Modified Cascade Ribonucleoproteins And Uses Thereof

Abstract

A clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for adaptive antiviral defence (Cascade); the Cascade protein complex comprising at least CRISPR-associated protein subunits Cas7, Cas5 and Cas6 which includes at least one subunit with an additional amino acid sequence possessing nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity. The Cascade complex with additional activity is combined with an RNA molecule to produce a ribonucleoprotein complex. The RNA molecule is selected to have substantial complementarity to a target sequence. Targeted ribonucleoproteins can be used as genetic engineering tools for precise cutting of nucleic acids in homologous recombination, non-homologous end joining, gene modification, gene integration, mutation repair or for their visualisation, transcriptional activation or repression. A pair of ribonucleotides fused to Fold dimers may be used to generate double-strand breakages in the DNA to facilitate these applications in a sequence-specific manner.

Description

[0001] The invention relates to the field of genetic engineering and more particularly to the area of gene and/or genome modification of organisms, including prokaryotes and eukaryotes. The invention also concerns methods of making site specific tools for use in methods of genome analysis and genetic modification, whether in vivo or in vitro. The invention more particularly relates to the field of ribonucleoproteins which recognise and associate with nucleic acid sequences in a sequence specific way.

[0002] Bacteria and archaea have a wide variety of defense mechanisms against invasive DNA. So called CRISPR/Cas defense systems provide adaptive immunity by integrating plasmid and viral DNA fragments in loci of clustered regularly interspaced short palindromic repeats (CRISPR) on the host chromosome. The viral or plasmid-derived sequences, known as spacers, are separated from each other by repeating host-derived sequences. These repetitive elements are the genetic memory of this immune system and each CRISPR locus contains a diverse repertoire of unique `spacer` sequences acquired during previous encounters with foreign genetic elements.

[0003] Acquisition of foreign DNA is the first step of immunization, but protection requires that the CRISPR is transcribed and that these long transcripts are processed into short CRISPR-derived RNAs (crRNAs) that each contains a unique spacer sequence complementary to a foreign nucleic acid challenger.

[0004] In addition to the crRNA, genetic experiments in several organisms have revealed that a unique set of CRISPR-associated (Cas) proteins is required for the steps of acquiring immunity, for crRNA biogenesis and for targeted interference. Also, a subset of Cas proteins from phylogenetically distinct CRISPR systems have been shown to assemble into large complexes that include a crRNA.

[0005] A recent re-evaluation of the diversity of CRISPR/Cas systems has resulted in a classification into three distinct types (Makarova K. et al (2011) Nature Reviews Microbiology--AOP 9 May 2011; doi:10.1038/nrmicro2577) that vary in cas gene content, and display major differences throughout the CRISPR defense pathway. (The Makarova classification and nomenclature for CRISPR-associated genes is adopted in the present specification.) RNA transcripts of CRISPR loci (pre-crRNA) are cleaved specifically in the repeat sequences by CRISPR associated (Cas) endoribonucleases in type I and type III systems or by RNase III in type II systems; the generated crRNAs are utilized by a Cas protein complex as a guide RNA to detect complementary sequences of either invading DNA or RNA. Cleavage of target nucleic acids has been demonstrated in vitro for the Pyrococcus furiosus type III-B system, which cleaves RNA in a ruler-anchored mechanism, and, more recently, in vivo for the Streptococcus thermophiles type II system, which cleaves DNA in the complementary target sequence (protospacer). In contrast, for type I systems the mechanism of CRISPR-interference is still largely unknown.

[0006] The model organism Escherichia coli strain K12 possesses a CRISPR/Cas type I-E (previously known as CRISPR subtype E (Cse)). It contains eight cas genes (cas1, cas2, cas3 and cse1, cse2, cas7, cas2, cas6e) and a downstream CRISPR (type-2 repeats). In Escherichia coli K12 the eight cas genes are encoded upstream of the CRISPR locus. Cas1 and Cas2 do not appear to be needed for target interference, but are likely to participate in new target sequence acquisition. In contrast, six Cas proteins: Cse1, Cse2, Cas3, Cas7, Cas5 and Cas6e (previously also known as CasA, CasB, Cas3, CasC/Cse4, CasD and CasE/Cse3 respectively) are essential for protection against lambda phage challenge. Five of these proteins: Cse1, Cse2, Cas7, Cas5 and Cas6e (previously known as CasA, CasB, CasC/Cse4, CasD and CasE/Cse3 respectively) assemble with a crRNA to form a multi-subunit ribonucleoprotein (RNP) referred to as Cascade.

[0007] In E. coli, Cascade is a 405 kDa ribonucleoprotein complex composed of an unequal stoichiometry of five functionally essential Cas proteins: Cse1.sub.1Cse2.sub.2Cas7.sub.6Cas5.sub.1Cas6e.sub.1 (i.e. under previous nomenclature CasA.sub.1B.sub.2C.sub.6D.sub.1E.sub.1) and a 61-nt CRISPR-derived RNA. Cascade is an obligate RNP that relies on the crRNA for complex assembly and stability, and for the identification of invading nucleic acid sequences. Cascade is a surveillance complex that finds and binds foreign nucleic acids that are complementary to the spacer sequence of the crRNA.

[0008] Jore et al. (2011) entitled "Structural basis for CRISPR RNA-guided DNA recognition by Cascade" Nature Structural & Molecular Biology 18: 529-537 describes how there is a cleavage of the pre-crRNA transcript by the Cas6e subunit of Cascade, resulting in the mature 61 nt crRNA being retained by the CRISPR complex. The crRNA serves as a guide RNA for sequence specific binding of Cascade to double stranded (ds) DNA molecules through base pairing between the crRNA spacer and the complementary protospacer, forming a so-called R-loop. This is known to be an ATP-independent process.

[0009] Brouns S. J. J., et al (2008) entitled "Small CRISPR RNAs guide antiviral defense in prokaryotes" Science 321: 960-964 teaches that Cascade loaded with a crRNA requires Cas3 for in vivo phage resistance.

[0010] Marraffini L. & Sontheimer E. (2010) entitled "CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea" Nature Reviews Genetics 11: 181-190 is a review article which summarises the state of knowledge in the art in the field. Some suggestions are made about CRISPR-based applications and technologies, but this is mainly in the area of generating phage resistant strains of domesticated bacteria for the dairy industry. The specific cleavage of RNA molecules in vitro by a crRNP complex in Pyrococcus furiosus is suggested as something which awaits further development. Manipulation of CRISPR systems is also suggested as a possible way of reducing transmission of antibiotic-resistant bacterial strains in hospitals. The authors stress that further research effort will be needed to explore the potential utility of the technology in these areas.

[0011] US2011236530 A1 (Manoury et al.) entitled "Genetic cluster of strains of Streptococcus thermophilus having unique rheological properties for dairy fermentation" discloses certain S. thermophilus strains which ferment milk so that it is highly viscous and weakly ropy. A specific CRISPR locus of defined sequence is disclosed.

[0012] US2011217739 A1 (Terns et al.) entitled "Cas6 polypeptides and methods of use" discloses polypeptides which have Cas6 endoribonuclease activity. The polypeptides cleave a target RNA polynucleotide having a Cas6 recognition domain and cleavage site. Cleavage may be carried out in vitro or in vivo. Microbes such as E. coli or Haloferax volcanii are genetically modified so as to express Cas6 endoribonuclease activity.

[0013] WO2010054154 (Danisco) entitled "Bifidobacteria CRISPR sequences" discloses various CRISPR sequences found in Bifidobacteria and their use in making genetically altered strains of the bacteria which are altered in their phage resistance characteristics.

[0014] US2011189776 A1 (Terns et al.) entitled "Prokaryotic RNAi-like system and methods of use" describes methods of inactivating target polynucleotides in vitro or in prokaryotic microbes in vivo. The methods use a psiRNA having a 5' region of 5-10 nucleotides chosen from a repeat from a CRISPR locus immediately upstream of a spacer. The 3' region is substantially complementary to a portion of the target polynucleotide. Also described are polypeptides having endonuclease activity in the presence of psiRNA and target polynucleotide.

[0015] EP2341149 A1 (Danisco) entitled "Use of CRISPR associated genes (CAS) describes how one or more Cas genes can be used for modulating resistance of bacterial cells against bacteriophage; particularly bacteria which provide a starter culture or probiotic culture in dairy products.

[0016] WO2010075424 (The Regents of the University of California) entitled "Compositions and methods for downregulating prokaryotic genes" discloses an isolated polynucleotide comprising a CRISPR array. At least one spacer of the CRISPR is complementary to a gene of a prokaryote so that is can down-regulate expression of the gene; particularly where the gene is associated with biofuel production.

[0017] WO2008108989 (Danisco) entitled "Cultures with improved phage resistance" discloses selecting bacteriophage resistant strains of bacteria and also selecting the strains which have an additional spacer having 100% identity with a region of phage RNA. Improved strain combinations and starter culture rotations are described for use in the dairy industry. Certain phages are described for use as biocontrol agents.

[0018] WO2009115861 (Institut Pasteur) entitled "Molecular typing and subtyping of Salmonella by identification of the variable nucleotide sequences of the CRISPR loci" discloses methods for detecting and identifying bacterial of the Salmonella genus by using their variable nucleotide sequences contained in CRISPR loci.

[0019] WO2006073445 (Danisco) entitled "Detection and typing of bacterial strains" describes detecting and typing of bacterial strains in food products, dietary supplements and environmental samples. Strains of Lactobacillus are identified through specific CRISPR nucleotide sequences.

[0020] Urnov F et al. (2010) entitled "Genome editing with engineered zinc finger nucleases" Nature 11: 636-646 is a review article about zinc finger nucleases and how they have been instrumental in the field of reverse genetics in a range of model organisms. Zinc finger nucleases have been developed so that precisely targeting genome cleavage is possible followed by gene modification in the subsequent repair process. However, zinc finger nucleases are generated by fusing a number of zinc finger DNA-binding domains to a DNA cleavage domain. DNA sequence specificity is achieved by coupling several zinc fingers in series, each recognising a three nucleotide motif A significant drawback with the technology is that new zinc fingers need to be developed for each new DNA locus which requires to be cleaved. This requires protein engineering and extensive screening to ensure specificity of DNA binding.

[0021] In the fields of genetic engineering and genomic research there is an ongoing need for improved agents for sequence/site specific nucleic acid detection and/or cleavage.

[0022] The inventors have made a surprising discovery in that certain bacteria expressing Cas3, which has helicase-nuclease activity, express Cas3 as a fusion with Cse1. The inventors have also unexpectedly been able to produce artificial fusions of Cse1 with other nuclease enzymes.

[0023] The inventors have also discovered that Cas3-independent target DNA recognition by Cascade marks DNA for cleavage by Cas3, and that Cascade DNA binding is governed by topological requirements of the target DNA.

[0024] The inventors have further found that Cascade is unable to bind relaxed target plasmids, but surprisingly Cascade displays high affinity for targets which have a negatively supercoiled (nSC) topology.

[0025] Accordingly in a first aspect the present invention provides a clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defence (Cascade), the Cascade protein complex, or portion thereof, comprising at least CRISPR-associated protein subunits: [0026] Cas7 (or COG 1857) having an amino acid sequence of SEQ ID NO:3 or a sequence of at least 18% identity therewith, [0027] Cas5 (or COG1688) having an amino acid sequence of SEQ ID NO:4 or a sequence of at least 17% identity therewith, and [0028] Cas6 (or COG 1583) having an amino acid sequence of SEQ ID NO:5 or a sequence of at least 16% identity therewith; and wherein at least one of the subunits includes an additional amino acid sequence providing nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity.

[0029] A subunit which includes an additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity is an example of what may be termed "a subunit linked to at least one functional moiety"; a functional moiety being the polypeptide or protein made up of the additional amino acid sequence. The transcription activating activity may be that leading to activation or upregulation of a desired genes; the transcription repressing activity leading to repressing or downregulation of a desired genes. The selection of the gene being due to the targeting of the cascade complex of the invention with an RNA molecule, as described further below.

[0030] The additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity is preferably formed of contiguous amino acid residues. These additional amino acids may be viewed as a polypeptide or protein which is contiguous and forms part of the Cas or Cse subunit(s) concerned. Such a polypeptide or protein sequence is preferably not normally part of any Cas or Cse subunit amino acid sequence. In other words, the additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity may be other than a Cas or Cse subunit amino acid sequence, or portion thereof, i.e. may be other than a Cas3 submit amino acid sequence or portion thereof.

[0031] The additional amino acid sequence with nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity may, as desired, be obtained or derived from the same organism, e.g. E. coli, as the Cas or Cse subunit(s).

[0032] Additionally and/or alternatively to the above, the additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity may be "heterologous" to the amino acid sequence of the Cas or Cse subunit(s). Therefore, the additional amino acid sequence may be obtained or derived from an organism different from the organism from which the Cas and/or Cse subunit(s) are derived or originate.

[0033] Throughout, sequence identity may be determined by way of BLAST and subsequent Cobalt multiple sequence alignment at the National Center for Biotechnology Information webserver, where the sequence in question is compared to a reference sequence (e.g. SEQ ID NO: 3, 4 or 5). The amino acid sequences may be defined in terms of percentage sequence similarity based on a BLOSUM62 matrix or percentage identity with a given reference sequence (e.g. SEQ ID NO:3, 4 or 5). The similarity or identity of a sequence involves an initial step of making the best alignment before calculating the percentage conservation with the reference and reflects a measure of evolutionary relationship of sequences.

[0034] Cas7 may have a sequence similarity of at least 31% with SEQ ID NO:3; Cas5 may have a sequence similarity of at least 26% with SEQ ID NO:4. Cas6 may have a sequence similarity of at least 27% with SEQ ID NO:5.

