groups" or "fluorophores" include luminescence, luminescent groups and suitable chromophores, respectively- In the present invention, the target RNA and aufmiicrobiaI may be labelled with luminescent labels and luminescence resonance energy transfer is indicative of complex formation. Suitable luminescent probes ilaclude, but are not limited to, the luminescent ions of europium and terbium introduced as lanthium chelates (Heyduk & Heyduk, 1997)- The lanthanide ions are also good donors for energy transfer to fluorescent groups (Selvin 1995). Luminescent groups containin lanthanide ions can be incorporated into nucleic acids utilizing an 'open cage' chelator phosphoramidite. Table 5 gives some preferred luminescent groups - In certain embodiments of the invention. the target RNA and antimicrobial may also be labelled with two chromophores, and a change in the absorption spectra of the label pair is used as a detection signal, as an alternative to measuring a change in fluorescence.

is MEASURABLE CHANGES In the method of the present invention. the labelled antimicrobial is capable of binding to the labelled target RNA, thereby forming a complex in which the donor present on one molecule comes into proximity with the acceptor on the other molecule. This results in reduced fluorescence of the complex compared to the uncomplexed fluorescence exhibited by the antimicrobial andlor target RNA when free in solution- 29 In the method of the invention, fluorescence intensity of the antimicrobial, the fluorescence intensity of the RNA target and the fluorescence intensity of the complex is measured at one or more wavelengths with a fluorescence spectrophotometer or microtitre plate reader. It is generally preferred that the antimicrobial and RNA target form a one-to-one complex and equirnolar concentrations of ant=crobml and RNA target are present in the bmding reaction. However, an excess of one reagent may be used without departing from the scope of the invention.

In some ernbodiments, a fraction of the antimicrobial molecules and RNA target molecules in the binding reaction can be replaced by unlabelled analogues. The optimal proportions of labelled and unlabelled antimicrobial and RNA target molecules can be determined by fitration of the difterent components and measuring the optimal concentrations required in order to obtain maximal FRET or fluorescent quenching.

The labelled RNA and labelled antimicrobial molecules are then mixed with a test compound and the fluorescence in the mixture is measured. If the test compound is able to bind to the region of the target RNA that binds to the antimicrobial, then a fraction of the antimicrobial will be prevented from binding to the RNA target- The proportions of the free antimicrobial, free test RNA and complex can be quantitatively determined by comparing the spectral properties of the complex, partially dissociated complex and the uncomplexed target RNA and antimicrobials. The amount of antimicrobial displacement will be a function of the relative affinity of the test compound for the target RNA compared to the antimicrobial and the - relative concentrations of the two molecules in the sample- Preferably, a variety of different concentrations of the molecule to-be-tested are compared to generate a binding curve- tp Saturation of the target RNA is reached when the fluorescence emission of the antimicrobial or RNA target molecule is restored to the levels obtained from the free molecules.

The concentration of compounds binding to RNA targets can be determined with a fluorescence standard curve depicting, the fluores=ce- of the labelled antimicrobial and target RNAs with varying known concentrations of competing unlabelled test compound.

In some of the invention, fluorescence resonance energy transfer between the donor and acceptor may give rise to a distinct fluorescence emission specmm of the complex which can be compared to the fluorescence emission spectra of the separate and target RNA molecules.

In some embodiments of the invention, FREI is detected by steady state measurements of the integrated emission intensity of the donor (le- the fluorescent dye that is excited by the light source used in the spectral measurement) andlor the acceptor (ie. the fluorescent dye which has a absorption spectrum that overlaps the emission specu= of the donor). In addition, FRET may be detected by time-resolved measurements in which the decay of donor fluoresce= is measured after a short pulse of excitation. In certain embodiments of the invention the donor is excited at a wavelength that does not itself result in efficient excitation of the acceptor, and FRET is detected by measuring, the excitation of the acceptor due to fer of a photon from the donor.

Typically, it is preferable to look for a signal (a positive), rather than for the absence of a signal (a negative) in an assay of the invention, but it will be appreciated that either or both may be followed.

31 TEST COMPOUND The present invention may be used to identify an antimicrobial or compound capable of binding to any target RNA, preferably as part of a screening process.

0 C1 As used herein, the term "test compound" refers to an agent comprising an andmicrobial, compound, molecule, or complex, that is being.tested for its ability to bind to a target RNA. Test compounds can be any agent, including, but not restricted to, antimicrobials, peprides, peptoids, proteins, lipids, metals, nucleotides, nucleosides, smaU organic molecules. polyamines, and combinations and derivatives thereof. Small organic molecules have a molecular weight of more than 50 and less than about 2,500 daltons, and most preferably between about 300 and about 800 daltons- Complex mixtures of substances, such as extracts containing natural products, or the products of mixed combinatorial eses, can also be tested and the component that binds to the target RNA can be purified from the mixture in a subsequent step. The test compound may be a close structural relative of a known antimicrobial that binds to the target RNA with higher zy than the known drug.

