Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/34—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6813—Hybridisation assays
  • C12Q1/6816—Hybridisation assays characterised by the detection means
  • C12Q1/6818—Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer

Definitions

• the invention relates to substrates for IRE-l ⁇ .
• the unfolded protein response is an intracellular signaling pathway which responds to the accumulation of misfolded proteins in the endoplasmic reticulum (ER) lumen.
• the UPR is increasingly recognized as a significant factor in many human diseases. Up-regulation of the UPR is thought to be important for tumor survival and B- cell autoimmunity, whereas UPR suppression is implicated in diseases such as Alzheimer's disease and type II diabetes.
• IRE-l ⁇ is a transmembrane signaling molecule with an N-terminal luminal domain inside the ER and a C-terminal kinase and RNase domain in the cytosol. The N-terminal luminal domain complexes with GRP78. IRE-l ⁇ is an ER stress sensor. When activated, IRE-l ⁇ induces transcription of endoplasmic reticulum stress response genes, such as GRP78 and GRP94, by activating the transcription factor XBP-I via specific RNA splicing.
• Antagonists of IRE-l ⁇ are useful for treating B-cell autoimmune diseases and cancer.
• Agonists of IRE-l ⁇ are useful for treating Alzheimer's disease and type II diabetes. It would, therefore, be useful to have methods of screening for IRE-l ⁇ agonist and antagonist molecules.
• FIG. 1 Spyro ruby-stained polyacrylamide gel showing a purified preparation of IRE-I ⁇ monomers and dimers.
• FIG. 2 Drawings of IRE-l ⁇ substrates.
• 33 base wild-type substrate 5'- GGGUCUGCUGAGUCC-GCAGCACUCAGAAGGCCC-3' (SEQ ID NO:1); 33 base mutant substrate 5'-GGGUCUGCUGAGUCCCCAGCACUCAGAAG-GCCC-S' (SEQ ID NO:2); 15 base wild-type substrate with 5' FAM and 3' BHQ-1TM moieties (5'- C AGUCCGC AGCACUG-3', SEQ ID NO:3); 15 base mutant substrate with 5' FAM and 3' BHQ-1TM moieties (5'-CAGUCCCCAGCACUG-S', SEQ ID NO:4).
• FIGS. 3A-C Photographs of polyacrylamide gels showing cleavage of an IRE-l ⁇ substrate.
• FIG. 3A radiant red stain
• FIG. 3B signal from cleaved 15 base FAM substrate.
• FIG. 3C radiant red stain.
• FIG. 4 Graph showing time course of IRE- l ⁇ RNase activity at 3 O 0 C.
• FIG. 5 Bar graph showing results of a competition assay to determine the activity of a 15 base substrate (SEQ ID NO:3) in the presence of a 33 base substrate (SEQ ID NO:1).
• FIG. 6 Graph showing results of a high-throughput assay of IRE- 1 ⁇ RNase activity
• the invention provides, inter alia, minimal substrates for IRE-l ⁇ which can be used in screening assays of the invention to identify agonists and antagonists of IRE-l ⁇ RNase activity, particularly human IRE-l ⁇ RNase activity.
• the invention also provides mutant substrates which IRE-l ⁇ does not cleave and which can be used as controls in the screening assays.
• IRE-l ⁇ substrates according to the invention are oligonucleotide molecules having an RNA loop and a nucleotide stem.
• the RNA loop contains a cleavage site for IRE-l ⁇ , preferably human IRE-l ⁇ .
• the RNA loop comprises the sequence 5'- CCGCAGC-3' (wild-type).
• RNA loops are those in which one or more nucleotides is altered with respect to the wild-type sequence, e.g., 5'-CCGAAGC-S', 5'- GCGAAGC-3', 5'-ACGAAGC-3', 5'-UCGAAGC-3', 5'-CCGAAGC-3', 5'-CGGAAGC- 3', 5'-CAGAAGC-3', 5'-CUGAAGC-3', 5'-CCGAAGC-3', 5'-CCAAAGC-3', 5'- CCUAAGC-3', 5'-CCGAAGC-3', 5'-CCGGAGC-3', 5'-CCGUAGC-3', 5'-CCGCAGC- 3', 5'-CCGAAGC-3', 5'-CCGAGGC-3', 5'-CCGAUGC-3' 5 5'-CCGACGC-3', 5'- CCGAAGC-3', 5'-CCGAAAC-S', 5'-CCGAAG
• the RNA loop can contain one or more altered nucleotides with respect to the wild-type sequence. If desired, a mutation can be introduced into the RNA loop to form a mutant substrate which IRE-l ⁇ cannot cleave.