TABLE-US-00001 For Cse1/CasA (502 AA): >gi|6130667|ref|NP_417240.1| CRISP RNA (crRNA) containing Cascade antiviral complex protein [Escherichia coli str. K-12 substr. MG1655] [SEQ ID NO: 1] MNLLIDNWIPVRPRNGGKVQIINLQSLYCSRDQWRLSLPRDDMELAALAL LVCIGQIIAPAKDDVEFRHRIMNPLTEDEFQQLIAPWIDMFYLNHAEHPF MQTKGVKANDVTPMEKLLAGVSGATNCAFVNQPGQGEALCGGCTAIALFN QANQAPGFGGGFKSGLRGGTPVTTFVRGIDLRSTVLLNVLTLPRLQKQFP NESHTENQPTWIKPIKSNESIPASSIGFVRGLFWQPAHIELCDPIGIGKC SCCGQESNLRYTGFLKEKFTFTVNGLWPHPHSPCLVTVKKGEVEEKFLAF TTSAPSWTQISRVVVDKIIQNENGNRVAAVVNQFRNIAPQSPLELIMGGY RNNQASILERRHDVLMFNQGWQQYGNVINEIVTVGLGYKTALRKALYTFA EGFKNKDFKGAGVSVHETAERHFYRQSELLIPDVLANVNFSQADEVIADL RDKLHQLCEMLFNQSVAPYAHHPKLISTLALARATLYKHLRELKPQGGPS NG For Cse2/CasB (160 AA): >gi|16130666|ref|NP_417239.1| CRISP RNA (crRNA) containing Cascade antiviral complex protein [Escherichia coli str. K-12 substr. MG1655] [SEQ ID NO: 2] MADEIDAMALYRAWQQLDNGSCAQIRRVSEPDELRDIPAFYRLVQPFGWE NPRHQQALLRMVFCLSAGKNVIRHQDKKSEQTTGISLGRALANSGRINER RIFQLIRADRTADMVQLRRLLTHAEPVLDWPLMARMLTWWGKRERQQLLE DFVLTTNKNA For Cas7/CasC/Cse4 (363 AA): >gi|16130665|ref|NP_417238.1| CRISP RNA (crRNA) containing Cascade antiviral complex protein [Escherichia coli str. K-12 substr. MG1655] [SEQ ID NO: 3] MSNFINIHVLISHSPSCLNRDDMNMQKDAIFGGKRRVRISSQSLKRAMRK SGYYAQNIGESSLRTIHLAQLRDVLRQKLGERFDQKIIDKTLALLSGKSV DEAEKISADAVTPWVVGEIAWFCEQVAKAEADNLDDKKLLKVLKEDIAAI RVNLQQGVDIALSGRMATSGMMTELGKVDGAMSIAHAITTHQVDSDIDWF TAVDDLQEQGSAHLGTQEFSSGVFYRYANINLAQLQENLGGASREQALEI ATHVVHMLATEVPGAKQRTYAAFNPADMVMVNFSDMPLSMANAFEKAVKA KDGFLQPSIQAFNQYWDRVANGYGLNGAAAQFSLSDVDPITAQVKQMPTL EQLKSWVRNNGEA For Cas5/CasD (224 AA): >gi|90111483|ref|NP_417237.2| CRISP RNA (crRNA) containing Cascade antiviral complex protein [Escherichia coli str. K-12 substr. MG1655] [SEQ ID NO: 4] MRSYLILRLAGPMQAWGQPTFEGTRPTGRFPTRSGLLGLLGACLGIQRDD TSSLQALSESVQFAVRCDELILDDRRVSVTGLRDYHTVLGAREDYRGLKS HETIQTWREYLCDASFTVALWLTPHATMVISELEKAVLKPRYTPYLGRRS CPLTHPLFLGTCQASDPQKALLNYEPVGGDIYSEESVTGHHLKFTARDEP MITLPRQFASREWYVIKGGMDVSQ For Cas6e/CasE (199 AA): >gi|16130663|ref|NP_417236.1| CRISPR RNA precursor cleavage enzyme; CRISP RNA (crRNA) containing Cascade antiviral complex protein [Escherichia coli str. K-12 substr. MG1655] [SEQ ID NO: 5] MYLSKVIIARAWSRDLYQLHQGLWHLFPNRPDAARDFLFHVEKRNTPEGC HVLLQSAQMPVSTAVATVIKTKQVEFQLQVGVPLYFRLRANPIKTILDNQ KRLDSKGNIKRCRVPLIKEAEQIAWLQRKLGNAARVEDVHPISERPQYFS GDGKSGKIQTVCFEGVLTINDAPALIDLVQQGIGPAKSMGCGLLSLAPL

[0035] In defining the range of sequence variants which fall within the scope of the invention, for the avoidance of doubt, the following are each optional limits on the extent of variation, to be applied for each of SEQ ID NO:1, 2, 3, 4 or 5 starting from the respect broadest range of variants as specified in terms of the respective percentage identity above. The range of variants therefore may therefore include: at least 16%, or at least 17%, or at least 18%, or at least 19%, or at least 20%, or at least 21%, or at least 22%, or at least 23%, or at least 24%, or at least 25%, or at least 26%, or at least 27%, or at least 28%, or at least 29%, or at least 30%, or at least 31%, or at least 32%, or at least 33%, or at least 34%, or at least 35%, or at least 36%, or at least 37%, or at least 38%, or at least 39%, or at least 40%, or at least 41%, or at least 42%, or at least 43%, at least 44%, or at least 45%, or at least 46%, or at least 47%, or at least 48%, or at least 49%, or at least 50%, or at least 51%, or at least 52%, or at least 53%, or at least 54%, or at least 55%, or at least 56%, or at least 57%, or at least 58%, or at least 59%, or at least 60%, or at least 61%, or at least 62%, or at least 63%, or at least 64%, or at least 65%, or at least 66%, or at least 67%, or at least 68%, or at least 69%, or at least 70%, or at least 71%, at least 72%, or at least 73%, or at least 74%, or at least 75%, or at least 76%, or at least 77%, or at least 78%, or at least 79%, or at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or at least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or 100% amino acid sequence identity.

[0036] Throughout, the Makarova et al. (2011) nomenclature is being used in the definition of the Cas protein subunits. Table 2 on page 5 of the Makarova et al. article lists the Cas genes and the names of the families and superfamilies to which they belong. Throughout, reference to a Cas protein or Cse protein subunit includes cross reference to the family or superfamily of which these subunits form part.

[0037] Throughout, the reference sequences of the Cas and Cse subunits of the invention may be defined as a nucleotide sequence encoding the amino acid sequence. For example, the amino acid sequence of SEQ ID NO:3 for Cas7 also includes all nucleic acid sequences which encode that amino acid sequence. The variants of Cas7 included within the scope of the invention therefore include nucleotide sequences of at least the defined amino acid percentage identities or similarities with the reference nucleic acid sequence; as well as all possible percentage identities or similarities between that lower limit and 100%.

[0038] The Cascade complexes of the invention may be made up of subunits derived or modified from more than one different bacterial or archaeal prokaryote. Also, the subunits from different Cas subtypes may be mixed.

[0039] In a preferred aspect, the Cas6 subunit is a Cas6e subunit of SEQ ID NO: 17 below, or a sequence of at least 16% identity therewith.

TABLE-US-00002 The sequence of a preferred Cas6e subunit is >gi|16130663|ref|NP_417236.1| CRISPR RNA precursor cleavage enzyme; CRISP RNA (crRNA) containing Cascade antiviral complex protein [Escherichia coli str. K-12 substr. MG1655]: [SEQ ID NO: 17] MYLSKVIIARAWSRDLYQLHQGLWHLFPNRPDAARDFLFHVEKRNTPEGC HVLLQSAQMPVSTAVATVIKTKQVEFQLQVGVPLYFRLRANPIKTILDNQ KRLDSKGNIKRCRVPLIKEAEQIAWLQRKLGNAARVEDVHPISERPQYFS GDGKSGKIQTVCFEGVLTINDAPALIDLVQQGIGPAKSMGCGLLSLAPL

[0040] The Cascade complexes, or portions thereof, of the invention--which comprise at least one subunit which includes an additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity--may further comprise a Cse2 (or YgcK-like) subunit having an amino acid sequence of SEQ ID NO:2 or a sequence of at least 20% identity therewith, or a portion thereof. Alternatively, the Cse subunit is defined as having at least 38% similarity with SEQ ID NO:2. Optionally, within the protein complex of the invention it is the Cse2 subunit which includes the additional amino acid sequence having nucleic acid or chromatin modifying activity.

[0041] Additionally or alternatively, the Cascade complexes of the invention may further comprise a Cse1 (or YgcL-like) subunit having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 9% identity therewith, or a portion thereof. Optionally within the protein complex of the invention it is the Cse1 subunit which includes the additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity.

[0042] In preferred embodiments, a Cascade complex of the invention is a Type I CRISPR-Cas system protein complex; more preferably a subtype I-E CRISPR-Cas protein complex or it can be based on a Type I-A or Type I-B complex. A Type I-C, D or F complex is possible. In particularly preferred embodiments based on the E. coli system, the subunits may have the following stoichiometries: Cse1.sub.1Cse2.sub.2Cas7.sub.6Cas5.sub.1 Cas6.sub.e or Cse1.sub.1Cse2.sub.2Cas7.sub.6Cas5.sub.1Cas6e.sub.1.

[0043] The additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity may be translationally fused through expression in natural or artificial protein expression systems, or covalently linked by a chemical synthesis step to the at least one subunit; preferably the at least one functional moiety is fused or linked to at least the region of the N terminus and/or the region of the C terminus of at least one of a Cse1, Cse2, Cas7, Cas5, Cas6 or Cas6e subunit. In particularly preferred embodiments, the additional amino acid sequence having nucleic acid or chromatin modifying activity is fused or linked to the N terminus or the C terminus of a Cse1, a Cse2 or a Cas5 subunit; more preferably the linkage is in the region of the N terminus of a Cse1 subunit, the N terminus of a Cse2 subunit, or the N terminus of a Cas7 subunit.

[0044] The additional amino acid sequence having nucleic acid or chromatin modifying, activating, repressing or visualising activity may be a protein; optionally selected from a helicase, a nuclease, a nuclease-helicase, a DNA methyltransferase (e.g. Dam), or DNA demethylase, a histone methyltransferase, a histone demethylase, an acetylase, a deacetylase, a phosphatase, a kinase, a transcription (co-)activator, an RNA polymerase submit, a transcription repressor, a DNA binding protein, a DNA structuring protein, a marker protein, a reporter protein, a fluorescent protein, a ligand binding protein (e.g. mCherry or a heavy metal binding protein), a signal peptide (e.g. Tat-signal sequence), a subcellular localisation sequence (e.g. nuclear localisation sequence) or an antibody epitope.

[0045] The protein concerned may be a heterologous protein from a species other than the bacterial species from which the Cascade protein subunits have their sequence origin.

[0046] When the protein is a nuclease, it may be one selected from a type II restriction endonuclease such as FokI, or a mutant or an active portion thereof. Other type II restriction endonucleases which may be used include EcoR1, EcoRV, BgII, BamHI, BsgI and BspMI. Preferably, one protein complex of the invention may be fused to the N terminal domain of Fold and another protein complex of the invention may be fused to the C terminal domain of FokI. These two protein complexes may then be used together to achieve an advantageous locus specific double stranded cut in a nucleic acid, whereby the location of the cut in the genetic material is at the design and choice of the user, as guided by the RNA component (defined and described below) and due to presence of a so-called "protospacer adjacent motif" (PAM) sequence in the target nucleic acid strand (also described in more detail below).

[0047] In a preferred embodiment, a protein complex of the invention has an additional amino acid sequence which is a modified restriction endonuclease, e.g. FokI. The modification is preferably in the catalytic domain. In preferred embodiments, the modified FokI is KKR Sharkey or ELD Sharkey which is fused to the Cse1 protein of the protein complex. In a preferred application of these complexes of the invention, two of these complexes (KKR Sharkey and ELD Sharkey) may be together in combination. A heterodimer pair of protein complexes employing differently modified FokI is has particular advantage in targeted double stranded cutting of nucleic acid. If homodimers are used then it is possible that there is more cleavage at non-target sites due to non-specific activity. A heterodimer approach advantageously increases the fidelity of the cleavage in a sample of material.

[0048] The Cascade complex with additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity defined and described above is a component part of an overall system of the invention which advantageously permits the user to select in a predetermined matter a precise genetic locus which is desired to be cleaved, tagged or otherwise altered in some way, e.g methylation, using any of the nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing entities defined herein. The other component part of the system is an RNA molecule which acts as a guide for directing the Cascade complex of the invention to the correct locus on DNA or RNA intending to be modified, cut or tagged.

[0049] The Cascade complex of the invention preferably also comprises an RNA molecule which comprises a ribonucleotide sequence of at least 50% identity to a desired target nucleic acid sequence, and wherein the protein complex and the RNA molecule form a ribonucleoprotein complex. Preferably the ribonucleoprotein complex forms when the RNA molecule is hybridized to its intended target nucleic acid sequence. The ribonucleoprotein complex forms when the necessary components of Cascade-functional moiety combination and RNA molecule and nucleic acid (DNA or RNA) are present together in suitable physiological conditions, whether in vivo or in vitro. Without wishing to be bound by any particular theory, the inventors believe that in the context of dsDNA, particularly negatively supercoiled DNA, the Cascade complex associating with the dsDNA causes a partial unwinding of the duplex strands which then allows the RNA to associate with one strand; the whole ribonucleoprotein complex then migrates along the DNA strand until a target sequence substantially complementary to at least a portion of the RNA sequence is reached, at which point a stable interaction between RNA and DNA strand occurs, and the function of the functional moiety takes effect, whether by modifying, nuclease cutting or tagging of the DNA at that locus.

[0050] In preferred embodiments, a portion of the RNA molecule has at least 50% identity to the target nucleic acid sequence; more preferably at least 95% identity to the target sequence. In more preferred embodiments, the portion of the RNA molecule is substantially complementary along its length to the target DNA sequence; i.e. there is only one, two, three, four or five mismatches which may be contiguous or non-contiguous. The RNA molecule (or portion thereof) may have at least 51%, or at least 52%, or at least 53%, or at least 54%, or at least 55%, or at least 56%, or at least 57%, or at least 58%, or at least 59%, or at least 60%, or at least 61%, or at least 62%, or at least 63%, or at least 64%, or least 65%, or at least 66%, or at least 67%, or at least 68%, or at least 69%, or at least 70%, or at least 71%, or at least 72%, or at least 73%, or at least 74%, or at least 75%, or at least 76%, or at least 77%, or at least 78%, or at least 79%, or at least 80%, or at least 81%, or at least 82%, or at least 83%, or at least 84%, or least 85%, or at least 86%, or at least 87%, or at least 88%, or at least 89%, or at least 90%, or at least 91%, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97%, or at least 98%, or at least 99%, or 100% identity to the target sequence.

[0051] The target nucleic acid may be DNA (ss or ds) or RNA.

[0052] In other preferred embodiments, the RNA molecule or portion thereof has at least 70% identity with the target nucleic acid. At such levels of identity, the target nucleic acid is preferably dsDNA.

[0053] The RNA molecule will preferably require a high specificity and affinity for the target nucleic acid sequence. A dissociation constant (K.sub.d) in the range 1 pM to 1 .mu.M, preferably 1-100 nM is desirable as determined by preferably native gel electrophoresis, or alternatively isothermal titration calorimetry, surface plasmon resonance, or fluorescence based titration methods. Affinity may be determined using an electrophoretic mobility shift assay (EMSA), also called gel retardation assay (see Semenova E et al. (2011) Proc. Natl. Acad. Sci. USA 108: 10098-10103).