Test compounds may be derived Itorn large libraries of synthetic or natural compounds. For instance, synthetic compound libraries are commercially available from Maybridge Chemical Co- (Trevillet, Cornwall, UK) or AIdrich (Milwaukee, WI)Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts may be used- Additionally, test compounds may be synthetically produced using combinatorial chemistry either as individual compounds or as mixtures.

32 1 ORDER OF AIDUNG A significant advantage of the method of the invention is that it measures equilibrium binding. The invention also exploits the principle that the most reliable type of assays for RNA-binding compounds are based on competition assays between the RNA-binding protem and the drug candidates.

In preferred embodiments of the invention, the target RNA, the antimicrobial, and the test compound are mixed, and the fluorescence of the mixture is compared to standards. Competitive Inbibitors of the binding of the antimicrobial prevent the formation of the antimicrobialtarget complex and therefore incrmse the amount of free target RNA and free antimicrobial in the reaction. Since the fluorescence of the free RNA and antimicrobial molecules is unquenched, the overall fluorescence in the reaction increases in direct relation to the amount of test compound in the binding reaction and its relative affinity for the target RNA compared to the antimicrobial.

In some embodiments of the invention, the test compound is first mixed with the laibelled RNA in order to form a complex in the absence of the labelled antimicrobial, and the antimicrobial is then added. Since the antimicrobial will only be able to bind to the free RNA in the reaction, there will be a reduced amount of complex formed between the antimicrobial and the targ get RNA compared to the amount of complex formed in the absence of test compound. As a result, the fluorescence of the mixture containing the test compound will be increased compared to a similar rae prepared in the absence of the test compound- In other embodiments, a complex is pre-formed between the labelled RNA and the labelled antimicrobial before addition of the test compound. If the test compound is able to 33 disrupt the complex formed between the labelled-RNA and the Labelled antimicrobial, or alter the equilibrimn binding state by binding to RNA that has dissociated from the antimicrobial, the amount of complex in the reaction will be reduced and the overall fluorescence of the mixture will. increase- In some circumst=ces, the test compound may itself be fluores=t andlor be capable of quenching the fluorescent group present on the target RNA andlor the antimicrobial. In preferred embodiments of the invention, the fluorescence of standards containing the test compound on its own, and m pairwise conibbiations, with the =get RNA or antimi al, are measured and these values are compared to the tluorescence of the complete test mixture containing the test compound, the fluorescent RNA and the andmicrobial.

Quenebing of fluorescence arising from the RNA due to the binding of the test compound to the RNA will result in a decrease in the signal arising from the RNA that is not complexed to the antimicrobial, but will not affect the fluorescent signal arising from the group on the antbmicrobial or the signal obtained from the RNA in a complex with the antirnicrobial. In this circumstance it is preferable to configure the donorlacceptor pairs on the RNA and the 2nt microbial such that an increase in the fluorescence of the antimicrobial is detectable when the formation of the complex between rhe antimicrobial and the RNA is blocked by the test compound.

QUANMATIVE NATURE OF IHE ASSAY An important feature of the invention is that the test compound competes for RNA binding ag a specific pre-defined antimicrobial. Ttds provides speefficity in the assay and 34 permats exclusion of compounds that bind to the target R-NA but do not interfere with Ibe binding of the antimicrobial. In preferred embodime nts, the antimicrobials are designed to bind to discrete regions in the target RNA that are involved in biological activity or function, to permit identification of compounds that are likely to have biological or pharmaceutical activity.

The invention allows the measurement of the dissociation constant (Rj between the:anthidcrobial and the target RNA. Kd is defined by equation [11:

-Kd _ IRAIPA [RP] Where [Rfl is the conce=ation of free RNA, []p] is the concentration of free ial, and [RP] is the concentration of the complex.

may be determined experunentaIly by incubating a pre-determined concentration of target RNA together with a series of concentrations of antimicrobial. An increase in the formation of complexes of the andmicrobial and the target RNA in solution results in a progressive increase in FRET andlor quenching. As the conceon of antimicrobial increases the spectral values approach a ma value asymptotically due to the formation in 15 solution of the ant=crobial-target RNA complex. In some embodiments of the invention the K.6 of an antimicrobial is determined by incubating a pre-determined concentration of ancrobial together with a series of concentrations of target RNA - Ile value for K,, is preferably determined by fitting the experimental data to a bindingcurve derived from equation [1] by least-squares fit regression analysis. Alternatively, Kd 35 values can be approximated by graphical analysis of the data using double reciprocal (Scatchard) or similar plots. K. values are physical-chemical constants that define the affinity between the antimicrobial and the target RNA- lle relative affinities of diffierent antimicrobial for target RNAs may be detemffied by comparing measured Kdvalues.