• the RNA loop of the mutant substrate comprises the sequence 5'-CCCCAGC-3'.
• Nucleotides in the nucleotide stem can be deoxyribonucleotides, ribonucleotides, and/or nucleotide analogs, such as DNA or phosphorothioates.
• the nucleotide stem comprises at least 4 and as many as 30 or more nucleotide base pairs. Preferably the nucleotide stem consists of 4, 5, 6, 7, 8, 9, or 10 nucleotide base pairs.
• the nucleotide stem can have one or more mismatches (bulges) and can have an overhang.
• the particular nucleotides in the stem are not important as long as at least 4 nucleotide base pairs are formed to stabilize the RNA loop.
• the basepairs need not be consecutive and may contain one, two, or more mismatches, as long as a stem is formed and one, two, or three basepairs are formed next to the loop.
• IRE-l ⁇ substrates of the invention can comprise a donor moiety and an acceptor moiety, which permits IRE-l ⁇ RNase activity to be detected using resonance energy transfer.
• the donor moiety is conjugated to one of the 5' or 3' ends of the oligonucleotide molecule, and the acceptor moiety is conjugated to the other of the 5' or 3' ends of the oligonucleotide molecule.
• the donor moiety and the acceptor moiety are in sufficient proximity to each other to exhibit a detectable resonance energy transfer when the donor is excited.
• the RNase activity of IRE-l ⁇ cleaves the substrate, which changes the distance or relative orientation between the donor and acceptor moieties and alters the resonance energy transfer between the moieties.
• the degree of alteration reflects RNase activity and can be detected qualitatively or quantitatively.
• a "donor moiety” is a fluorophore or a luminescent moiety.
• the absorption spectrum of the "acceptor moiety” overlaps the emission spectrum of the donor moiety.
• the acceptor moiety does not need to be fluorescent and can be a fluorophore, chromophore, or quencher.
• both the donor and acceptor moieties are fluorescent proteins.
• both the donor and acceptor moieties are luminescent moieties.
• either one of the donor or acceptor moieties can be a fluorescent protein while the other moiety is a luminescent moiety.
• the acceptor moiety is a "quencher moiety.”
• FRET fluorescence resonance energy transfer
• LRET luminescent resonance energy transfer
• BRET bioluminescent resonance energy transfer
• Suitable acceptor moieties include, for example, a coumarin, a xanthene, a fluorescein, a fluorescent protein, a circularly permuted fluorescent protein, a rhodol, a rhodamine, a resorufin, a cyanine, a difluoroboradiazaindacene, a phthalocyanine, an indigo, a benzoquinone, an anthraquinone, an azo compound, a nitro compound, an indoaniline, a diphenylmethane, a triphenylmethane, and a zwitterionic azopyridinium compound.
• Suitable donor moieties include, but are not limited to, a coumarin, a xanthene, a rhodol, a rhodamine, a resorufin, a cyanine, a bimane, an acridine, an isoindole, a dansyl dye, an aminophthalic hydrazide " an aminophthalimide, an aminonaphthalimide, an aminobenzofuran, an aminoquinoline, a dicyanohydroquinone, a semiconductor fluorescent nanocrystal, a fluorescent protein, a circularly permuted fluorescent protein, and fluorescent lanthanide chelate.
• either or both of the donor and acceptor moieties is a fluorescent protein.
• Suitable fluorescent proteins include green fluorescent proteins (GFP), red fluorescent proteins (RFP), yellow fluorescent proteins (YFP), and cyan fluorescent proteins (CFP).
• GFP green fluorescent proteins
• RFP red fluorescent proteins
• YFP yellow fluorescent proteins
• CFP cyan fluorescent proteins
• Useful fluorescent proteins also include mutants and spectral variants of these proteins which retain the ability to fluoresce.
• RFPs include Discosoma RFPs, such Discosoma DsRed (SEQ ID NO:9) or a mutant thereof which includes an Ilel25Arg mutation, or a non-oligomerizing tandem DsRed containing, for example, two RJFP monomers linked by a peptide linker.
• a non-oligomerizing tandem RFP can contain two DsRed monomers or two mutant DsRed- I125R monomers linked by a peptide (having, for example, the amino acid sequence shown in SEQ ID NO: 10).