[0054] The RNA molecule is preferably modelled on what are known from nature in prokaryotes as CRISPR RNA (crRNA) molecules. The structure of crRNA molecules is already established and explained in more detail in Jore et al. (2011) Nature Structural & Molecular Biology 18: 529-537. In brief, a mature crRNA of type I-E is often 61 nucleotides long and consists of a 5' "handle" region of 8 nucleotides, the "spacer" sequence of 32 nucleotides, and a 3' sequence of 21 nucleotides which form a hairpin with a tetranucleotide loop. However, the RNA used in the invention does not have to be designed strictly to the design of naturally occurring crRNA, whether in length, regions or specific RNA sequences. What is clear though, is that RNA molecules for use in the invention may be designed based on gene sequence information in the public databases or newly discovered, and then made artificially, e.g. by chemical synthesis in whole or in part. The RNA molecules of the invention may also be designed and produced by way of expression in genetically modified cells or cell free expression systems and this option may include synthesis of some or all of the RNA sequence.

[0055] The structure and requirements of crRNA has also been described in Semenova E et al. (2011) Proc. Natl. Acad. Sci. USA 108: 10098-10103. There is a so-called "SEED" portion forming the 5' end of the spacer sequence and which is flanked 5' thereto by the 5' handle of 8 nucleotides. Semenova et al. (2011) have found that all residues of the SEED sequence should be complementary to the target sequence, although for the residue at position 6, a mismatch may be tolerated. Similarly, when designing and making an RNA component of a ribonucleoprotein complex of the invention directed at a target locus (i.e. sequence), the necessary match and mismatch rules for the SEED sequence can be applied.

[0056] The invention therefore includes a method of detecting and/or locating a single base change in a target nucleic acid molecule comprising contacting a nucleic acid sample with a ribonucleoprotein complex of the invention as hereinbefore described, or with a Cascade complex and separate RNA component of the invention as hereinbefore described, and wherein the sequence of the RNA component (including when in the ribonucleoprotein complex) is such that it discriminates between a normal allele and a mutant allele by virtue of a single base change at position 6 of a contiguous sequence of 8 nucleotide residues.

[0057] In embodiments of the invention, the RNA molecule may have a length in the range of 35-75 residues. In preferred embodiments, the portion of the RNA which is complementary to and used for targeting a desired nucleic acid sequence is 32 or 33 residues long. (In the context of a naturally occurring crRNA, this would correspond to the spacer portion; as shown in FIG. 1 of Semenova et al. (2011)).

[0058] A ribonucleoprotein complex of the invention may additionally have an RNA component comprising 8 residues 5' to the RNA sequence which has at least substantial complementarity to the nucleic acid target sequence. (The RNA sequence having at least substantial complementarity to the nucleic acid target sequence would be understood to correspond in the context of a crRNA as being the spacer sequence. The 5' flanking sequence of the RNA would be considered to correspond to the 5' handle of a crRNA. This is shown in FIG. 1 of Semenova et al. (2011)).

[0059] A ribonucleoprotein complex of the invention may have a hairpin and tetranucleotide loop forming sequence 3' to the RNA sequence which has at least substantial complementarity to the DNA target sequence. (In the context of crRNA, this would correspond to a 3' handle flanking the spacer sequence as shown in FIG. 1 of Semenova et al. (2011)).

[0060] In some embodiments, the RNA may be a CRISPR RNA (crRNA).

[0061] The Cascade proteins and complexes of the invention may be characterised in vitro in terms of its activity of association with the RNA guiding component to form a ribonucleoprotein complex in the presence of the target nucleic acid (which may be DNA or RNA). An electrophoretic mobility shift assay (EMSA) may be used as a functional assay for interaction of complexes of the invention with their nucleic acid targets. Basically, Cascade-functional moiety complex of the invention is mixed with nucleic acid targets and the stable interaction of the Cascade-functional moiety complex is monitored by EMSA or by specific readout out the functional moiety, for example endonucleolytic cleavage of target DNA at the desired site. This can be determined by further restriction fragment length analysis using commercially available enzymes with known specificities and cleavage sites in a target DNA molecule.

[0062] Visualisation of binding of Cascade proteins or complexes of the invention to DNA or RNA in the presence of guiding RNA may be achieved using scanning/atomic force microscopy (SFM/AFM) imaging and this may provide an assay for the presence of functional complexes of the invention.

[0063] The invention also provides a nucleic acid molecule encoding at least one clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein subunit selected from: [0064] a. a Cse1 subunit having an amino acid sequence of SEQ ID NO: 1 or a sequence of at least 9% identity therewith; [0065] b. a Cse2 subunit having an amino acid sequence of SEQ ID NO:2 or a sequence of at least 20% identity therewith; [0066] c. a Cas7 subunit having an amino acid sequence of SEQ ID NO:3 or a sequence of at least 18% identity therewith; [0067] d. a Cas5 subunit having an amino acid sequence of SEQ ID NO:4 or a sequence of at least 17% identity therewith; [0068] e. a Cas6 subunit having an amino acid sequence of SEQ ID NO:5 or a sequence of at least 16% identity therewith; and wherein at least a, b, c, d or e includes an additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity.

[0069] The additional amino acid sequence having nucleic acid or chromatin modifying, visualising, transcription activating or transcription repressing activity is preferably fused to the CRISPR-associated protein subunit.

[0070] In the nucleic acids of the invention defined above, the nucleotide sequence may be that which encodes the respective SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:5, or in defining the range of variant sequences thereto, it may be a sequence hybridisable to that nucleotide sequence, preferably under stringent conditions, more preferably very high stringency conditions. A variety of stringent hybridisation conditions will be familiar to the skilled reader in the field. Hybridization of a nucleic acid molecule occurs when two complementary nucleic acid molecules undergo an amount of hydrogen bonding to each other known as Watson-Crick base pairing. The stringency of hybridization can vary according to the environmental (i.e. chemical/physical/biological) conditions surrounding the nucleic acids, temperature, the nature of the hybridization method, and the composition and length of the nucleic acid molecules used. Calculations regarding hybridization conditions required for attaining particular degrees of stringency are discussed in Sambrook et al., Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001); and Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology--Hybridization with Nucleic Acid Probes Part I, Chapter 2 (Elsevier, New York, 1993). The T.sub.m is the temperature at which 50% of a given strand of a nucleic acid molecule is hybridized to its complementary strand. The following is an exemplary set of hybridization conditions and is not limiting:

Very High Stringency (Allows Sequences that Share at Least 90% Identity to Hybridize) Hybridization: 5x SSC at 65.degree. C. for 16 hours Wash twice: 2x SSC at room temperature (RT) for 15 minutes each Wash twice: 0.5x SSC at 65.degree. C. for 20 minutes each High Stringency (Allows Sequences that Share at Least 80% Identity to Hybridize) Hybridization: 5x-6x SSC at 65.degree. C.-70.degree. C. for 16-20 hours Wash twice: 2x SSC at RT for 5-20 minutes each Wash twice: 1x SSC at 55.degree. C.-70.degree. C. for 30 minutes each Low Stringency (Allows Sequences that Share at Least 50% Identity to Hybridize) Hybridization: 6x SSC at RT to 55.degree. C. for 16-20 hours Wash at least twice: 2x-3x SSC at RT to 55.degree. C. for 20-30 minutes each.

[0071] The nucleic acid molecule may be an isolated nucleic acid molecule and may be an RNA or a DNA molecule.

[0072] The additional amino acid sequence may be selected from a helicase, a nuclease, a nuclease-helicase (e.g. Cas3), a DNA methyltransferase (e.g. Dam), a DNA demethylase, a histone methyltransferase, a histone demethylase, an acetylase, a deacetylase, a phosphatase, a kinase, a transcription (co-)activator, an RNA polymerase subunit, a transcription repressor, a DNA binding protein, a DNA structuring protein, a marker protein, a reporter protein, a fluorescent protein, a ligand binding protein (e.g. mCherry or a heavy metal binding protein), a signal peptide (e.g. Tat-signal sequence), a subcellular localisation sequence (e.g. nuclear localisation sequence), or an antibody epitope. The additional amino acid sequence may be, or from a different protein from the organism from which the relevant Cascade protein subunit(s) are derived.

[0073] The invention includes an expression vector comprising a nucleic acid molecule as hereinbefore defined. One expression vector may contain the nucleotide sequence encoding a single Cascade protein subunit and also the nucleotide sequence encoding the additional amino acid sequence, whereby on expression the subunit and additional sequence are fused. Other expression vectors may comprise nucleotide sequences encoding just one or more Cascade protein subunits which are not fused to any additional amino acid sequence.

[0074] The additional amino acid sequence with nucleic acid or chromatin modifying activity may be fused to any of the Cascade subunits via a linker polypeptide. The linker may be of any length up to about 60 or up to about 100 amino acid residues. Preferably the linker has a number of amino acids in the range 10 to 60, more preferably 10-20. The amino acids are preferably polar and/or small and/or charged amino acids (e.g. Gln, Ser, Thr, Pro, Ala, Glu, Asp, Lys, Arg, His, Asn, Cys, Tyr). The linker peptide is preferably designed to obtain the correct spacing and positioning of the fused functional moiety and the subunit of Cascade to which the moiety is fused to allow proper interaction with the target nucleotide.

[0075] An expression vector of the invention (with or without nucleotide sequence encoding amino acid residues which on expression will be fused to a Cascade protein subunit) may further comprise a sequence encoding an RNA molecule as hereinbefore defined. Consequently, such expression vectors can be used in an appropriate host to generate a ribonucleoprotein of the invention which can target a desired nucleotide sequence.

[0076] Accordingly, the invention also provides a method of modifying, visualising, or activating or repressing transcription of a target nucleic acid comprising contacting the nucleic acid with a ribonucleoprotein complex as hereinbefore defined. The modifying may be by cleaving the nucleic acid or binding to it.

[0077] The invention also includes a method of modifying, visualising, or activating or repressing transcription of a target nucleic acid comprising contacting the nucleic acid with a Cascade protein complex as hereinbefore defined, plus an RNA molecule as hereinbefore defined.

[0078] In accordance with the above methods, the modification, visualising, or activating or repressing transcription of a target nucleic acid may therefore be carried out in vitro and in a cell free environment; i.e. the method is carried out as a biochemical reaction whether free in solution or whether involving a solid phase. Target nucleic acid may be bound to a solid phase, for example.

[0079] In a cell free environment, the order of adding each of the target nucleic acid, the Cascade protein complex and the RNA molecule is at the option of the average skilled person. The three components may be added simultaneously, sequentially in any desired order, or separately at different times and in a desired order. Thus it is possible for the target nucleic acid and RNA to be added simultaneously to a reaction mix and then the Cascade protein complex of the invention to be added separately and later in a sequence of specific method steps.

[0080] The modification, visualising, or activating or repressing transcription of a target nucleic acid may be made in situ in a cell, whether an isolated cell or as part of a multicellular tissue, organ or organism. Therefore in the context of whole tissue and organs, and in the context of an organism, the method can be carried out in vivo or it can be carried out by isolating a cell from the whole tissue, organ or organism and then returning the cell treated with ribonucleoprotein complex to its former location, or a different location, whether within the same or a different organism. Thus the method would include allografts, autografts, isografts and xenografts.

[0081] In these embodiments, the ribonucleoprotein complex or the Cascade protein complex of the invention requires an appropriate form of delivery into the cell, which will be well known to persons of skill in the art, including microinjection, whether into the cell cytoplasm or into the nucleus.

[0082] Also when present separately, the RNA molecule requires an appropriate form of delivery into a cell, whether simultaneously, separately or sequentially with the Cascade protein complex. Such forms of introducing RNA into cells are well known to a person of skill in the art and may include in vitro or ex vivo delivery via conventional transfection methods. Physical methods, such as microinjection and electroporation, as well as calcium co-precipitation, and commercially available cationic polymers and lipids, and cell-penetrating peptides, cell-penetrating particles (gene-gun) may each be used. For example, viruses may be used as delivery vehicles, whether to the cytoplasm and/or nucleus--e.g. via the (reversible) fusion of Cascade protein complex of the invention or a ribonucleoprotein complex of the invention to the viral particle. Viral delivery (e.g. adenovirus delivery) or Agrobacterium-mediated delivery may be used.

[0083] The invention also includes a method of modifying visualising, or activating or repressing transcription of a target nucleic acid in a cell, comprising transfecting, transforming or transducing the cell with any of the expression vectors as hereinbefore described. The methods of transfection, transformation or transduction are of the types well known to a person of skill in the art. Where there is one expression vector used to generate expression of a Cascade complex of the invention and when the RNA is added directly to the cell then the same or a different method of transfection, transformation or transduction may be used. Similarly, when there is one expression vector being used to generate expression of a Cascade-functional fusion complex of the invention and when another expression vector is being used to generate the RNA in situ via expression, then the same or a different method of transfection, transformation or transduction may be used.

[0084] In other embodiments, mRNA encoding the Cascade complex of the invention is introduced into a cell so that the Cascade complex is expressed in the cell. The RNA which guides the Cascade complex to the desired target sequence is also introduced into the cell, whether simultaneously, separately or sequentially from the mRNA, such that the necessary ribonucleoprotein complex is formed in the cell.

[0085] In the aforementioned methods of modifying or visualising a target nucleic acid, the additional amino acid sequence may be a marker and the marker associates with the target nucleic acid; preferably wherein the marker is a protein; optionally a fluorescent protein, e.g. green fluorescent protein (GFP) or yellow fluorescent protein (YFP) or mCherry. Whether in vitro, ex vivo or in vitro, then methods of the invention can be used to directly visualise a target locus in a nucleic acid molecule, preferably in the form of a higher order structure such as a supercoiled plasmid or chromosome, or a single stranded target nucleic acid such as mRNA. Direct visualisation of a target locus may use electron micrography, or fluorescence microscopy.

[0086] Other kinds of label may be used to mark the target nucleic acid including organic dye molecules, radiolabels and spin labels which may be small molecules.

[0087] In methods of the invention described above, the target nucleic acid is DNA; preferably dsDNA although the target can be RNA; preferably mRNA.

[0088] In methods of the invention for modifying, visualising, activating transcription or repressing transcription of a target nucleic acid wherein the target nucleic acid is dsDNA, the additional amino acid sequence with nucleic acid or chromatin modifying activity may be a nuclease or a helicase-nuclease, and the modification is preferably a single stranded or a double stranded break at a desired locus. In this way unique sequence specific cutting of DNA can be engineered by using the Cascade-functional moiety complexes. The chosen sequence of the RNA component of the final ribonucleoprotein complex provides the desired sequence specificity for the action of the additional amino acid sequence.