In preferred embodiments, the binding constant of a test compound relative to the andmicrobial (K), is measured by incubating a pre- determined concenn-ation. of target RNA and ant=crobial, together with a series of different compound concentrations- The concentrations of target RNA and antimicrobial molecules are chosen to give a measurable amount of complex formation; preferably gre:ater than 10% complex formation and most preferably greater than 50% complex formation. The most preferable starting conditions are obtained using equimolar concentrations of antimicrobial and target RNA molecules at concentrafions that are greater than 5 x Kd of the antimicrobial-target RNA- Under these circunistances essentially all of the antimicrobial and target RNA is found in the complex- I is then determined by measuring the inhibition of complex formation as a flinction of the amount of test compound added. A formal description of the binding equilibrium is as follows- [R) + [P) [R) + [11 where [R] is the target RNA concentration, [P] isantimicrobial concentration, [11 is the inhibitor (i.e., ten compound) concentration, [RP] is the concentration of the complex formed between the antimicrobial and the target RNA; and RM is the concentration of the complex formed between the test compound and the target RNA. It follows that:

36 K., - [RA IPA [RP] and Ki - [RA IIA IRn where ld is the dissociation cot between the target RNA and the antimicrobial, K, is the dissociation complex between the test compound and the target RNA, N is the free RNA concewation; [P,] is the free antirni ial concentration; and A is the free test compound (inln-bitor) concentration.

Hence [R] - [RP] - [Pt) JP] - W]; and Combining the equations yields the cubic'equation [21 in which Kd and 1 are related to the experimentally determined values for [R), [P), [I] and [RP]:

W33 (y-d- 1) + + + (2K,-Y-J(P1 + + "][P] {(Kd-2y"^ - Y-, [P] - KdR] Kdys',} + y, [Rj [p]2 = 0 is 37 equation [2) 1 Solutions of equation [21 by regressional analysis yield values for K, However, in practice, it is prele to lify equation (2] to a quadratic equation by approximating certain of the starting conditions. A typical simplification occurs when K, > > Y. and therefore the experimental inhibitor concentration is much greater than the total RNA, under conditions 5 where the antimicrobial is partially displaced from the RNA by inhibitor, hence, [] = (11. Reworking the above derivation, with this simplification, then yields the quadratic equation:

K 1±RJ +1p]+MIRI = 0 which has the solution -K I-f-111 +IP]+[R] I++L[.R] - 4[PI[R] [RP] = i-)] K K i) equation [31 equation [4] is If a value of K has already been determined for the antimicrobial, 'Values of K, for various inhibitors can be determined by non-linear regression analysis of data of [RP] against [I].

An alternative method to estimate Y.', which has been applied in the examples given 20 below, is to fit the data to the equation:

38 FI = [AjW.'] + M where: FI is the experimentally measured fluorescence intensity. B,., is the ma fluorescent signal (determined by measuring the fluorescence of the antimicrobial combined with inhibitor); and M is the inhibitor concentration- This simplified method ignores the effect of andmicrobial binding on reducing the free RNA concentration, but is a useful simplification when lc., > > id - LIBRARY SCREG (including high througbput screens) lle present invention also encompasses high-througbput screening methods for idg compounds that bind to a target RNA. Preferably, all the biochemicú steps for this assay are performed in a single solution in, for instance, a test tabe or microtitre plate, and the test compounds are analyzed initially at a single compound conemiu-adon. For the purposes of high throughput screening, the experimental conditions are adjusted to ar- hieve a proportion of test compounds identified as "positive" compounds from amongst the total compounds screened- The assay is preferably set to identify compounds with an appreciable affinity towards the target RNA e- g., when 0. 1 % to 1 % of the total test compounds from a large compound library are shown to bind to a given target RNA with a KI, of 101zM or less (e.g- lgM, 10OnM, lOnM, or less).

KITS USEFUL ACCORDING TO THE DWENTION The invention also provides a Idt for determining whether a test compound binds to a target RNA, the kit comprising (a) a target RNA labelled with a donor group or an 39 acceptor group and (b) an antimicrobial labelled with. a complementary acceptor or donor group, wherein the andmicrobial and the target RNA are capable of binding to each other in an orientation that permits the donor group to come into sufficient pro to the acceptor group to permit fluorescent resonance energy tramfer andlor quenching - Ibe kits will include the. components useful in the inventive methods, as well as packaging materials therefor.

MEASUREMENTS OF RNA BINDING COMPOUND lle invention may be embodied as a clinical assay or method for derennining the presence of an RNA-binding compound in a biological sample such as the senim or tissues of a subject. Many drugs, including RNA-binding compounds such as antibiotics, are routinely assayed for their scrum levels when administered to patients to prevent administration of toxic levels of compounds- The invention thus provides a method for determining the amount of a predetermined RNA-binding compound in a subject or biological sample. In this method a complex consisting of a labelled target RNA specifically bound to a labelled antimicrobial is mixed with a sample to be analysed (c-g., a serum sample or tissue extract from a subject)- 'Ite level of RNA-binding compound in the sample is determined by comparing the level of fluorescence emitted by the labelled target RNA and/or labelled antimicrobial in the presence of the sample with the level of fluorescence obtained using a known amount of the RNA-binding compound of interest. In some embodiments of this merhod, the antimicrobial is unrelated to the RNA-bindine, compound of interest; in other embodiments it is a fluorescent version of the compound of interest.