• Useful GFPs include an Aequorea GFP (e.g., SEQ ID NO: 11), a Renilla GFP, a Phialidium GFP, and related fluorescent proteins for example, a cyan fluorescent protein (CFP), a yellow fluorescent protein (YFP), or a spectral variant of the CFP or YFP.
• CFP (cyan) and YFP (yellow) are color variants of GFP.
• CFP and YFP contain 6 and 4 mutations, respectively. They are Tyr66Try, Phe66Leu, Ser65Thr, Asnl45Ile, Metl53Thr, and Vall63Ala in CFP and Ser65Gly, Vall68Leu, Ser72Ala, and Thr203Tyr.
• Spectral variants include an enhanced GFP (EGFP; SEQ ID NO: 12), an enhanced CFP (ECFP; SEQ ID NO: 13), an enhanced YFP (EYFP; SEQ ID NO: 14), and an EYFP with V68L and Q69K mutations.
• Other examples of fluorescent proteins comprising mutations are Aequorea GFP with one or more mutations at amino acid residues A206, L221 or F223 of SEQ ID NO:11 (e.g., mutations A206K, L221K, F223R, Q80R); mutations L221K and F223R of ECFP (SEQ ID NO:13), and EYFP-V68L/Q69K of SEQ ID NO:14.
• GFP-related fluorescent proteins include those having one or more folding mutations, and fragments of the proteins that are fluorescent, for example, an A. victoria GFP from which the two N-terminal amino acid residues have been removed.
• these fluorescent proteins contain different aromatic amino acids within the . central chromophore and fluoresce at a distinctly shorter wavelength than the wild type GFP species.
• the engineered GFP proteins designated P4 and P4-3 contain, in addition to other mutations, the substitution Y66H; and the engineered GFP proteins designated W2 and W7 contain, in addition to other mutations, Y66W.
• Folding mutations include the substitutions F64L, V68L, S72A, T44A, F99S, Y145F, N1461, M153T, M153A, V163A, 1167T 5 S175G, S205T, and N212K.
• Luminescent moieties useful in an IRE-l ⁇ substrate include lanthanides, which can be in the form of a chelate, including a lanthanide complex containing the chelate (e.g, ⁇ - diketone chelates of cerium, praseodymium, neodymium, promethium, samarium, europium, gadolinium, terbium, dysprosium, holmium, erbium, thulium, or ytterbium).
• Lanthanide chelates are well known in the art. See Soini and Kojola, Clin. Chem. 29, 65, 1983; Hemmila et al., Anal. Biochem.
• Suitable ⁇ -diketones are, for example, 2-naphthoyltrifluoroacetone (2- NTA), 1-naphthoyltrifluoroacetone (1-NTA), p-methoxybenzoyltrifluoroacetone (MO- BTA), ⁇ -fluorobenzoyltrifiuoroacetone (F-BTA), benzoyltrifluoroacetone (BTA), furoyltrifluoroacetone (FTA), naphthoylfuroylmethane (NFM), dithenoylmethane (DTM), and dibenzoylmethane (DBM). See also US 20040146895.
• 2- NTA 2-naphthoyltrifluoroacetone
• NTA 1-naphthoyltrifluoroacetone
• MO- BTA p-methoxybenzoyltrifluoroacetone
• F-BTA ⁇ -fluorobenzoyl
• Luminescent proteins include, but are not limited to, lux proteins (e.g., luxCDABE from Vibrio ⁇ scherii), luciferase proteins (e.g., firefly luciferase, Gaussia luciferase, Pleuromamma luciferase, and luciferase proteins of other beetles, Dinoflagellates (Gonylaulax; Pyrocystis;), Annelids (Dipocardia), Molluscs (Lativa), and Crustacea (Vargula; Cypridina), and green fluorescent proteins of bioluminescent coelenterates (e.g., Aequorea Victoria, Renilla mullerei, Renilla reniformis; see Prendergast et al, Biochemistry 17, 3448-53, 1978; Ward et al, Photochem.
• lux proteins e.g., luxCDABE from Vibrio ⁇ scherii
• Firefly luciferase is available from Sigma, St. Louis, MO, and Boehringer Mannheim Biochemicals, Indianapolis, IN. Recombinant ⁇ produced firefly luciferase is available from Promega Corporation, Madison, WI. Jellyfish aequorin and luciferase from Renilla are commercially available from Sealite Sciences, Bogart, GA.