[0089] Therefore, the invention also provides a method of non-homologous end joining of a dsDNA molecule in a cell at a desired locus to remove at least a part of a nucleotide sequence from the dsDNA molecule; optionally to knockout the function of a gene or genes, wherein the method comprises making double stranded breaks using any of the methods of modifying a target nucleic acid as hereinbefore described.

[0090] The invention further provides a method of homologous recombination of a nucleic acid into a dsDNA molecule in a cell at a desired locus in order to modify an existing nucleotide sequence or insert a desired nucleotide sequence, wherein the method comprises making a double or single stranded break at the desired locus using any of the methods of modifying a target nucleic acid as hereinbefore described.

[0091] The invention therefore also provides a method of modifying, activating or repressing gene expression in an organism comprising modifying, activating transcription or repressing transcription of a target nucleic acid sequence according to any of the methods hereinbefore described, wherein the nucleic acid is dsDNA and the functional moiety is selected from a DNA modifying enzyme (e.g. a demethylase or deacetylase), a transcription activator or a transcription repressor.

[0092] The invention additionally provides a method of modifying, activating or repressing gene expression in an organism comprising modifying, activating transcription or repressing transcription of a target nucleic acid sequence according to any of the methods hereinbefore described, wherein the nucleic acid is an mRNA and the functional moiety is a ribonuclease; optionally selected from an endonuclease, a 3' exonuclease or a 5' exonuclease.

[0093] In any of the methods of the invention as described above, the cell which is subjected to the method may be a prokaryote. Similarly, the cell may be a eukaryotic cell, e.g. a plant cell, an insect cell, a yeast cell, a fungal cell, a mammalian cell or a human cell. When the cell is of a mammal or human then it can be a stem cell (but may not be any human embryonic stem cell). Such stem cells for use in the invention are preferably isolated stem cells. Optionally in accordance with any method the invention a cell is transfected in vitro.

[0094] Preferably though, in any of the methods of the invention, the target nucleic acid has a specific tertiary structure, optionally supercoiled, more preferably wherein the target nucleic acid is negatively supercoiled. Advantageously, the ribonucleoprotein complexes of the invention, whether produced in vitro, or whether formed within cells, or whether formed within cells via expression machinery of the cell, can be used to target a locus which would otherwise be difficult to get access to in order to apply the functional activity of a desired component, whether labelling or tagging of a specific sequence, modification of nucleic acid structure, switching on or off of gene expression, or of modification of the target sequence itself involving single or double stranded cutting followed by insertion of one or more nucleotide residues or a cassette.

[0095] The invention also includes a pharmaceutical composition comprising a Cascade protein complex or a ribonucleoprotein complex of the invention as hereinbefore described.

[0096] The invention further includes a pharmaceutical composition comprising an isolated nucleic acid or an expression vector of the invention as hereinbefore described.

[0097] Also provided is a kit comprising a Casacade protein complex of the invention as hereinbefore described plus an RNA molecule of the invention as hereinbefore described.

[0098] The invention includes a Cascade protein complex or a ribonucleoprotein complex or a nucleic acid or a vector, as hereinbefore described for use as a medicament.

[0099] The invention allows a variety of possibilities to physically alter DNA of prokaryotic or eukaryotic hosts at a specified genomic locus, or change expression patterns of a gene at a given locus. Host genomic DNA can be cleaved or modified by methylation, visualized by fluorescence, transcriptionally activated or repressed by functional domains such as nucleases, methylases, fluorescent proteins, transcription activators or repressors respectively, fused to suitable Cascade-subunits. Moreover, the RNA-guided RNA-binding ability of Cascade permits the monitoring of RNA trafficking in live cells using fluorescent Cascade fusion proteins, and provides ways to sequester or destroy host mRNAs causing interference with gene expression levels of a host cell.

[0100] In any of the methods of the invention, the target nucleic acid may be defined, preferably so if dsDNA, by the presence of at least one of the following nucleotide triplets: 5'-CTT-3',5'-CAT-3',5'-CCT-3', or 5'-CTC-3' (or 5'-CUU-3',5'-CAU-3',5'-CCU-3', or 5'-CTC-3' if the target is an RNA). The location of the triplet is in the target strand adjacent to the sequence to which the RNA molecule component of a ribonucleoprotein of the invention hybridizes. The triplet marks the point in the target strand sequence at which base pairing with the RNA molecule component of the ribonucleoprotein does not take place in a 5' to 3' (downstream) direction of the target (whilst it takes place upstream of the target sequence from that point subject to the preferred length of the RNA sequence of the RNA molecule component of the ribonucleoprotein of the invention). In the context of a native type I CRISPR system, the triplets correspond to what is known as a "PAM" (protospacer adjacent motif). For ssDNA or ssRNA targets, presence of one of the triplets is not so necessary.

[0101] The invention will now be described in detail and with reference to specific examples and drawings in which:

[0102] FIG. 1 shows the results of gel-shift assays where Cascade binds negatively supercoiled (nSC) plasmid DNA but not relaxed DNA. A) Gel-shift of nSC plasmid DNA with J3-Cascade, containing a targeting (J3) crRNA. pUC-.lamda. was mixed with 2-fold increasing amounts of J3-Cascade, from a pUC-.lamda.:Cascade molar ratio of 1:0.5 up to a 1:256 molar ratio. The first and last lanes contain only pUC-.lamda.. B) Gel-shift as in (A) with R44-Cascade containing a non-targeting (R44) cRNA. C) Gel-shift as in (A) with Nt.BspQI nicked pUC-.lamda.. D) Gel-shift as in (A) with PdmI linearized pUC-.lamda.. E) Fit of the fraction pUC-.lamda. bound to J3-Cascade plotted against the concentration of free J3-Cascade gives the dissociation constant (Kd) for specific binding. F) Fit of the fraction pUC-.lamda. bound to R44-Cascade plotted against the concentration of free R44-Cascade gives the dissociation constant (Kd) for non-specific binding. G) Specific binding of Cascade to the protospacer monitored by restriction analysis, using the unique BsmI restriction site in the protospacer sequence. Lane 1 and 5 contain only pUC-.lamda.. Lane 2 and 6 contain pUC-.lamda. mixed with Cascade. Lane 3 and 7 contain pUC-.lamda. mixed with Cascade and subsequent BsmI addition. Lane 4 and 8 contain pUC-.lamda. mixed with BsmI. H) Gel-shift of pUC-.lamda. bound to Cascade with subsequent Nt.BspQI cleavage of one strand of the plasmid. Lane 1 and 6 contain only pUC-.lamda.. Lane 2 and 7 contain pUC-.lamda. mixed with Cascade. Lane 3 and 8 contain pUC-.lamda. mixed with Cascade and subsequent Nt.BspQI nicking Lane 4 and 9 contain pUC-.lamda. mixed with Cascade, followed by addition of a ssDNA probe complementary to the displaced strand in the R-loop and subsequent nicking with Nt.BspQI. Lane 5 and 10 contain pUC-.lamda. nicked with Nt.BspQI. H) Gel-shift of pUC-.lamda. bound to Cascade with subsequent Nt.BspQI nicking of the plasmid. Lane 1 and 6 contain only pUC-.lamda.. Lane 2 and 7 contain pUC-.lamda. mixed with Cascade. Lane 3 and 8 contain pUC-.lamda. mixed with Cascade and subsequent Nt.BspQI cleavage. Lane 4 and 9 contain pUC-.lamda. mixed with Cascade, followed by addition of a ssDNA probe complementary to the displaced strand in the R-loop and subsequent cleavage with Nt.BspQI. Lane 5 and 10 contain pUC-.lamda. cleaved with Nt.BspQI. I) Gel-shift of pUC-.lamda. bound to Cascade with subsequent EcoRI cleavage of both strands of the plasmid. Lane 1 and 6 contain only pUC-.lamda.. Lane 2 and 7 contain pUC-.lamda. mixed with Cascade. Lane 3 and 8 contain pUC-.lamda. mixed with Cascade and subsequent EcoRI cleavage. Lane 4 and 9 contain pUC-.lamda. mixed with Cascade, followed by addition of a ssDNA probe complementary to the displaced strand in the R-loop and subsequent cleavage with EcoRI. Lane 5 and 10 contain pUC-.lamda. cleaved with EcoRI.

[0103] FIG. 2 shows scanning force micrographs demonstrating how Cascade induces bending of target DNA upon protospacer binding. A-P) Scanning force microscopy images of nSC plasmid DNA with J3-Cascade containing a targeting (J3) crRNA. pUC-.lamda. was mixed with J3-Cascade at a pUC-.lamda.:Cascade ratio of 1:7. Each image shows a 500.times.500 nm surface area. White dots correspond to Cascade.

[0104] FIG. 3 shows how BiFC analysis reveals that Cascade and Cas3 interact upon target recognition. A) Venus fluorescence of cells expressing Cascade.DELTA.Cse1 and CRISPR 7Tm, which targets 7 protospacers on the phage .lamda. genome, and Cse1-N155Venus and Cas3-C85Venus fusion proteins. B) Brightfield image of the cells in (A). C) Overlay of (A) and (B). D) Venus fluorescence of phage .lamda. infected cells expressing Cascade.DELTA.Cse1 and CRISPR 7Tm, and Cse1-N155Venus and Cas3-C85Venus fusion proteins. E) Brightfield image of the cells in (G). F) Overlay of (G) and (H). G) Venus fluorescence of phage .lamda. infected cells expressing Cascade.DELTA.Cse1 and non-targeting CRISPR R44, and N155Venus and C85Venus proteins. H) Brightfield image of the cells in (J). I) Overlay of (J) and (K). J) Average of the fluorescence intensity of 4-7 individual cells of each strain, as determined using the profile tool of LSM viewer (Carl Zeiss).

[0105] FIG. 4 shows Cas3 nuclease and helicase activities during CRISPR-interference. A) Competent BL21-AI cells expressing Cascade, a Cas3 mutant and CRISPR J3 were transformed with pUC-.lamda.. Colony forming units per microgram pUC-.lamda. (cfu/.mu.g DNA) are depicted for each of the strains expressing a Cas3 mutant. Cells expressing wt Cas3 and CRISPR J3 or CRISPR R44 serve as positive and negative controls, respectively. B) BL21-AI cells carrying Cascade, Cas3 mutant, and CRISPR encoding plasmids as well as pUC-.lamda. are grown under conditions that suppress expression of the cas genes and CRISPR. At t=0 expression is induced. The percentage of cells that lost pUC-.lamda. over time is shown, as determined by the ratio of ampicillin sensitive and ampicillin resistant cells.

[0106] FIG. 5 shows how a Cascade-Cas3 fusion complex provides in vivo resistance and has in vitro nuclease activity. A) Coomassie Blue stained SDS-PAGE of purified Cascade and Cascade-Cas3 fusion complex. B) Efficiency of plaquing of phage .lamda. on cells expressing Cascade-Cas3 fusion complex and a targeting (J3) or non-targeting (R44) CRISPR and on cells expressing Cascade and Cas3 separately together with a targeting (J3) CRISPR. C) Gel-shift (in the absence of divalent metal ions) of nSC target plasmid with J3-Cascade-Cas3 fusion complex. pUC-.lamda. was mixed with 2-fold increasing amounts of J3-Cascade-Cas3, from a pUC-.lamda.:J3-Cascade-Cas3 molar ratio of 1:0.5 up to a 1:128 molar ratio. The first and last lane contain only pUC-.lamda.. D) Gel-shift (in the absence of divalent metal ions) of nSC non-target plasmid with J3-Cascade-Cas3 fusion complex. pUC-p7 was mixed with 2-fold increasing amounts of J3-Cascade-Cas3, from a pUC-p7:J3-Cascade-Cas3 molar ratio of 1:0.5 up to a 1:128 molar ratio. The first and last lane contain only pUC-p7. E) Incubation of nSC target plasmid (pUC-.lamda., left) or nSC non-target plasmid (pUC-p7, right) with J3-Cascade-Cas3 in the presence of 10 mM MgCl.sub.2. Lane 1 and 7 contain only plasmid. F) Assay as in (E) in the presence of 2 mM ATP. G) Assay as in (E) with the mutant J3-Cascade-Cas3K320N complex. H) Assay as in (G) in the presence of 2 mM ATP.

[0107] FIG. 6 is a schematic diagram showing a model of the CRISPR-interference type I pathway in E. coli.

[0108] FIG. 7 is a schematic diagram showing how a Cascade-FokI fusion embodiment of the invention is used to create Fold dimers which cuts dsDNA to produce blunt ends as part of a process of non-homologous end joining or homologous recombination.

[0109] FIG. 8 shows how BiFC analysis reveals that Cascade and Cas3 interact upon target recognition. Overlay of Brightfield image and Venus fluorescence of cells expressing Cascade without Cse1, Cse1-N155Venus and Cas3-C85Venus and either CRISPR 7Tm, which targets 7 protospacers on the phage Lambda genome, or the non-targeting CRISPR R44. Cells expressing CRISPR 7Tm are fluorescent only when infected with phage Lambda, while cells expressing CRISPR R44 are non-fluorescent. The highly intense fluorescent dots (outside cells) are due to light-reflecting salt crystals. White bars correspond to 10 micron.

[0110] FIG. 9 shows pUC-.lamda. sequences of 4 clones [SEQ ID NOs: 39-42] encoding CRISPR J3, Cascade and Cas3 (wt or S483AT485A) indicate that these are escape mutants carrying (partial) deletions of the protospacer or carrying a single point mutation in the seed region, which explains the inability to cure these plasmids.

[0111] FIG. 10 shows sequence alignments of cas3 genes from organisms containing the Type I-E CRISPR/Cas system. Alignment of cas3-cse1 genes from Streptomyces sp. SPB78 (1.sup.st sequence, Accession Number: ZP.sub.--07272643.1) [SEQ ID NO: 43], in Streptomyces griseus (2.sup.nd sequence, Accession Number YP.sub.--001825054) [SEQ ID NO: 44], and in Catenulispora acidiphila DSM 44928 (3.sup.rd sequence, Accession Number YP.sub.--003114638) [SEQ ID NO: 45] and an artificial E. coli Cas3-Cse1 fusion protein [SEQ ID NO: 46] which includes the polypeptide linker sequence from S. griseus.

[0112] FIG. 11 shows the design of a Cascade.sup.KKR/ELD nuclease pair in which Fold nuclease domains are mutated such that only heterodimers consisting of KKR and ELD nuclease domains are and the distance between the opposing binding sites may be varied to determine the optimal distance between a Cascade nuclease pair.

[0113] FIG. 12 is a schematic diagram showing genome targeting by a Cascade-Fold nuclease pair.

[0114] FIG. 13 shows an SDS PAGE gel of Cascade-nuclease complexes.

[0115] FIG. 14 shows electrophoresis gels of in vitro cleavage assays of Cascade.sup.KKR/ELD on plasmid DNA.