The invention also provides a kit for determining the level of an RNAbinding compound of interest in a subject or sample, comprising (a) RNA labelled with a donor group or an acceptor gmup and which is specificafly bound by the compound of interest (b) a antimicrobial labelled with a complementary acceptor or donor group, wherein the anthnicrobial and the target RNA are capable of binding to each other in an orientation that permits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer andlor quenching. The kit preferably further comprises a sample of the compound of interest in unlabelled and uncomplexed form, with which to prepare a standard fluorescence curve.

Typically, a scrum or blood sample. or a tissue extract, is taken from a patient and contacted with the complex. The fluorescence of the complex is then measured and compared to a standard curve depicting the fluorescence of the complex in the presence of knoWn concentrations of the RNA-binding compound of interest.

In this, and other, aspects of the invention, it may be desirable to add a ribonuclease inhibitor to the sample or to themixture of the sample and complex to prevent degradation of the RNA. As an alternative, the fluorescently labelled target RNA could be protected by the inclusion of modified bases, sugars or backbone modifications as described aboveEXAMPLES

41 1 1 The following examples illustrate the preferred modes of making, and practicing the present invention, but do not limit the scope of the invention- The meThod of the invention is illustrated by the binding of a fluorescently labeled antibiotic to a fluorescently labelled RNA target and the competitive inhibition of binding by unlabelled antibiotic. The fluorescently labelled anti-biotic used here is paramomycin, which contacts a specific region in the 16S rRNA A site (Fourmy et aL, 1998, S. Mol. Biol. M:333)- Ile fitiorescently labelled RNA is a small, 25 nucleotide RNA that mimics the double helical region of the 16S A site that is bound by paramomycin. The ability to detect a competitive inhibitor of binding of the fluorescently labelled antibiotic is 10 demonstrated with unlabeled anti-biotic, either neomycin or paramomycinIn fin-ther examples, the identification'of model RNA targets that are useM according to the invention are described for the OTPase center of 23S rRNA, the Ll (E site) of 23S rRNA, and the spectinomycin binding site of 16S rRNA.

is EXAMPLE1

Identifying a model sequence for the A site, the site of action for a number of aminoglycoside antibiotics.

A number of antibiotics bind to the 16S rRNA in a variety of subregions of the rRNA, as illustrated in FIG. 1. Several aminoglycoside antibiotics, including paramomycin, bind the 16S rRNA in the subregion that is part of the ri- bosome acceptor site or A site, which is where amino acids (acylated to tRNAs) enter the ribosorne to activate elongation of the nascent peptide (Spalin and Prescott, 1996, supra)- The A site of 42 the 16S rRNA can be reduced to generate small ribosomal sub domains that maintain the essential features of the RNA target (Gutell et aL, 1993, Schnase et al., 1996), as shown in FIG. 5. The RNA target can be constructed from two small olioorl-bonueleotides. Alternatively the ends of the double stranded RNA can be linked by.a loop. The bacterial A 5 site is highly conserved, as shown for several bacteria in PIGS - 5 and 13.

1. Synthesis of DABCYL-labelled A site RNA:

5'-CCGUCACACCUUCGGGUGAAGUCG G -Y(SEQ ID No. 1) An oligoribonucleotide of the sequ= shown above contg a S' dabcyl group was synthesized by XERAGON using TOM phospharamidite chemistry. It was purified by gel electrophoresis in a 20 % acrylamide gel containing 7M urea, and extracted from the gel by electroelurion (Fourmy et aL, 1998, 1. Mol- Biol. 277:333).

2. Synffiesis of Paramomycin-TAMRA Paramomycin TA was synthesized by reacting 55mg paramomycin sulphate in sodium bicarbonate (6mL 0.067M in 30% dimethyl formamide (D" with Smg was diluted and purified by anion exchange chromatography, and reversed phase HPLC (WaRg et al., 1997, Blochem. 36:768).

43 3. Demonstration of quenching due to FRET between TAMRA-labe-11ed Paramomycin and DABCYL-labelled A site RNA.

FIG. 6 shows an experiment in which complex formation between a fluorescently labelled target RNA (DABCYL-labelled A site RNA) and a fluorescently labelled antibiotic (paramomycin-TAMRA) is measured by quenching in the complex due to fluorescent resonance energy transfer In this experiment, a small RNA derived from the 16S A site (see FIG. 5) was used as the target RNA or A site RNA - The interaction between paramomycin-TA and A site RNA.was, measured utilizing paramomyein-TAMRA as a donor and DABCYL- A site RNA as an acceptor. Each measurement was made in a 2mL euvette, in a Perkin Elmer LS50B fluorimeter- Increasing amounts of DABCYL-A site RNA (corresponding to the amounts shown in FIG. 6) were added to a solution of 25nM paramomycin- TAMRA in the presence of 50mM Tris.HCI pH7.5, SOmM KCl, 0. 1 % DMSO 0.00007% Triton X- 100 and 0Jug/mL BSA- For each titration point emission spectra were aquired using a fixed wavelength of 544 am with the excitation slits set to Sum and the emission slits set to S=.