• DNA sequences of the aequorin and other luciferases employed for preparation of some substrates of the invention can be derived from a variety of sources.
• cDNA can be prepared from mRNA isolated from the species disclosed above. See Faust, et al, Biochem. 18, 1106-19, 1979; De Wet et al, Proc. Natl. Acad. ScL USA 82, 7870-73, 1985.
• Luciferase substrates are well known and include coelenterazine (available from Molecular Probes, Eugene, OR) and ENDURENTM. These cell-permeable reagents can be directly administered to cells, as is known in the art. Luciferin compounds " can be prepared according to the methods disclosed by Hori et al, Biochemistry 14, 2371-76, 1975; Hori et al, Proc. Natl Acad. ScI USA 74, 4285-87, 1977).
• the acceptor moiety is a quencher moiety, preferably a "dark quencher” (or “black hole quencher”) as is known in the art.
• a "dark quencher” or “black hole quencher”
• the change in conformation which occurs with RNase activity eliminates quenching, resulting in an increase in energy emission from the donor moiety.
• "Dark quenchers” themselves do not emit photons. Use of a “dark quencher” reduces or eliminates background fluorescence or luminescence which would otherwise occur as a result of energy transfer from the donor moiety.
• Suitable quencher moieties include BLACK HOLE QUENCHERTM dyes (e.g., BHQ-0TM, BHQ- 1TM, BHQ-2TM, BHQ-3TM), which are available from Biosearch Technologies, Inc., and QSYTM dyes available from Invitrogen. Suitable quencher moieties are disclosed, for example, in US 2005/0118619; US 2005/0112673; and US 2004/0146959.
• BLACK HOLE QUENCHERTM dyes e.g., BHQ-0TM, BHQ- 1TM, BHQ-2TM, BHQ-3TM
• QSYTM dyes available from Invitrogen.
• Suitable quencher moieties are disclosed, for example, in US 2005/0118619; US 2005/0112673; and US 2004/0146959.
• any suitable fluorophore may be used as the donor moiety provided its spectral properties are favorable for use with the chosen dark quencher.
• the donor moiety can be, for example, a Cy-dye, Texas Red, a BODIPYTM dye, or an Alexa dye.
• the fluorophore is an aromatic or heteroaromatic compound and can be a pyrene, anthracene, naphthalene, acridine, stilbene, indole, benzindole, oxazole, thiazole, benzothiazole, cyanine, carbocyanine, salicylate, anthranilate, coumarin, a fluorescein (e.g., fluorescein, tetrachlorofiuorescein, hexachlorofiuorescein), rhodamine, tetramethyl-rhodamine, or other like compound.
• a fluorescein e.g., fluorescein, tetrachlorofiuorescein, hexachlorofiuorescein
• rhodamine tetramethyl-rhodamine, or other like compound.
• Suitable fluorescent moieties for use with dark quenchers include xanthene dyes, such as fluorescein or rhodamine dyes, including 6-carboxyfluorescein (FAM), 27'-dimethoxy-4 l 5'-dichloro-6-carboxyfluorescein (JOE), tetrachlorofluorescein (TET), 6-carboxyrhodamme (R6G), N,N,N;N'-tetramethyl-6-carboxyrhodamine (TAMRA), 6-carboxy-X-rhodamine (ROX).
• Suitable fluorescent reporters also include the naphthylamine dyes that have an amino group in the alpha or beta position.
• naphthylamino compounds include l-dimethylaminonaphthyl-5-sulfonate, 1- anilino-8-naphthalene sulfonate and 2-p-toluidinyl-6-naphthalene sulfonate, 5-(2'- aminoethyl)aminonaphthalene-l -sulfonic acid (EDANS).
• fluorescent moieties include coumarins, such as 3-phenyl-7- isocyanatocoumarin; acridines, such as 9-isothiocyanatoacridin- e and acridine orange; N-(p-(2-benzoxazolyl)phenyl)maleimide; cyanines, such as indodicarbocyanine 3 (Cy3), indodicarbocyanine 5 (Cy5), indodicarbocyanine 5.5 (Cy5.5), 3-l-carboxy-pentyl)-3'- ethyl-5,5'-dimethy- loxacarbocyanine (CyA); lH,5H,lH,15H-Xantheno[2,3,4-ij:5,6,7- i'j'jdiquinol- izin-18-ium, 9-[2(or 4)-[[[6-[2,5-dioxo-l-pyrroli
• IRE-l ⁇ substrates of the invention can be used in a variety of systems to detect, monitor, and quantitate IRE-l ⁇ RNase activity. Such assays can be used, for example, to monitor RNase activity or to identify a test compound as an agonist or antagonist of IRE-l ⁇ activity.