[0116] FIG. 15 shows Cascade.sup.KKR/ELD cleavage patterns and frequency [SEQ ID NO: 47].

EXAMPLES

Materials and Methods Used

Strains, Gene Cloning, Plasmids and Vectors

[0117] E. coli BL21-AI and E. coli BL21 (DE3) strains were used throughout. Table 1 lists all plasmids used in this study. The previously described pWUR408, pWUR480, pWUR404 and pWUR547 were used for production of Strep-tag II R44-Cascade, and pWUR408, pWUR514 and pWUR630 were used for production of Strep-tag II J3-Cascade (Jore et al., (2011) Nature Structural & Molecular Biology 18, 529-536; Semenova et al., (2011) Proceedings of the National Academy of Sciences of the United States of America 108, 10098-10103.) pUC-.lamda. (pWUR610) and pUC-p7 (pWUR613) have been described elsewhere (Jore et al., 2011; Semenova et al., 2011). The C85Venus protein is encoded by pWUR647, which corresponds to pET52b (Novagen) containing the synthetic GA1070943 construct (Table 2) (Geneart) cloned between the BamHI and NotI sites. The N155Venus protein is encoded by pWUR648, which corresponds to pRSF1b (Novagen) containing the synthetic GA1070941 construct (Table 2) (Geneart) cloned between the NotI and XhoI sites. The Cas3-C85Venus fusion protein is encoded by pWUR649, which corresponds to pWUR647 containing the Cas3 amplification product using primers BG3186 and BG3213 (Table 3) between the NcoI and BamHI sites. The CasA-N155Venus fusion protein is encoded by pWUR650, which corresponds to pWUR648 containing the CasA amplification product using primers BG3303 and BG3212 (Table 3) between the NcoI and BamHI sites. CRISPR 7Tm is encoded by pWUR651, which corresponds to pACYCDuet-1 (Novagen) containing the synthetic GA1068859 construct (Table 2) (Geneart) cloned between the NcoI and KpnI sites. The Cascade encoding pWUR400, the Cascade.DELTA.Cse1 encoding WUR401 and the Cas3 encoding pWUR397 were described previously (Jore et al., 2011). The Cas3H74A encoding pWUR652 was constructed using site directed mutagenesis of pWUR397 with primers BG3093, BG3094 (Table 3).

TABLE-US-00003 TABLE 1 Plasmids used Description and order Restriction Plasmids of genes (5'-3') sites Primers Source pWUR397 cas3 inpRSF-1b, no 1 tags pWUR400 casA-casB-casC-casD- 1 casE in pCDF-1b, no tags pWUR401 casB-casC-casD-casE 1 in pCDF-1b, no tags pWUR404 casE in pCDF-1b, no 1 tags pWUR408 casA in pRSF-1b, no 1 tags pWUR480 casB with Strep-tag II 1 (N-term)-casC-casD in pET52b pWUR514 casB with Strep-tag II 2 (N-term)-casC-casD- CasE in pET52b pWUR547 E. coli R44 CRISPR, 7x 2 spacer nr. 2, in pACYCDuet-1 pWUR613 pUC-p7; pUC19 2 containing R44- protospacer on a 350 bp phage P7 amplicon pWUR630 CRISPR poly J3, 5x NcoI/KpnI This spacer J3 in study pACYCDuet-1 pWUR610 pUC-.lamda.; pUC19 3 containing J3- protospacer on a 350 bp phage A, amplicon pWUR647 C85Venus; GA1070943 BamHI/NotI This (Table S1) in pET52b study pWUR648 N155Venus; NotI/XhoI This GA1070941 (Table S1) study in pRSF1b pWUR649 cas3-C85Venus; NcoI/BamHI BG3186 + This pWUR647 containing BG3213 study cas3 amplicon pWUR650 casA-N155Venus NcoI/NotI BG3303 + This pWUR648 containing BG3212 study casA amplicon pWUR651 CRISPR 7Tm; NcoI/KpnI This GA1068859 (Table S1) study in pACYCDuet-1 casB with Strep-tag II This (N-term)-casC-casD- study CasE in pCDF-1b cas3-casA fusion This study cas3H74A-CasA fusion This study cas3D75A-CasA fusion This study cas3K320N-CasA This fusion study cas3D452N-CasA This fusion study Source 1 in the table above is Brouns et al (2008) Science 321, 960-964. Source 2 in the table above is Jore et al (2011) Nature Structural & Molecular Biology 18: 529-537.

TABLE-US-00004 TABLE 2 Synthetic Constructs GA1070943 ACTGGAAAGCGGGCAGTGAAAGGAAGGCCCATGAGGCCAGTTAATTAAGC GGATCCTGGCGGCGGCAGCGGCGGCGGCAGCGACAAGCAGAAGAACGGCA TCAAGGCGAACTTCAAGATCCGCCACAACATCGAGGACGGCGGCGTGCAG CTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCT GCTGCCCGACAACCACTACCTGAGCTACCAGTCCGCCCTGAGCAAAGACC CCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCC GGGATCACTCTCGGCATGGACGAGCTGTACAAGTAAGCGGCCGCGGCGCG CCTAGGCCTTGACGGCCTTCCTTCAATTCGCCCTATAGTGAG [SEQ ID NO: 6] GA1070941 CACTATAGGGCGAATTGGCGGAAGGCCGTCAAGGCCGCATTTAATTAAGC GGCCGCAGGCGGCGGCAGCGGCGGCGGCAGCATGGTGAGCAAGGGCGAGG AGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTA AACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTA CGGCAAGCTGACCCTGAAGCTCATCTGCACCACCGGCAAGCTGCCCGTGC CCTGGCCCACCCTCGTGACCACCCTCGGCTACGGCCTGCAGTGCTTCGCC CGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCC CGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACT ACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGC ATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCA CAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCACGGCCTAAC TCGAGGGCGCGCCCTGGGCCTCATGGGCCTTCCGCTCACTGCCCGCTTTC CAG [SEQ ID NO: 7] GA1068859 CACTATAGGGCGAATTGGCGGAAGGCCGTCAAGGCCGCATGAGCTCCATG GAAACAAAGAATTAGCTGATCTTTAATAATAAGGAAATGTTACATTAAGG TTGGTGGGTTGTTTTTATGGGAAAAAATGCTTTAAGAACAAATGTATACT TTTAGAGAGTTCCCCGCGCCAGCGGGGATAAACCGGGCCGATTGAAGGTC CGGTGGATGGCTTAAAAGAGTTCCCCGCGCCAGCGGGGATAAACCGCCGC AGGTACAGCAGGTAGCGCAGATCATCAAGAGTTCCCCGCGCCAGCGGGGA TAAACCGACTTCTCTCCGAAAAGTCAGGACGCTGTGGCAGAGTTCCCCGC GCCAGCGGGGATAAACCGCCTACGCGCTGAACGCCAGCGGTGTGGTGAAT GAGTTCCCCGCGCCAGCGGGGATAAACCGGTGTGGCCATGCACGCCTTTA ACGGTGAACTGGAGTTCCCCGCGCCAGCGGGGATAAACCGCACGAACTCA GCCAGAACGACAAACAAAAGGCGAGTTCCCCGCGCCAGCGGGGATAAACC GGCACCAGTACGCGCCCCACGCTGACGGTTTCTGAGTTCCCCGCGCCAGC GGGATAAACCGCAGCTCCCATTTTCAAACCCAGGTACCCTGGGCCTCATG GGCCTTCCGCTCACTGCCCGCTTTCCAG [SEQ ID NO: 8] GA1047360 GAGCTCCCGGGCTGACGGTAATAGAGGCACCTACAGGCTCCGGTAAAACG GAAACAGCGCTGGCCTATGCTTGGAAACTTATTGATCAACAAATTGCGGA TAGTGTTATTTTTGCCCTCCCAACACAAGCTACCGCGAATGCTATGCTTA CGAGAATGGAAGCGAGCGCGAGCCACTTATTTTCATCCCCAAATCTTATT CTTGCTCATGGCAATTCACGGTTTAACCACCTCTTTCAATCAATAAAATC ACGCGCGATTACTGAACAGGGGCAAGAAGAAGCGTGGGTTCAGTGTTGTC AGTGGTTGTCACAAAGCAATAAGAAAGTGTTTCTTGGGCAAATCGGCGTT TGCACGATTGATCAGGTGTTGATTTCGGTATTGCCAGTTAAACACCGCTT TATCCGTGGTTTGGGAATTGGTAGATCTGTTTTAATTGTTAATGAAGTTC ATGCTTACGACACCTATATGAACGGCTTGCTCGAGGCAGTGCTCAAGGCT CAGGCTGATGTGGGAGGGAGTGTTATTCTTCTTTCCGCAACCCTACCAAT GAAACAAAAACAGAAGCTTCTGGATACTTATGGTCTGCATACAGATCCAG TGGAAAATAACTCCGCATATCCACTCATTAACTGGCGAGGTGTGAATGGT GCGCAACGTTTTGATCTGCTAGCGGATCCGGTACC [SEQ ID NO: 9]

TABLE-US-00005 TABLE 3 Primers BG3186 ATAGCGCCATGGAACCTTTTAAATATATATGCCATTA [SEQ ID NO: 10] BG3213 ACAGTGGGATCCGCTTTGGGATTTGCAGGGATGACTCTGGT [SEQ ID NO: 11] BG3303 ATAGCGTCATGAATTTGCTTATTGATAACTGGATTCCTGTA CG [SEQ ID NO: 12] BG3212 ACAGTGGCGGCCGCGCCATTTGATGGCCCTCCTTGCGGTTT TAA [SEQ ID NO: 13] BG3076 CGTATATCAAACTTTCCAATAGCATGAAGAGCAATGAAAAA TAAC [SEQ ID NO: 14] BG3449 ATGATACCGCGAGACCCACGCTC [SEQ ID NO: 15] BG3451 CGGATAAAGTTGCAGGACCACTTC [SEQ ID NO: 16]

Protein Production and Purification

[0118] Cascade was expressed and purified as described (Jore et al., 2011). Throughout purification a buffer containing 20 mM HEPES pH 7.5, 75 mM NaCl, 1 mM DTT, 2 mM EDTA was used for resuspension and washing. Protein elution was performed in the same buffer containing 4 mM desthiobiotin. The Cascade-Cas3 fusion complex was expressed and purified in the same manner, with washing steps being performed with 20 mM HEPES pH 7.5, 200 mM NaCl and 1 mM DTT, and elution in 20 mM HEPES pH 7.5, 75 mM NaCl, 1 mM DTT containing 4 mM desthiobiotin.

Electrophoretic Mobility Shift Assay

[0119] Purified Cascade or Cascade subsomplexes were mixed with pUC-.lamda. in a buffer containing 20 mM HEPES pH 7.5, 75 mM NaCl, 1 mM DTT, 2 mM EDTA, and incubated at 37.degree. C. for 15 minutes. Samples were run overnight on a 0.8% TAE Agarose gel and post-stained with SybR safe (Invitrogen) 1:10000 dilution in TAE for 30 minutes. Cleavage with BsmI (Fermentas) or Nt.BspQI (New England Biolabs) was performed in the HEPES reaction buffer supplemented with 5 mM MgCl.sub.2.

Scanning Force Microscopy

[0120] Purified Cascade was mixed with pUC-.lamda. (at a ratio of 7:1, 250 nM Cascade, 35 nM DNA) in a buffer containing 20 mM HEPES pH 7.5, 75 mM NaCl, 0.2 mM DTT, 0.3 mM EDTA and incubated at 37.degree. C. for 15 minutes. Subsequently, for AFM sample preparation, the incubation mixture was diluted 10.times. in double distilled water and MgCl.sub.2 was added at a final concentration of 1.2 mM. Deposition of the protein-DNA complexes and imaging was carried out as described before (Dame et al., (2000) Nucleic Acids Res. 28: 3504-3510).

Fluorescence Microscopy

[0121] BL21-AI cells carrying CRISPR en cas gene encoding plasmids, were grown overnight at 37.degree. C. in Luria-Bertani broth (LB) containing ampicillin (100 .mu.g/ml), kanamycin (50 .mu.g/ml), streptomycin (50 .mu.g/ml) and chloramphenicol (34 .mu.g/ml). Overnight culture was diluted 1:100 in fresh antibiotic-containing LB, and grown for 1 hour at 37.degree. C. Expression of cas genes and CRISPR was induced for 1 hour by adding L-arabinose to a final concentration of 0.2% and IPTG to a final concentration of 1 mM. For infection, cells were mixed with phage Lambda at a Multiplicity of Infection (MOI) of 4. Cells were applied to poly-L-lysine covered microscope slides, and analyzed using a Zeiss LSM510 confocal laser scanning microscope based on an Axiovert inverted microscope, with a 40.times. oil immersion objective (N.A. of 1.3) and an argon laser as the excitation source (514 nm) and detection at 530-600 nm. The pinhole was set at 203 .mu.m for all measurements.

pUC-.lamda. Transformation Studies

[0122] LB containing kanamycin (50 .mu.g/ml), streptomycin (50 .mu.g/ml) and chloramphenicol (34 .mu.g/ml) was inoculated from an overnight pre-inoculum and grown to an OD.sub.600 of 0.3. Expression of cas genes and CRISPR was induced for 45 minutes with 0.2% L-arabinose and 1 mM IPTG. Cells were collected by centrifugation at 4.degree. C. and made competent by resuspension in ice cold buffer containing 100 mM RbCl.sub.2, 50 mM MnCl.sub.2, 30 mM potassium acetate, 10 mM CaCl.sub.2 and 15% glycerol, pH 5.8. After a 3 hour incubation, cells were collected and resuspended in a buffer containing 10 mM MOPS, 10 mM RbC1, 75 mM CaCl.sub.2, 15% glycerol, pH 6.8. Transformation was performed by adding 80 ng pUC-.lamda., followed by a 1 minute heat-shock at 42.degree. C., and 5 minute cold-shock on ice. Next cells were grown in LB for 45 minutes at 37.degree. C. before plating on LB-agar plates containing 0.2% L-arabinose, 1 mM IPTG, ampicillin (100 .mu.g/ml), kanamycin (50 .mu.g/ml), streptomycin (50 .mu.g/ml) and chloramphenicol (34 .mu.g/ml).

[0123] Plasmid curing was analyzed by transforming BL21-AI cells containing cas gene and CRISPR encoding plasmids with pUC-.lamda., while growing the cells in the presence of 0.2% glucose to suppress expression of the T7-polymerase gene. Expression of cas genes and CRISPR was induced by collecting the cells and re-suspension in LB containing 0.2% arabinose and 1 mM IPTG. Cells were plated on LB-agar containing either streptomycin, kanamycin and chloramphenicol (non-selective for pUC-.lamda.) or ampicillin, streptomycin, kanamycin and chloramphenicol (selective for pUC-.lamda.). After overnight growth the percentage of plasmid loss can be calculated from the ratio of colony forming units on the selective and non-selective plates.