Emission spectra were acquired over the range 570-60Onm. This range encompasses the emission spectrim of the donor (TAI1RA). A reduction in donor intensity was observed, which is due to fluorescence resonance energy transfer taldng place between the two dyes upon the antibiotic binding to the A site RNA. The donor ratio presented is the difference in donor intensity on addition of DABCYL-A site RNA stock solution as a proportion of the total donor intensity in the absence of acceptor- 44 EXAMPLE2

Binding of par=omyein-TAMRA to A site RNA measured in a fluorescent plate reader.

TO facilitate screening of competitive binding by the antimicrobial-RNA FRET assay, test compounds (andmicrobials) are measured in plates containing multiple wells. To demonstrate the ability of the assay to be utilized in this format, measurements were made in a 96-well plate reader (Wallac victor) with a fixed wavelength of 544= and emission at 590 nm, as shown in FIG. 7.] was determined by an initial measurement of a 95 gL solution of 2SuM paramomyein-TAMRA in the presence of 50MM Tris-HCI pH7.5, 8OmM KCL 0. 1 % DMSO 0.'00007 % Triton X-100 and 0. Sug/mL 13SA. 1, (the final measurement) was then measured following the addition of 5 ILL of a 20 X DABCYLA site RNA stock solution (corresponding to the amounts shown in FIG. 7).

is EXAMPLE3

Inhibition of paramomycin-TAMRA to A site binding by 1OgM Neomycin.

In the method of this invention, the ability of compounds to bind to rRNA is measured by competition binding assays involving an andmicrobiaYtarcl,, et RNA pair and the compound to be tested. An important illustration of the method is to demonstrate that unlabelled antimicrobials can act as competitive inhibitors of the binding of the labelled 20 antimicrobials.

A control experiment of this type which demonstrates the use of unlabelled neomycin as a competitor is shown in FIG. 8. Binding of paramomyein-TA to A site RNA was measured in a fluorescent plate reader. Measurements were made in a 96-well plate reader (Wallac victor) with a fixed wavelength of 544= and emission at 590 mn.

was determined by an initial measurement of a 95 gL soIution of 25uM paramomycin-TANIRA in the presence of 5OmM Tris-HCI pH7.5, SOmM KCI, 0. 1 % DMSO 0.00007 % Triton X-100 and 0.5ug/mL BSA presence of 1OgM NeomycinI (The final measurement) was then measured following the addition of 5 gL of a 20 X DABCYL-A site RNA stock solution (corresponding to the amounts shown in the figure).

As shown in FIG- 8, a slight reduction in fluoresence in the presence of the neomycin competitor was observed compared to that of the control without neomycin, demonstrating the ability of the assay to detect binding of a competitor antibiotic to the target RNA- EXAMPLE 4

Lihibition of paramomycin-TA to A site binding by 15gM Paramomycin.

To further illustrate that the method of this invention can be applied to measure the competitive binding of test antimicrobials or compounds in assays involving an antimicrobialltarget RNA pair, unlabelled paramomycin was used as a competitor in the parmomyein-TAMRA and DABCYL-A site RNA assay The results of testing unlabelled paramomycin as a compezitive inhibitor of the binding of fluorescenyly-labelled paramomycin to tluoreseently-labened A site RNA is shown in FIG- 9- Binding of paramomycin-TAMRA to A site RNA was measured in a fluorescent plate reader. Measurements were made in a 96-well plate reader (Wallac victor) with a fixed wavelength of 544= and emission at 590 nm. 1 was determined by an initial 46 measurement of a 95 gL solution of 25nM paramomycia-TAMPA in the presence of SOmM TrisSCI PH7.5, SOmM M. 0. 1 % DMSO 0.00007 % Triton X-100 and O. Sug/niL BSA presence of 15pM Neomycin. I (the final measurement) was then measured following the addition of 5 gL of a 20 X DABCYL-A site RNA stock solution (corresponding to the amounts shown in FIG. 9). The results of the assay are in aent with those obtained usmg neomycin as the competitive antibiotic, finther indicatmg the ability of the method of the invention to measure competitive binding assays involving an andmicrobialltarget RNA pair and an antimicrobial (or other compound) to be tested.

EXAMPLE 5

A model sequence for the LI site (the E site), the site of action of the oxazolidinones.

An antimicrobial-binding fragment (sub-region) of an antimicrobialbinding RNA useful according to the invention is identified from known antibiotic binding fragments available in the art. Such fragments serve as target RNAs. The complete 23S rRNA is bound in a variety of subregions by a number of antibiotics, including but not limited to those from the cIasses aminoglycoside, oxazolidinone, macrolide, tetracyclins, and thiazole as illu= in FIG. 2- The oxazolidinone antibiotics, as exemplified but not limited to those shown in FIG. 4, bind the 23S rRNA in the L1 or E site. Identification of a candidate model target RNA for the Ll site is shown in FIG. 11, which shows reduction of 23S rRNA to generate small ribosomal sub domains that maintain the essential featwes of the RNA target (OutcIl et al-, 1993; Schnare et, al-, 1996). In this case the RNA target is 47 characterized by intra helical hydrogen bonding and is likely to dictate that the RNA target be constructed from a relatively long oligoribonuelcotide- The RNA folding may be further stabilized by the inclusion of the ri-bosomal protein Ll.