• a test compound which increases IRE-l ⁇ RNase activity ⁇ i.e., an agonist) is a potential therapeutic agent (or lead compound for developing a therapeutic agent) for treating Alzheimer's disease and type II diabetes.
• a test compound which decreases IRE-l ⁇ RNase activity i.e., an antagonist
• Assays can be carried out quantitatively or qualitatively, using either full-length IRE-l ⁇ or a portion of IRE-l ⁇ comprising the active site for RNase activity, including the cytoplasmic domain and the kinase and RNAse domains.
• the structure and functional domains of IRE-l ⁇ are well understood. See, e.g., Sidrauski & Walter, Cell 90, 1-20, 1997; Tirasophon et al., Genes & Devel. 14, 2725-2736, 2000; Dong et al, RNA 7, 361- 73, 2001; Calfon et al., Nature 415, 92-202, 2002 Liu et al., J. Biol. Chem.
• changes in resonance energy transfer are used to indicate RNase activity.
• a change in resonance energy transfer can readily be detected using methods well known in the art. See, e.g., US 2005/0118619; US 2002/0137115; US 2003/0165920; US 2003/0186229; US 2004/0137479; US 2005/0026234; US 2005/0054573; US 2005/0118619; U.S. Patent 6,773,885; U.S. Patent 6,803,201; U.S. Patent 6,818,420; Ayoub et al, 2002; Boute et al, 2002; Domin et al, Prog. Biomed. Optics and Imaging, Proc.
• RET resonance energy transfer
• RNase activity can also be used.
• the relative mass of cleaved and uncleaved products is detected, for example, using mass spectroscopy. See, e.g., U.S. Patent 5,506,348.
• a detectable label such as a fluorescent compound, is linked to either the 3' or 5' end of the substrate, and cleavage of the substrate is detected using relative size, such as by capillary electrophoresis.
• relative size such as by capillary electrophoresis.
• Test compounds See, e.g., Camilleri, ed., Capillary Electrophoresis: Theory and Practice (New Directions in Organic and Biological Chemistry Series), 1997; Heller, Analysis of Nucleic Acids By Capillary Electrophoresis, Chromatographia CE Series Volume 1, 1997; Altria, ed., Capillary Electrophoresis Guidebook: Principles, Operation, and Applications (Methods in Molecular Biology, volume 52), 1996; Guttman et al., Anal. Chem. 62, 137-146, 1990; and U.S. Patents 5,571,680, 5,110,424, and 5,567,292. Test compounds
• Test compounds can be pharmacologic agents already known in the art or . can be compounds previously unknown to have any pharmacological activity.
• the compounds can be naturally occurring or designed in the laboratory. They can be isolated from microorganisms, animals, or plants, and can be produced recombinantly, or synthesized by chemical methods known in the art. If desired, test compounds can be obtained using any of the numerous combinatorial library methods known in the art, including but not limited to, biological libraries, spatially addressable parallel solid phase or solution phase libraries, synthetic library methods requiring deconvolution, the "one-bead one-compound” library method, and synthetic library methods using affinity chromatography selection.
• Screening methods of the invention can be used in high through-put screening formats. Using high throughput screening, many discrete compounds can be tested in parallel so that large numbers of test compounds can be quickly screened.
• the most widely established techniques utilize 96- well microtiter plates, however 384- or 1536- plates also can be used.
• 96- well microtiter plates As is known in the art, a variety of instruments, materials, pipettors, robotics, plate washers, and plate readers are commercially available.
• a fusion protein comprising glutathione S transferase (GST) and human IRE-l ⁇ (GST- IRE- l ⁇ ) was obtained from a 500 ml baculovirus-infected insect cell culture.
• the insect cells were lysed by suspending the cells in Buffer A (25 mM Tris-HCl pH7.5, 50 mM KCl, 5 mM MgCl 2 , 1 mM EDTA, 2.5 mM DTT, 0.1 mM ATP, 10% sterile glycerol, 0.005% NP-40, 1 ⁇ g/mL leupeptin, 100 mM NaF, 100 mM NaVO 4 , 100 mM PMSF; 30 mLs per 500 mL culture), transferring the suspension to a high speed centrifuge tube, and sonicating the suspension on ice. The sonicated preparation was spun at 13000 x g for 30 minutes at 4°C.