Phage Lambda Infection Studies

[0124] Host sensitivity to phage infection was tested using a virulent phage Lambda (.lamda..sub.vir), as in (Brouns et al (2008) Science 321, 960-964). The sensitivity of the host to infection was calculated as the efficiency of plaquing (the plaque count ratio of a strain containing an anti-.lamda. CRISPR to that of the strain containing a non-targeting R44CRISPR) as described in Brouns et al (2008).

Example 1

Cascade Exclusively Binds Negatively Supercoiled Target DNA

[0125] The 3 kb pUC19-derived plasmid denoted pUC-.lamda., contains a 350 bp DNA fragment corresponding to part of the J gene of phage .lamda., which is targeted by J3-Cascade (Cascade associated with crRNA containing spacer J3 (Westra et al (2010) Molecular Microbiology 77, 1380-1393). The electrophoretic mobility shift assays show that Cascade has high affinity only for negatively supercoiled (nSC) target plasmid. At a molar ratio of J3-Cascade to pUC-.lamda. of 6:1 all nSC plasmid was bound by Cascade, (see FIG. 1A), while Cascade carrying the non-targeting crRNA R44 (R44-Cascade) displayed non-specific binding at a molar ratio of 128:1 (see FIG. 1B). The dissociation constant (Kd) of nSC pUC-.lamda. was determined to be 13.+-.1.4 nM for J3-Cascade (see FIG. 1E) and 429.+-.152 nM for R44-Cascade (see FIG. 1F). J3-Cascade was unable to bind relaxed target DNA with measurable affinity, such as nicked (see FIG. 1C) or linear pUC-.lamda. (see FIG. 1D), showing that Cascade has high affinity for larger DNA substrates with a nSC topology.

[0126] To distinguish non-specific binding from specific binding, the BsmI restriction site located within the protospacer was used. While adding BsmI enzyme to pUC-.lamda. gives a linear product in the presence of R44-Cascade (see FIG. 1G, lane 4), pUC-.lamda. is protected from BsmI cleavage in the presence of J3-Cascade (see FIG. 1G, lane 7), indicating specific binding to the protospacer. This shows that Cas3 is not required for in vitro sequence specific binding of Cascade to a protospacer sequence in a nSC plasmid.

[0127] Cascade binding to nSC pUC-.lamda. was followed by nicking with Nt.BspQI, giving rise to an OC topology. Cascade is released from the plasmid after strand nicking, as can be seen from the absence of a mobility shift (see FIG. 1H, compare lane 8 to lane 10). In contrast, Cascade remains bound to its DNA target when a ssDNA probe complementary to the displaced strand is added to the reaction before DNA cleavage by Nt.BspQI (see FIG. 1H, lane 9). The probe artificially stabilizes the Cascade R-loop on relaxed target DNA. Similar observations are made when both DNA strands of pUC-.lamda. are cleaved after Cascade binding (see FIG. 1I, lane 8 and lane 9).

Example 2

Cascade Induces Bending of Bound Target DNA

[0128] Complexes formed between purified Cascade and pUC-.lamda. were visualized. Specific complexes containing a single bound J3-Cascade complex were formed, while unspecific R44-Cascade yields no DNA bound complexes in this assay under identical conditions. Out of 81 DNA molecules observed 76% were found to have J3-Cascade bound (see FIG. 2A-P). Of these complexes in most cases Cascade was found at the apex of a loop (86%), whereas a small fraction only was found at non-apical positions (14%). These data show that Cascade binding causes bending and possibly wrapping of the DNA, probably to facilitate local melting of the DNA duplex.

Example 3

Naturally Occurring Fusions of Cas3 and Cse1: Cas3 Interacts with Cascade Upon Protospacer Recognition

[0129] Figure S3 shows sequence analysis of cas3 genes from organisms containing the Type I-E CRISPR/Cas system reveals that Cas3 and Cse1 occur as fusion proteins in Streptomyces sp. SPB78 (Accession Number: ZP.sub.--07272643.1), in Streptomyces griseus (Accession Number YP.sub.--001825054), and in Catenulispora acidiphila DSM 44928 (Accession Number YP.sub.--003114638).

Example 4

Bimolecular Fluorescence Complementation (BiFC) Shows how a Cse1 Fusion Protein Forming Part of Cascade Continues to Interact with Cas3

[0130] BiFC experiments were used to monitor interactions between Cas3 and Cascade in vivo before and after phage .lamda. infection. BiFC experiments rely on the capacity of the non-fluorescent halves of a fluorescent protein, e.g., Yellow Fluorescent Protein (YFP) to refold and to form a fluorescent molecule when the two halves occur in close proximity. As such, it provides a tool to reveal protein-protein interactions, since the efficiency of refolding is greatly enhanced if the local concentrations are high, e.g., when the two halves of the fluorescent protein are fused to interaction partners. Cse1 was fused at the C-terminus with the N-terminal 155 amino acids of Venus (Cse1-N155Venus), an improved version of YFP (Nagai et al (2002) Nature Biotechnology 20, 87-90). Cas3 was C-terminally fused to the C-terminal 85 amino acids of Venus (Cas3-C85Venus).

[0131] BiFC analysis reveals that Cascade does not interact with Cas3 in the absence of invading DNA (FIG. 3ABC, FIG. 3P and FIG. 8). Upon infection with phage .lamda., however, cells expressing Cascade.DELTA.Cse1, Cse1-N155Venus and Cas3-C85Venus are fluorescent if they co-express the anti-.lamda. CRISPR 7Tm (FIG. 3DEF, FIG. 3P and FIG. 8). When they co-express a non-targeting CRISPR R44 (FIG. 3GHI, FIG. 3P and FIG. 8), the cells remain non-fluorescent. This shows that Cascade and Cas3 specifically interact during infection upon protospacer recognition and that Cse1 and Cas3 are in close proximity of each other in the Cascade-Cas3 binary effector complex.

[0132] These results also show quite clearly that a fusion of Cse1 with an heterologous protein does not disrupt the ribonucleoprotein formation of Cascade and crRNA, nor does it disrupt the interaction of Cascade and Cas3 with the target phage DNA, even when the Cas3 itself is also a fusion protein.

Example 5

Preparing a Designed Cas3-Cse1 Fusion Gives a Protein with In Vivo Functional Activity

[0133] Providing in vitro evidence for Cas3 DNA cleavage activity required purified and active Cas3. Despite various solubilization strategies, Cas3 overproduced (Howard et al (2011) Biochem. J. 439, 85-95) in E. coli BL21 is mainly present in inactive aggregates and inclusion bodies. Cas3 was therefore produced as a Cas3-Cse1 fusion protein, containing a linker identical to that of the Cas3-Cse1 fusion protein in S. griseus (see FIG. 10). When co-expressed with Cascade.DELTA.Cse1 and CRISPR J3, the fusion-complex was soluble and was obtained in high purity with the same apparent stoichiometry as Cascade (FIG. 5A). When functionality of this complex was tested for providing resistance against phage .lamda. infection, the efficiency of plaquing (eop) on cells expressing the fusion-complex J3-Cascade-Cas3 was identical as on cells expressing the separate proteins (FIG. 5B).

[0134] Since the J3-Cascade-Cas3 fusion-complex was functional in vivo, in vitro DNA cleavage assays were carried out using this complex. When J3-Cascade-Cas3 was incubated with pUC-.lamda. in the absence of divalent metals, plasmid binding was observed at molar ratios similar to those observed for Cascade (FIG. 5C), while a-specific binding to a non-target plasmid (pUC-p7, a pUC19 derived plasmid of the same size as pUC-.lamda., but lacking a protospacer) occurred only at high molar ratios (FIG. 5D), indicating that a-specific DNA binding of the complex is also similar to that of Cascade alone.

[0135] Interestingly, the J3-Cascade-Cas3 fusion complex displays magnesium dependent endonuclease activity on nSC target plasmids. In the presence of 10 mM Mg.sup.2+J3-Cascade-Cas3 nicks nSC pUC-.lamda. (FIG. 5E, lane 3-7), but no cleavage is observed for substrates that do not contain the target sequence (FIG. 5E, lane 9-13), or that have a relaxed topology. No shift of the resulting OC band is observed, in line with previous observations that Cascade dissociates spontaneously after cleavage, without requiring ATP-dependent Cas3 helicase activity. Instead, the helicase activity of Cas3 appears to be involved in exonucleolytic plasmid degradation. When both magnesium and ATP are added to the reaction, full plasmid degradation occurred (FIG. 5H).

[0136] The inventors have found that Cascade alone is unable to bind protospacers on relaxed DNA. In contrast, the inventors have found that Cascade efficiently locates targets in negatively supercoiled DNA, and subsequently recruits Cas3 via the Cse1 subunit. Endonucleolytic cleavage by the Cas3 HD-nuclease domain causes spontaneous release of Cascade from the DNA through the loss of supercoiling, remobilizing Cascade to locate new targets. The target is then progressively unwound and cleaved by the joint ATP-dependent helicase activity and HD-nuclease activity of Cas3, leading to complete target DNA degradation and neutralization of the invader.

[0137] Referring to FIG. 6 and without wishing to be bound to any particular theory, a mechanism of operation for the CRISPR-interference type I pathway in E. coli may involve (1) First, Cascade carrying a crRNA scans the nSC plasmid DNA for a protospacer, with adjacent PAM. Whether during this stage strand separation occurs is unknown. (2) Sequence specific protospacer binding is achieved through basepairing between the crRNA and the complementary strand of the DNA, forming an R-loop. Upon binding, Cascade induces bending of the DNA. (3) The Cse1 subunit of Cascade recruits Cas3 upon DNA binding. This may be achieved by Cascade conformational changes that take place upon nucleic acid binding. (4) The HD-domain (darker part) of Cas3 catalyzes Mg.sup.2+-dependent nicking of the displaced strand of the R-loop, thereby altering the topology of the target plasmid from nSC to relaxed OC. (5a and 5b) The plasmid relaxation causes spontaneous dissociation of Cascade. Meanwhile Cas3 displays ATP-dependent exonuclease activity on the target plasmid, requiring the helicase domain for target dsDNA unwinding and the HD-nuclease domain for successive cleavage activity. (6) Cas3 degrades the entire plasmid in an ATP-dependent manner as it processively moves along, unwinds and cleaves the target dsDNA.

Example 6

Preparation of Artificial Cas-Strep Tag Fusion Proteins and Assembly of Cascade Complexes

[0138] Cascade complexes are produced and purified as described in Brouns et al (2008) Science 321: 960-4 (2008), using the expression plasmids listed in Supplementary Table 3 of Jore et al (2011) Nature Structural & Molecular Biology 18: 529-537. Cascade is routinely purified with an N-terminal Strep-tag II fused to CasB (or CasC in CasCDE). Size exclusion chromatography (Superdex 200 HR 10/30 (GE)) is performed using 20 mM Tris-HCl (pH 8.0), 0.1 M NaCl, 1 mM dithiotreitol. Cascade preparations (.about.0.3 mg) are incubated with DNase I (Invitrogen) in the presence of 2.5 mM MgCl.sub.2 for 15 min at 37.degree. C. prior to size exclusion analysis. Co-purified nucleic acids are isolated by extraction using an equal volume of phenol:chloroform:isoamylalcohol (25:24:1) pH 8.0 (Fluka), and incubated with either DNase I (Invitrogen) supplemented with 2.5 mM MgCl.sub.2 or RNase A (Fermentas) for 10 min at 37.degree. C. Cas subunit proteins fused to the amino acid sequence of Strep-Tag are produced.

[0139] Plaque assays showing the biological activity of the Strep-Tag Cascade subunits are performed using bacteriophage Lambda and the efficiency of plaquing (EOP) was calculated as described in Brouns et al (2008).

[0140] For purification of crRNA, samples are analyzed by ion-pair reversed-phased-HPLC on an Agilent 1100 HPLC with UV.sub.260nm detector (Agilent) using a DNAsep column 50 mm.times.4.6 mm I. D. (Transgenomic, San Jose, Calif.). The chromatographic analysis is performed using the following buffer conditions: A) 0.1 M triethylammonium acetate (TEAA) (pH 7.0) (Fluka); B) buffer A with 25% LC MS grade acetonitrile (v/v) (Fisher). crRNA is obtained by injecting purified intact Cascade at 75.degree. C. using a linear gradient starting at 15% buffer B and extending to 60% B in 12.5 min, followed by a linear extension to 100% B over 2 min at a flow rate of 1.0 ml/min. Hydrolysis of the cyclic phosphate terminus was performed by incubating the HPLC-purified crRNA in a final concentration of 0.1 M HCl at 4.degree. C. for 1 hour. The samples are concentrated to 5-10 .mu.l on a vacuum concentrator (Eppendorf) prior to ESI-MS analysis.

[0141] Electrospray Ionization Mass spectrometry analysis of crRNA is performed in negative mode using an UHR-TOF mass spectrometer (maX is) or an HCT Ultra PTM Discovery instrument (both Bruker Daltonics), coupled to an online capillary liquid chromatography system (Ultimate 3000, Dionex, UK). RNA separations are performed using a monolithic (PS-DVB) capillary column (200 .mu.m.times.50 mm I.D., Dionex, UK). The chromatography is performed using the following buffer conditions: C) 0.4 M 1,1,1,3,3,3,-Hexafluoro-2-propanol (HFIP, Sigma-Aldrich) adjusted with triethylamine (TEA) to pH 7.0 and 0.1 mM TEAA, and D) buffer C with 50% methanol (v/v) (Fisher). RNA analysis is performed at 50.degree. C. with 20% buffer D, extending to 40% D in 5 min followed by a linear extension to 60% D over 8 min at a flow rate of 2 .mu.l/min.

[0142] Cascade protein is analyzed by native mass spectrometry in 0.15 M ammonium acetate (pH 8.0) at a protein concentration of 5 .mu.M. The protein preparation is obtained by five sequential concentration and dilution steps at 4.degree. C. using a centrifugal filter with a cut-off of 10 kDa (Millipore). Proteins are sprayed from borosilicate glass capillaries and analyzed on a LCT electrospray time-of-flight or modified quadrupole time-of-flight instruments (both Waters, UK) adjusted for optimal performance in high mass detection (see Tahallah N et al (2001) Rapid Commun Mass Spectrom 15: 596-601 (2001) and van den Heuvel, R. H. et al. Anal Chem 78: 7473-83 (2006). Exact mass measurements of the individual Cas proteins were acquired under denaturing conditions (50% acetonitrile, 50% MQ, 0.1% formic acid). Sub-complexes in solution were generated by the addition of 2-propanol to the spray solution to a final concentration of 5% (v/v). Instrument settings were as follows; needle voltage .about.1.2 kV, cone voltage .about.175 V, source pressure 9 mbar. Xenon was used as the collision gas for tandem mass spectrometric analysis at a pressure of 1.5 10.sup.-2 mbar. The collision voltage varied between 10-200 V.