EXAMPLE 6

A model "ence for the GTPase center, the site of action of the thiazole antibiotics.

In addition to the L1 site, the 23S rRNA is bound by antibiotics in other subregions, including its GTPase center, as shown in FIG. 2. The GTPase center contains the binding site for the anti-biotic thiostrepton. Identification of a target RNA for the thiostrepron binding site is shown in FIG. 12, which shows reduction of 23S rkNA to generate small ribosomal sub domains that maintain the essential features of the RNA target (Gutell et al., 1993; Schnare et al., 1996). In this instance, the RNA target comprises a number of structural motifs, including two hairpin loops, a helical junction and a number of potentially unpaired bases. This potential complexity necessitates that the RNA target be constructed from a relatively long oligoribonucleotide- The RNA folding may be flirther stabilized by the inclusion of the fibosonial protein L 11 - EXAMPLE 7

A model sequence for the spectinomycin site.

As illustrated in FIG. 1, a number of antibiotics bind the 16S rRNA in a variety of subregions. The antibiotic spectinomycin binds the subreggion of 16S rRNA depicted in 48 FIGS. 12 and 16. A model sequence for the spectinomycin binding site can be identified by reduction of the 16S rRNA to generate small ribosomal domains that maintain the essential features of the RNA tarZet (GuteIt et aL, 1993; Schnare et al., 1996). In this case the RNA target comprises a short double suanded RNA sequence next to a complex 3 helical junction. The RNA target may be constxucted from a relatively Iongoligoribonucleotide in which the arms of the helical junction are shortened and Enked by loops. Ile target may be further reduced such that it consists of the double helical region alone. This region of the bacterial nbosorne is highly conserved, as shown for several bacteria in FIGS. 12 and 16. In FIG. 12, the Escherichla Coli RNA sequence is shown and the mutational differences for the gram-positive bacteria Bacillus subtilis are shown in brackets.

49 Table 1. The following molecules are antimicrobials that contain anuine groups that are appropriate for the introduction of fluorescent dyes. ThCY are CXaMPICS and we not a limiting set- c-lass Antibiotic T Rget rRNA NucleoTidrs(s) Warence Aminoglycoside Amikacin A site 16S 1408 Pnimmananan ct aL, 1998, J.

Infect Dis. 177:1573 Aminoglycosidc; Apramycin A site 165 1408 1419 1494 Woodcock et al., 1991, EMBO J. 10.3099 Aminoglycoside Bekanamycin A site 16S Hw et al., 1998, Biistry 37.656 Aininoglycoside Gent=ficin A site (L6) 16S 1408 14191494 Yoshizawa et al., 1998, UMO J. 17:6437 Aminoglycosidc Hygromycin 3 A site 16S 1491 3495 Moa=d md Noller, 1987, Nature 327:389 Aminoglycosidc Kanamycin A site 16S 1408 14J9 1494 Beauclerk and Cundlifte, 1987, J. Mol. Biol. 193:661 An-tinoglycoside Kasuycin P site 16S 794926 Woodcock c: al., 1991, EMBO L 10:3099 Ami-noglycoside Ncernin A site 165 1408 1419 1494 Woodcock et al., 1991, EMBO J. 103M Arninoglycoside Neomycin A sitc 16S 1408 14191494 Recht ct al., 1999, S. Mol.

Biol. 286.33 Aminoglycoside Paromomyein A sim 16S 1408 1419 1491 1494 1Fourmy et al., 1998, L Mol Biol. 277:333 Amimoglycoz:ide Sis=ycin Kojic et al--- 1992, X.

Bactedol. 174.7868 Aminoglycoside Specdnomycin SS binding sfte 16S 1063-1065 1191-1193 Moazed and Noller 1987, Naram 327.389 Arninoglycoside Tobramycin A site 16S 1408 Pramnananan et al., 1999, J Infect. Dis. 177:1573 Cyclic Peptide Viomycin 23S 913914 Moazed and Nolle:i 1987, Siochimic 69:879 Table 2. The following molecules are antimicrobials that contain ketone groups that are appropriate for the introduction of fluorescent dyes. They are examples and are not a limiting set- Class Antibioti Tar rRNA Nurleotides(s efimce peptidy, Umsforwe Gauthier et al., 1988;, Mol. GenGenet- 214:192 Douthwaite and Aa 1993, J. Mol. Biol. 232.725 Rodriguez-Fonseca et al.' 1995, 1. MOL Biol. 247:224 Muhk et aL, 1983, MS Lett. 152:125; OehIer et al., 1997, Nucleic Acids Rm 25.1219 Macrolide Spiramycin 23S 2611 Macrolide (14) Erithromyciii peptidyl erase 23S. 2057 2058 2059 2447 2505 2611 Macrolide (16) Tylosin peptidyl 23S trmsferase Tetracycline Chlortetracycline A (P) site 165 (23S) 51 Table 3. The following molecules areantimicrobials that contain aldehyde groups that are appropriate for the introduction of fluorescent dyes. They are examples and are not a Iiiniting set.