• the GST tag was removed using PRESCISSIONTM PROTEASE cleavage.
• Cleavage buffer (825 ⁇ L Buffer B, 350 ⁇ l sterile glycerol, and 35 ⁇ l PRESCISSIONTM PROTEASE per mL of beads) was added to the column and incubated for 4 hours at 4 0 C with tumbling. The final product was collected by collecting flow-thru from the column. As shown in FIG. 1, this method provides a high yield and a highly pure preparation of IRE- l ⁇ protein.
• the IRE-l ⁇ monomer used in the assays described below comprises amino acids 462-977 of IRE-l ⁇ (linker, kinase, and RNAse domains) with GPLGSPEF (amino acids 1-8 of SEQ ID NO: 15) at the end terminus from the linker region of the GST vector.
• An IRE-l ⁇ protein preparation obtained as described in Example 1 was tested at various dilutions for RNase activity using four substrates: a 33 base wild-type substrate 5'- GGGUCUGCUGAGUCCGCAGC ACUC AGAAGGCCC-3' (SEQ ID NO:1), a 15 base wild-type substrate 5'-C AGUCCGC AGC ACUG-3' (SEQ ID NO:3) labeled with FAM (5') and BHQ-1TM (3'), a 33 base mutant substrate 5'-GGGUCUGCUGAGUCCCCAG- CACUCAGAAGGCCC-3' (SEQ ID NO:2), and a 15 base mutant substrate 5'- C AGUCCCC AGC ACUG-3' (SEQ ID NO:4) labeled with FAM (5 r ) and BHQ (3').
• reaction mixture comprising IX reaction buffer
• IX reaction buffer is 100 mM Hepes pH 7.5, 250 mM KOAc, 2.5 mM MgCl 2 ), 3mM DTT, and 0.4% polyethylene glycol water
• Twenty-five nanoliters of a 1 mM test compound solution were added to test wells.
• Three ⁇ l of a 128 ng/ml IRE-l ⁇ preparation were added to each test well and to positive control wells (final concentration 5.82 ng/well).
• Negative control wells contained only reaction mixture and test compound.
• IRE-l ⁇ cleaves both wild-type substrates with high specific activity, but does not cleave either of the mutant substrates.
• the enzyme retains activity at a 1 :20 dilution, and the activity appears to be dose dependent.
• Specific human IRE-l ⁇ activity was confirmed using additional 33 base stem-loop substrates with single point mutations in the loop, as shown in FIG. 3C.
• the structure on the right designates the wild type stem-loop substrate, which also is shown in FIG. 2. Circled residues show wild type residues which were changed to single point mutations (boxed). Mutants are labeled with numbers on the corresponding gel on the left. The experiment was performed in identical fashion as that in FIG. 3A with the exception of using all 5 mutant substrates with or with out the presence of recombinant purified human IRE-l ⁇ .
• IRE-l ⁇ digested the wild type substrate with little if any digestion of the other substrates, indicated by the lack of a lower molecular weight band.
• the lanes are: 1, wild type substrate in reaction buffer, no IRE-l ⁇ ; 2, mutant substrate #1 in reaction buffer, no IRE-l ⁇ ; 3, mutant substrate #2 in reaction buffer, no IRE-l ⁇ ; 4, mutant substrate #3 in reaction buffer, no IRE-l ⁇ ; 5, mutant substrate #4 in reaction buffer, no IRE-l ⁇ ; 6, mutant substrate #5 in reaction buffer, no IRE-l ⁇ ; 7, wild type substrate in reaction buffer, with IRE-l ⁇ ; 8, mutant substrate #1 in reaction buffer, with IRE-l ⁇ ; 9, mutant substrate #2 in reaction buffer, with IRE-l ⁇ ; 10, mutant substrate #3 in reaction buffer, with IRE-l ⁇ ; 11, mutant substrate #4 in reaction buffer, with IRE- l ⁇ ; and 12, mutant substrate #5 in reaction buffer, with IRE-l ⁇ .
• This example demonstrates a competition assay using a 15 base wild-type dual-labeled substrate (SEQ ID NO:3) as the readout. Increasing amounts of either unlabeled wild- type (SEQ ID NO:1) or mutant 33 base substrate (SEQ ID NO:2) were incubated in the standard reaction as described in Example 2 for 1 hour at 30 0 C.

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