[0143] Electrophoretic mobility shift assays (EMSA) are used to demonstrate the functional activity of Cascade complexes for target nucleic acids. EMSA is performed by incubating Cascade, CasBCDE or CasCDE with 1 nM labelled nucleic acid in 50 mM Tris-Cl pH 7.5, 100 mM NaCl. Salmon sperm DNA (Invitrogen) is used as competitor. EMSA reactions are incubated at 37.degree. C. for 20-30 min prior to electrophoresis on 5% polyacrylamide gels. The gels are dried and analyzed using phosphor storage screens and a PMI phosphor imager (Bio-Rad). Target DNA binding and cleavage activity of Cascade is tested in the presence of 1-10 mM Ca, Mg or Mn-ions.

[0144] DNA targets are gel-purified long oligonucleotides (Isogen Life Sciences or Biolegio), listed in Supplementary Table 3 of Jore et al (2011). The oligonucleotides are end-labeled using .gamma..sup.32P-ATP (PerkinElmer) and T4 kinase (Fermentas). Double-stranded DNA targets are prepared by annealing complementary oligonucleotides and digesting remaining ssDNA with Exonuclease I (Fermentas). Labelled RNA targets are in vitro transcribed using T7 Maxiscript or T7 Mega Shortscript kits (Ambion) with .alpha..sup.32P-CTP (PerkinElmer) and removing template by DNase I (Fermentas) digestion. Double stranded RNA targets are prepared by annealing complementary RNAs and digesting surplus ssRNA with RNase T1 (Fermentas), followed by phenol extraction.

[0145] Plasmid mobility shift assays are performed using plasmid pWUR613 containing the R44 protospacer. The fragment containing the protospacer is PCR-amplified from bacteriophage P7 genomic DNA using primers BG3297 and BG 3298 (see Supplementary Table 3 of Jore et al (2011). Plasmid (0.4 .mu.g) and Cascade were mixed in a 1:10 molar ratio in a buffer containing 5 mM Tris-HCl (pH 7.5) and 20 mM NaCl and incubated at 37.degree. C. for 30 minutes. Cascade proteins were then removed by proteinase K treatment (Fluka) (0.15 U, 15 min, 37.degree. C.) followed by phenol/chloroform extraction. RNA-DNA complexes were then treated with RNaseH (Promega) (2 U, 1 h, 37.degree. C.).

[0146] Strep-Tag-Cas protein subunit fusions which form Cascade protein complexes or active sub-complexes with the RNA component (equivalent to a crRNA), have the expected biological and functional activity of scanning and specific attachment and cleavage of nucleic acid targets. Fusions of the Cas subunits with the amino acid chains of fluorescent dyes also form Cascade complexes and sub-complexes with the RNA component (equivalent to crRNA) which retains biological and functional activity and allows visualisation of the location of a target nucleic acid sequence in ds DNA for example.

Example 7

A Cascade-Nuclease Pair and Test of Nuclease Activity In Vitro

[0147] Six mutations designated "Sharkey" have been introduced by random mutagenesis and screening to improve nuclease activity and stability of the non-specific nuclease domain from Flavobacterium okeanokoites restriction enzyme Fold (see Guo, J., et al. (2010) J. Mol. Biol. 400: 96-107). Other mutations have been introduced that reduce off-target cleavage activity. This is achieved by engineering electrostatic interactions at the FokI dimer interface of a ZFN pair, creating one FokI variant with a positively charged interface (KKR, E490K, 1538K, H537R) and another with a negatively charged interface (ELD, Q486E, 1499L, N496D) (see Doyon, Y., et al. (2011) Nature Methods 8: 74-9). Each of these variants is catalytically inactive as a homodimer, thereby reducing the frequency of off-target cleavage.

Cascade-Nuclease Design

[0148] We translationally fused improved FokI nucleases to the N-terminus of Cse1 to generate variants of Cse1 being FokI.sup.KKR-Cse1 and FokI.sup.ELD-Cse1, respectively. These two variants are co-expressed with Cascade subunits (Cse2, Cas7, Cas5 and Cas6e), and one of two distinct CRISPR plasmids with uniform spacers. This loads the Cascade.sup.KKR complex with uniform P7-crRNA, and the Cascade.sup.ELD complex with uniform M13g8-crRNA. These complexes are purified using the N-terminally Strepll-tagged Cse2 as described in Jore, M. M., et al., (2011) Nat. Struct. Mol. Biol. 18(5): 529-536. Furthermore an additional purification step can be carried out using an N-terminally HIS-tagged FokI, to ensure purifying full length and intact Cascade-nuclease fusion complexes.

[0149] The nucleotide and amino acid sequences of the fusion proteins used in this example were as follows:

TABLE-US-00006 >nucleotide sequence of FokI-(Sharkey-ELD)-Cse1 [SEQ ID NO: 18] ATGGCTCAACTGGTTAAAAGCGAACTGGAAGAGAAAAAAAGTGAACTGCG CCACAAACTGAAATATGTGCCGCATGAATATATCGAGCTGATTGAAATTG CACGTAATCCGACCCAGGATCGTATTCTGGAAATGAAAGTGATGGAATTT TTTATGAAAGTGTACGGCTATCGCGGTGAACATCTGGGTGGTAGCCGTAA ACCGGATGGTGCAATTTATACCGTTGGTAGCCCGATTGATTATGGTGTTA TTGTTGATACCAAAGCCTATAGCGGTGGTTATAATCTGCCGATTGGTCAG GCAGATGAAATGGAACGTTATGTGGAAGAAAATCAGACCCGTGATAAACA TCTGAATCCGAATGAATGGTGGAAAGTTTATCCGAGCAGCGTTACCGAGT TTAAATTCCTGTTTGTTAGCGGTCACTTCAAAGGCAACTATAAAGCACAG CTGACCCGTCTGAATCATATTACCAATTGTAATGGTGCAGTTCTGAGCGT TGAAGAACTGCTGATTGGTGGTGAAATGATTAAAGCAGGCACCCTGACCC TGGAAGAAGTTCGTCGCAAATTTAACAATGGCGAAATCAACTTTGCGGAT CCCACCAACCGCGCGAAAGGCCTGGAAGCGGTGAGCGTGGCGAGCatgaa tttgcttattgataactggattcctgtacgcccgcgaaacggggggaaag tccaaatcataaatctgcaatcgctatactgcagtagagatcagtggcga ttaagtttgccccgtgacgatatggaactggccgctttagcactgctggt ttgcattgggcaaattatcgccccggcaaaagatgacgttgaatttcgac atcgcataatgaatccgctcactgaagatgagtttcaacaactcatcgcg ccgtggatagatatgttctaccttaatcacgcagaacatccctttatgca gaccaaaggtgtcaaagcaaatgatgtgactccaatggaaaaactgttgg ctggggtaagcggcgcgacgaattgtgcatttgtcaatcaaccggggcag ggtgaagcattatgtggtggatgcactgcgattgcgttattcaaccaggc gaatcaggcaccaggttttggtggtggttttaaaagcggtttacgtggag gaacacctgtaacaacgttcgtacgtgggatcgatcttcgttcaacggtg ttactcaatgtcctcacattacctcgtcttcaaaaacaatttcctaatga atcacatacggaaaaccaacctacctggattaaacctatcaagtccaatg agtctatacctgcttcgtcaattgggtttgtccgtggtctattctggcaa ccagcgcatattgaattatgcgatcccattgggattggtaaatgttcttg ctgtggacaggaaagcaatttgcgttataccggttttcttaaggaaaaat ttacctttacagttaatgggctatggccccatccgcattccccttgtctg gtaacagtcaagaaaggggaggttgaggaaaaatttcttgctttcaccac ctccgcaccatcatggacacaaatcagccgagttgtggtagataagatta ttcaaaatgaaaatggaaatcgcgtggcggcggttgtgaatcaattcaga aatattgcgccgcaaagtcctcttgaattgattatggggggatatcgtaa taatcaagcatctattcttgaacggcgtcatgatgtgttgatgtttaatc aggggtggcaacaatacggcaatgtgataaacgaaatagtgactgttggt ttgggatataaaacagccttacgcaaggcgttatatacctttgcagaagg gtttaaaaataaagacttcaaaggggccggagtctctgttcatgagactg cagaaaggcatttctatcgacagagtgaattattaattcccgatgtactg gcgaatgttaatttttcccaggctgatgaggtaatagctgatttacgaga caaacttcatcaattgtgtgaaatgctatttaatcaatctgtagctccct atgcacatcatcctaaattaataagcacattagcgcttgcccgcgccacg ctatacaaacatttacgggagttaaaaccgcaaggagggccatcaaatgg ctga >protein sequence of FokI-(Sharkey-ELD)-Cse1 [SEQ ID NO: 19] MAQLVKSELEEKKSELRHKLKYVPHEYIELIEIARNPTQDRILEMKVMEF FMKVYGYRGEHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQ ADEMERYVEENQTRDKHLNPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQ LTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINFAD PTNRAKGLEAVSVASMNLLIDNWIPVRPRNGGKVQIINLQSLYCSRDQWR LSLPRDDMELAALALLVCIGQIIAPAKDDVEFRHRIMNPLTEDEFQQLIA PWIDMFYLNHAEHPFMQTKGVKANDVTPMEKLLAGVSGATNCAFVNQPGQ GEALCGGCTAIALFNQANQAPGFGGGFKSGLRGGTPVTTFVRGIDLRSTV LLNVLTLPRLQKQFPNESHTENQPTWIKPIKSNESIPASSIGFVRGLFWQ PAHIELCDPIGIGKCSCCGQESNLRYTGFLKEKFTFTVNGLWPHPHSPCL VTVKKGEVEEKFLAFTTSAPSWTQISRVVVDKIIQNENGNRVAAVVNQFR NIAPQSPLELIMGGYRNNQASILERRHDVLMFNQGWQQYGNVINEIVTVG LGYKTALRKALYTFAEGFKNKDFKGAGVSVHETAERHFYRQSELLIPDVL ANVNFSQADEVIADLRDKLHQLCEMLFNQSVAPYAHHPKLISTLALARAT LYKHLRELKPQGGPSNG* >nucleotide sequence of FokI-(Sharkey-KKR)-Cse1 [SEQ ID NO: 20] ATGGCTCAACTGGTTAAAAGCGAACTGGAAGAGAAAAAAAGTGAACTGCG CCACAAACTGAAATATGTGCCGCATGAATATATCGAGCTGATTGAAATTG CACGTAATCCGACCCAGGATCGTATTCTGGAAATGAAAGTGATGGAATTT TTTATGAAAGTGTACGGCTATCGCGGTGAACATCTGGGTGGTAGCCGTAA ACCGGATGGTGCAATTTATACCGTTGGTAGCCCGATTGATTATGGTGTTA TTGTTGATACCAAAGCCTATAGCGGTGGTTATAATCTGCCGATTGGTCAG GCAGATGAAATGCAGCGTTATGTGAAAGAAAATCAGACCCGCAACAAACA TATTAACCCGAATGAATGGTGGAAAGTTTATCCGAGCAGCGTTACCGAGT TTAAATTCCTGTTTGTTAGCGGTCACTTCAAAGGCAACTATAAAGCACAG CTGACCCGTCTGAATCGTAAAACCAATTGTAATGGTGCAGTTCTGAGCGT TGAAGAACTGCTGATTGGTGGTGAAATGATTAAAGCAGGCACCCTGACCC TGGAAGAAGTTCGTCGCAAATTTAACAATGGCGAAATCAACTTTGCGGAT CCCACCAACCGCGCGAAAGGCCTGGAAGCGGTGAGCGTGGCGAGCatgaa tttgcttattgataactggattcctgtacgcccgcgaaacggggggaaag tccaaatcataaatctgcaatcgctatactgcagtagagatcagtggcga ttaagtttgccccgtgacgatatggaactggccgctttagcactgctggt ttgcattgggcaaattatcgccccggcaaaagatgacgttgaatttcgac atcgcataatgaatccgctcactgaagatgagtttcaacaactcatcgcg ccgtggatagatatgttctaccttaatcacgcagaacatccctttatgca gaccaaaggtgtcaaagcaaatgatgtgactccaatggaaaaactgttgg ctggggtaagcggcgcgacgaattgtgcatttgtcaatcaaccggggcag ggtgaagcattatgtggtggatgcactgcgattgcgttattcaaccaggc gaatcaggcaccaggttttggtggtggttttaaaagcggtttacgtggag gaacacctgtaacaacgttcgtacgtgggatcgatcttcgttcaacggtg ttactcaatgtcctcacattacctcgtcttcaaaaacaatttcctaatga atcacatacggaaaaccaacctacctggattaaacctatcaagtccaatg agtctatacctgcttcgtcaattgggtttgtccgtggtctattctggcaa ccagcgcatattgaattatgcgatcccattgggattggtaaatgttcttg ctgtggacaggaaagcaatttgcgttataccggttttcttaaggaaaaat ttacctttacagttaatgggctatggccccatccgcattccccttgtctg gtaacagtcaagaaaggggaggttgaggaaaaatttcttgctttcaccac ctccgcaccatcatggacacaaatcagccgagttgtggtagataagatta ttcaaaatgaaaatggaaatcgcgtggcggcggttgtgaatcaattcaga aatattgcgccgcaaagtcctcttgaattgattatggggggatatcgtaa taatcaagcatctattcttgaacggcgtcatgatgtgttgatgtttaatc aggggtggcaacaatacggcaatgtgataaacgaaatagtgactgttggt ttgggatataaaacagccttacgcaaggcgttatatacctttgcagaagg gtttaaaaataaagacttcaaaggggccggagtctctgttcatgagactg cagaaaggcatttctatcgacagagtgaattattaattcccgatgtactg gcgaatgttaatttttcccaggctgatgaggtaatagctgatttacgaga caaacttcatcaattgtgtgaaatgctatttaatcaatctgtagctccct atgcacatcatcctaaattaataagcacattagcgcttgcccgcgccacg ctatacaaacatttacgggagttaaaaccgcaaggagggccatcaaatgg ctga >protein sequence of FokI-(Sharkey-KKR)-Cse1 [SEQ ID NO: 21] MAQLVKSELEEKKSELRHKLKYVPHEYIELIEIARNPTQDRILEMKVMEF FMKVYGYRGEHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQ ADEMQRYVKENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQ LTRLNRKTNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINFAD PTNRAKGLEAVSVASMNLLIDNWIPVRPRNGGKVQIINLQSLYCSRDQWR LSLPRDDMELAALALLVCIGQIIAPAKDDVEFRHRIMNPLTEDEFQQLIA PWIDMFYLNHAEHPFMQTKGVKANDVTPMEKLLAGVSGATNCAFVNQPGQ GEALCGGCTAIALFNQANQAPGFGGGFKSGLRGGTPVTTFVRGIDLRSTV LLNVLTLPRLQKQFPNESHTENQPTWIKPIKSNESIPASSIGFVRGLFWQ PAHIELCDPIGIGKCSCCGQESNLRYTGFLKEKFTFTVNGLWPHPHSPCL VTVKKGEVEEKFLAFTTSAPSWTQISRVVVDKIIQNENGNRVAAVVNQFR NIAPQSPLELIMGGYRNNQASILERRHDVLMFNQGWQQYGNVINEIVTVG LGYKTALRKALYTFAEGFKNKDFKGAGVSVHETAERHFYRQSELLIPDVL ANVNFSQADEVIADLRDKLHQLCEMLFNQSVAPYAHHPKLISTLALARAT LYKHLRELKPQGGPSNG* >nucleotide sequence of His.sub.6-Dual-monopartite NLS SV40-FokI-(Sharkey-KKR)-Cse1 [SEQ ID NO: 22] ATGcatcaccatcatcaccacCCGAAAAAAAAGCGCAAAGTGGATCCGAA GAAAAAACGTAAAGTTGAAGATCCGAAAGACATGGCTCAACTGGTTAAAA