CIass Ant-biotic Tmet rRNA NucleotidesLs) Reference Oxazolidinone DuPont 721 E site, LI 23S 2113 21142118 Matassova et al., binding site (165) 2119 2153 (864) 1999, RNA 5.939 Woodcock et aL, A site 915 199 1, EIMO J.

Arninoglycoside Seeptomycin region, S12, 16S 523911-915 10:3099:

SS?, LI 1? Spickler et al., 1997, J. Mol. Biol. 273:586 52 Table 4. The following molecules are antimdcr that contain dehydrobutyrene and dehydroalanine groups that are appropnate for the introduction of fluorescent dyes. They are examples and are not a limiting set.

Class Antibiotic Target LRNA Nucleotides(s) Reference GTPase Cundliffe and TI3iazole Nosihepti& associated 23S 1067 Thompson, 198 1, J.

centre Gen. Microbiol.

126:185 GTpase Thiazole Thiostrepton associated 23S 10671095 Egebjerg et al., 1989, centre EAMO 1, 9.607 53 Table 5. Typical. values of Rc, Donor Acceptor Ro (A) Fluorescein Tetramethylrhodamine 55 IAEDANS Fluorescein 46 EDANS DABCYL 33 Fluorescein Fluorescein 44 BODEPY FL BODEPY FL 57 RO is the distance at which 50% of excited donors are deactivated by FRET. Data from Hangland, RP- 1996. Handbook of Fluorescent Probes and Research Chemicals, 6th edition. Molecular Probes, Inc. Eugene OR, USA.

54 Table 6. FRET-pairs suitable for use in the method of this invention.

D-ci i9A A=- por (a) dQnols Fluorescein Fluorescein EDANS Dansyl Cy3 Tryptophan, Fluorescein Tetramethyl rhodaminc Fluorescein DABCYL Fluorescein is Tetrachlorofitoresecin bl a dmw Europium Terbium Terbium Tetramethylrhodamine Cy-3 DABCYL Fluorescein Cy-5 AEDANS Tetr=erhyl rhodamine 'DABCYL DABCYL Cy-3 Rexachlorofluorescein cy-S cy-S Tetramethyl rhodaminc Cy-3 :55 Table 7. -Antitwnor antimicrobials acting on tRNA.

Antibiotic Tar get Reference Enediynes tRNAhe Sugiura et al., 1997, Bioorg- Me-d.

Chem- 5. 1229 Colicin E5 (Nuclease) tRNA(Tyr, His, Asn, Asp), Ogawa et al., 1999, Science 283:2097 anticodon loop 56 Table 8. Adclitional classes of antimicrobials.

class Antibiotic Alkaloid Narciclasine Alkaloid Emetine N-glycosidase Ricin Nuclease Nuclease Colicin E3 alp-ha-Sarcin Nucleoside Puromycin derivative Nucleoside derivative Pyrrolidine d&zivative Target rkNA Nuclootides(s) peptidyl t-dnsferast 23S ? yeast S 14 binding 16S site? elongation factor 23S bindi-eg sic A site elongation factor 23S binding site A site (SOS) 23S SpaTsomycin peptidyl transferase 23S Anisomycin peptidyl transferase 23S Sesquiterpene: Fusarenon X peptidyl transferase 23S Sesquiterpene T2 toxin 2660 14931494 266012661 25022504 2602,2603 24472452 2453 peptidyl umisferase 23S 2394 Streptogramin Virginiamycin peptidyl transferase 23S 20592394 A M1 2503 (MLS group) Sireptograrnin Vernamycin B peptidyl transferase 23S 7522062 B 2505 (MLS group) Refitrence Rod.riguez-Fonseca et al., 1995, S- Mol. Biol247:224 Fewell and Woolford, 1999, Mol. Cell. Biol. 19:826 Endo and Tsuragi, 198 & J. BiolChern. 263:8735 Bowman et al., 1971, Nature New Biol. 234:133 Moazed et al., 1988, Nature 334:362 Jaynes EN et aL, Biochemistry 1978 Feb 21;17(4):561- 9 Lazaro E, et al., j Mol Biol 1996 Aug 16;261(2):231-9 Rodriguez-Fonseca et al., 1 ' 9951 J. Mol. Biol. 247:224 Jimenez and Vazquez Eur J Biochem 1975 Jun;54(2):483-92 Rodriguez-Fonseca et aL, 1995, L Mol- Biol. 247:224 Porse andGarrett J Mol Biol 1999 Feb 19;286(2)..375-87 Moazed and Noller 1987 Biochimie Aug;69(g):879-84 57 Refireaces:

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   67 CLAIMS 1 - A method for determining whether a test compound binds to a target RNA, the method comprising the steps of.

   (a) contacting the test compound with a pair of indicator molecules comprising an antin-derobial labelled with a donor group or an acceptor group and the target RNA labelled with a complementary acceptor or donor group, the pair being capable of binding to each other in an orientation that permits the donor group to come into sufficient proxirdty to the acceptor group to permit fluorescent resonance energy transfer andlor quenching to take place; and (b) measuring the fluorescence of the target RNA and the antimicrobial in the presence of the test compound and comparing this value to the fluorescence of a standard.

   2. A method according to claim 1, in which the standard comprises the indicator pair in the presence or absence of test compound, the fluorescently-labened target RNA, in the presence or absence of test compound, or the fluorescently- labelled antimicrobial molecule in the presence or absence of test compound.

   3. A method for the identification of a compound d= binds to a target RNA from within a plurality of test compounds, comprising the steps of the method a=rding to claim 1 preceded by the initial step of providing a plurality of " compounds.

   4. A method according to any of clai 1 or 3, comprising the steps of 68 I") contacting a test compound with an indicator complex, the indicator complex Vaj comprising a fluorescently-labelled antimicrobial bound to a fluorescently labelled target RNA in an orientation that permits the fluorescent groups present on each molecule to come into sufficient proximity to permit fluorescent. resonance energy transfer to take place; and (b) measuring the fluorescence of the target RNA and the antimicrobial in the presence of the test compound and comparing this value to the fluorescence of a standard- 5. A me according to any one of claims 1 or 3, wherein the antimicrobial is selected fTom The antimicrobial classes aminoglycoside, cyclic pepride, macrolide, tetracycline, oxazolidinone, thiazole, protein, glycoprotein, alkylold, nuclease, or Nglycosidase.

   is 6. A method according to any one of claims 1 or 3, in which the antimicrobial binds the target RNA with a M of betw= 1X10-'2 and IXIC M.

   7 - A method according to any one of claims 1 or 3, in which the target RNA is between 5 and about 750 nucleotides in length.

   8- A method according to any one of claims 1 or 3, in which the target RNA is chemically modified.

   69 9- A method according to any one of claims 1 or 3, in which the target RNA is derived from bacterial, viral, fimgal, or eukaryotic RNA- 10. A method according to claim 9, in which [he target RNA is 16S ribosomal RNA11. A method according to claim 10, in which the target RNA is an antimicrobial binding fragment of the 16S ribosomal RNA.

   12- A method according to claim 10, in which the target RNA is 23S ribosomal RNA.

   13 - A method according to claim 10, in which the target RNA is an antimicrobial binding fragment of the 23S ribosomal RNA.

   is 14. A method according to any one of claims 1 or 3, in which the target RNA and the antimicrobial are fluorescently labelled by covalent attachment of a fluorescent group.

   - A method according to claim 14, in which the target RNA is fluorescently labelled ax the 3' or 5' end of a strand within the target RNA, or within the chain of the target RNA.

   16. A method according to any one of clairns 1 or 3, in which the antinderobial or the target RNA molecule is adhered to a solid support.

   17. A method according to any one of claims 1 or 3, in which either (i) the. donor is attached to the target RNA, and the acceptor is attached to the antimicrobial, or (ii) the donor is attached to the acrobia and the acceptor is attached to the target RNA- 18. A method according to any one of claims 1 or 3, in which the acceptor is able to quench the fluorescence of the donor after binding of the target RNA and the 10 antimicrobial.

   19- A method according to any one of claims 1 or 3, in which the target MA, the antimicrobial, and the test compound are mixed, and the fluorescence of the mixture is compared to standards.

   20. A method according to any one of chtims 1 or 3, in which the test compound is first mixed with the labelled RNA in order to form a complex in the absence of the labelled antimicrobial, and the antimicrobial is then added.

   21. A method according to any one of claims 1 to 20, in which a complex is pre-formed. between the labelled RNA and the labelled antimicrobial before addition of the test compound- 71 22. A kit for determining whether a test compound binds to a target RNA, the Idt comprising (a) a target RNA labelled with a donor group or an accepter group and (b) an antimicrobial with a complementaq acceptor or donor group, wherein the antimicrobial and the target RNA are capable of binding to each other in an orientation that pernlits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy transfer andlor quenching.

   23 - A method for determining. the presence in a biological sample of a compound that binds to a target RNA molecule, comprising (a) contacting the sample with a pair of indicator molecules comprising an antimicrobial labelled with a donor group or an acceptor group and the target RNA labelled with a complementary acceptor or donor group, the pair being capable of bluding to each other in an orientation that permits the donor group to come into sufficient proximity to the acceptor group to permit fluorescent resonance energy U-dnsfer and/or quenchingto take place; and (b) measuring the fluorescence of the target RNA and the andrfficrobial in the presence of the test compound and comparing this value to the fluorescence of a standard as an indication of binding.

   24- The method of claim 23, said biological sample comprising a tissue or fluid from. a mmmnml- 72 25. The method of claim 23, said biological sample comprising a plant extract.

   26. The method of clairn 23, said biological sample comprising a prokaryotic extract.

   73)