GCGAACTGGAAGAGAAAAAAAGTGAACTGCGCCACAAACTGAAATATGTG CCGCATGAATATATCGAGCTGATTGAAATTGCACGTAATCCGACCCAGGA TCGTATTCTGGAAATGAAAGTGATGGAATTTTTTATGAAAGTGTACGGCT ATCGCGGTGAACATCTGGGTGGTAGCCGTAAACCGGATGGTGCAATTTAT ACCGTTGGTAGCCCGATTGATTATGGTGTTATTGTTGATACCAAAGCCTA TAGCGGTGGTTATAATCTGCCGATTGGTCAGGCAGATGAAATGCAGCGTT ATGTGAAAGAAAATCAGACCCGCAACAAACATATTAACCCGAATGAATGG TGGAAAGTTTATCCGAGCAGCGTTACCGAGTTTAAATTCCTGTTTGTTAG CGGTCACTTCAAAGGCAACTATAAAGCACAGCTGACCCGTCTGAATCGTA AAACCAATTGTAATGGTGCAGTTCTGAGCGTTGAAGAACTGCTGATTGGT GGTGAAATGATTAAAGCAGGCACCCTGACCCTGGAAGAAGTTCGTCGCAA ATTTAACAATGGCGAAATCAACTTTGCGGATCCCACCAACCGCGCGAAAG GCCTGGAAGCGGTGAGCGTGGCGAGCatgaatttgcttattgataactgg attcctgtacgcccgcgaaacggggggaaagtccaaatcataaatctgca atcgctatactgcagtagagatcagtggcgattaagtttgccccgtgacg atatggaactggccgctttagcactgctggtttgcattgggcaaattatc gccccggcaaaagatgacgttgaatttcgacatcgcataatgaatccgct cactgaagatgagtttcaacaactcatcgcgccgtggatagatatgttct accttaatcacgcagaacatccctttatgcagaccaaaggtgtcaaagca aatgatgtgactccaatggaaaaactgttggctggggtaagcggcgcgac gaattgtgcatttgtcaatcaaccggggcagggtgaagcattatgtggtg gatgcactgcgattgcgttattcaaccaggcgaatcaggcaccaggtttt ggtggtggttttaaaagcggtttacgtggaggaacacctgtaacaacgtt cgtacgtgggatcgatcttcgttcaacggtgttactcaatgtcctcacat tacctcgtcttcaaaaacaatttcctaatgaatcacatacggaaaaccaa cctacctggattaaacctatcaagtccaatgagtctatacctgcttcgtc aattgggtttgtccgtggtctattctggcaaccagcgcatattgaattat gcgatcccattgggattggtaaatgttcttgctgtggacaggaaagcaat ttgcgttataccggttttcttaaggaaaaatttacctttacagttaatgg gctatggccccatccgcattccccttgtctggtaacagtcaagaaagggg aggttgaggaaaaatttcttgctttcaccacctccgcaccatcatggaca caaatcagccgagttgtggtagataagattattcaaaatgaaaatggaaa tcgcgtggcggcggttgtgaatcaattcagaaatattgcgccgcaaagtc ctcttgaattgattatggggggatatcgtaataatcaagcatctattctt gaacggcgtcatgatgtgttgatgtttaatcaggggtggcaacaatacgg caatgtgataaacgaaatagtgactgttggtttgggatataaaacagcct tacgcaaggcgttatatacctttgcagaagggtttaaaaataaagacttc aaaggggccggagtctctgttcatgagactgcagaaaggcatttctatcg acagagtgaattattaattcccgatgtactggcgaatgttaatttttccc aggctgatgaggtaatagctgatttacgagacaaacttcatcaattgtgt gaaatgctatttaatcaatctgtagctccctatgcacatcatcctaaatt aataagcacattagcgcttgcccgcgccacgctatacaaacatttacggg agttaaaaccgcaaggagggccatcaaatggctga >protein sequence of His.sub.6-Dual-monopartite NLS SV40-FokI-(Sharkey-KKR)-Cse1 [SEQ ID NO: 23] MHHHHHHPKKKRKVDPKKKRKVEDPKDMAQLVKSELEEKKSELRHKLKYV PHEYIELIEIARNPTQDRILEMKVMEFFMKVYGYRGEHLGGSRKPDGAIY TVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVKENQTRNKHINPNEW WKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNRKTNCNGAVLSVEELLIG GEMIKAGTLTLEEVRRKFNNGEINFADPTNRAKGLEAVSVASMNLLIDNW IPVRPRNGGKVQIINLQSLYCSRDQWRLSLPRDDMELAALALLVCIGQII APAKDDVEFRHRIMNPLTEDEFQQLIAPWIDMFYLNHAEHPFMQTKGVKA NDVTPMEKLLAGVSGATNCAFVNQPGQGEALCGGCTAIALFNQANQAPGF GGGFKSGLRGGTPVTTFVRGIDLRSTVLLNVLTLPRLQKQFPNESHTENQ PTWIKPIKSNESIPASSIGFVRGLFWQPAHIELCDPIGIGKCSCCGQESN LRYTGFLKEKFTFTVNGLWPHPHSPCLVTVKKGEVEEKFLAFTTSAPSWT QISRVVVDKIIQNENGNRVAAVVNQFRNIAPQSPLELIMGGYRNNQASIL ERRHDVLMFNQGWQQYGNVINEIVTVGLGYKTALRKALYTFAEGFKNKDF KGAGVSVHETAERHFYRQSELLIPDVLANVNFSQADEVIADLRDKLHQLC EMLFNQSVAPYAHHPKLISTLALARATLYKHLRELKPQGGPSNG* >nucleotide sequence of His.sub.6-Dual-monopartite NLS SV40-FokI (Sharkey-ELD)-Cse1 [SEQ ID NO: 24] ATGcatcaccatcatcaccacCCGAAAAAAAAGCGCAAAGTGGATCCGAA GAAAAAACGTAAAGTTGAAGATCCGAAAGACATGGCTCAACTGGTTAAAA GCGAACTGGAAGAGAAAAAAAGTGAACTGCGCCACAAACTGAAATATGTG CCGCATGAATATATCGAGCTGATTGAAATTGCACGTAATCCGACCCAGGA TCGTATTCTGGAAATGAAAGTGATGGAATTTTTTATGAAAGTGTACGGCT ATCGCGGTGAACATCTGGGTGGTAGCCGTAAACCGGATGGTGCAATTTAT ACCGTTGGTAGCCCGATTGATTATGGTGTTATTGTTGATACCAAAGCCTA TAGCGGTGGTTATAATCTGCCGATTGGTCAGGCAGATGAAATGGAACGTT ATGTGGAAGAAAATCAGACCCGTGATAAACATCTGAATCCGAATGAATGG TGGAAAGTTTATCCGAGCAGCGTTACCGAGTTTAAATTCCTGTTTGTTAG CGGTCACTTCAAAGGCAACTATAAAGCACAGCTGACCCGTCTGAATCATA TTACCAATTGTAATGGTGCAGTTCTGAGCGTTGAAGAACTGCTGATTGGT GGTGAAATGATTAAAGCAGGCACCCTGACCCTGGAAGAAGTTCGTCGCAA ATTTAACAATGGCGAAATCAACTTTGCGGATCCCACCAACCGCGCGAAAG GCCTGGAAGCGGTGAGCGTGGCGAGCatgaatttgcttattgataactgg attcctgtacgcccgcgaaacggggggaaagtccaaatcataaatctgca atcgctatactgcagtagagatcagtggcgattaagtttgccccgtgacg atatggaactggccgctttagcactgctggtttgcattgggcaaattatc gccccggcaaaagatgacgttgaatttcgacatcgcataatgaatccgct cactgaagatgagtttcaacaactcatcgcgccgtggatagatatgttct accttaatcacgcagaacatccctttatgcagaccaaaggtgtcaaagca aatgatgtgactccaatggaaaaactgttggctggggtaagcggcgcgac gaattgtgcatttgtcaatcaaccggggcagggtgaagcattatgtggtg gatgcactgcgattgcgttattcaaccaggcgaatcaggcaccaggtttt ggtggtggttttaaaagcggtttacgtggaggaacacctgtaacaacgtt cgtacgtgggatcgatcttcgttcaacggtgttactcaatgtcctcacat tacctcgtcttcaaaaacaatttcctaatgaatcacatacggaaaaccaa cctacctggattaaacctatcaagtccaatgagtctatacctgatcgtca attgggtttgtccgtggtctattctggcaaccagcgcatattgaattatg cgatcccattgggattggtaaatgttcttgctgtggacaggaaagcaatt tgcgttataccggttttcttaaggaaaaatttacctttacagttaatggg ctatggccccatccgcattccccttgtctggtaacagtcaagaaagggga ggttgaggaaaaatttcttgctttcaccacctccgcaccatcatggacac aaatcagccgagttgtggtagataagattattcaaaatgaaaatggaaat cgcgtggcggcggttgtgaatcaattcagaaatattgcgccgcaaagtcc tcttgaattgattatggggggatatcgtaataatcaagcatctattcttg aacggcgtcatgatgtgttgatgtttaatcaggggtggcaacaatacggc aatgtgataaacgaaatagtgactgttggtttgggatataaaacagcctt acgcaaggcgttatatacctttgcagaagggtttaaaaataaagacttca aaggggccggagtctctgttcatgagactgcagaaaggcatttctatcga cagagtgaattattaattcccgatgtactggcgaatgttaatttttccca ggctgatgaggtaatagctgatttacgagacaaacttcatcaattgtgtg aaatgctatttaatcaatctgtagctccctatgcacatcatcctaaatta ataagcacattagcgcttgcccgcgccacgctatacaaacatttacggga gttaaaaccgcaaggagggccatcaaatggctga >protein sequence of His.sub.6-Dual-monopartite NLS SV40-FokI-(Sharkey-ELD)-Cse1 [SEQ ID NO: 25] MHHHHHHPKKKRKVDPKKKRKVEDPKDMAQLVKSELEEKKSELRHKLKYV PHEYIELIEIARNPTQDRILEMKVMEFFMKVYGYRGEHLGGSRKPDGAIY TVGSPIDYGVIVDTKAYSGGYNLPIGQADEMERYVEENQTRDKHLNPNEW WKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIG GEMIKAGTLTLEEVRRKFNNGEINFADPTNRAKGLEAVSVASMNLLIDNW IPVRPRNGGKVQIINLQSLYCSRDQWRLSLPRDDMELAALALLVCIGQII APAKDDVEFRHRIMNPLTEDEFQQLIAPWIDMFYLNHAEHPFMQTKGVKA NDVTPMEKLLAGVSGATNCAFVNQPGQGEALCGGCTAIALFNQANQAPGF GGGFKSGLRGGTPVTTFVRGIDLRSTVLLNVLTLPRLQKQFPNESHTENQ PTWIKPIKSNESIPASSIGFVRGLFWQPAHIELCDPIGIGKCSCCGQESN LRYTGFLKEKFTFTVNGLWPHPHSPCLVTVKKGEVEEKFLAFTTSAPSWT QISRVVVDKIIQNENGNRVAAVVNQFRNIAPQSPLELIMGGYRNNQASIL ERRHDVLMFNQGWQQYGNVINEIVTVGLGYKTALRKALYTFAEGFKNKDF KGAGVSVHETAERHFYRQSELLIPDVLANVNFSQADEVIADLRDKLHQLC EMLFNQSVAPYAHHPKLISTLALARATLYKHLRELKPQGGPSNG*

DNA Cleavage Assay

[0150] The specificity and activity of the complexes was tested using an artificially constructed target plasmid as a substrate. This plasmid contains M13 and P7 binding sites on opposing strands such that both FokI domains face each other (see FIG. 11). The distance between the Cascade binding sites varies between 25 and 50 basepairs with 5 bp increments. As the binding sites of Cascade need to be flanked by any of four known PAM sequences (5'-protospacer-CTT/CAT/CTC/CCT-3' this distance range gives sufficient flexibility to design such a pair for almost any given sequence.

[0151] The sequences of the target plasmids used are as follows. The number indicated the distance between the M13 and P7 target sites. Protospacers are shown in bold, PAMs underlined:

[0152] Sequences of the target plasmids. The number indicates the distance between the M13 and P7 target sites. (protospacers in bold, PAMs underlined)

TABLE-US-00007 >50 bp [SEQ ID NO: 26] gaattcACAACGGTGAGCAAGTCACTGTTGGCAAGCCAGGATCTGAACAA TACCGTCTTGCTTTCGAGCGCTAGCTCTAGAACTAGTCCTCAGCCTAGGC CTCGTTCCGAAGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCATAGGC GGCCTTTAACTCggatcc >45 bp [SEQ ID NO: 27] gaattcACAACGGTGAGCAAGTCACTGTTGGCAAGCCAGGATCTGAACAA TACCGTCTTTTCGAGCGCTAGCTCTAGAACTAGTCCTCAGCCTAGGCCTC GTTCAAGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCATAGGCGGCCT TTAACTCggatcc >40 bp [SEQ ID NO: 28] gaattcACAACGGTGAGCAAGTCACTGTTGGCAAGCCAGGATCTGAACAA TACCGTCTTCGAGCGCTAGCTCTAGAACTAGTCCTCAGCCTAGGCCTCGA AGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCATAGGCGGCCTTTAAC TCggatcc >35 bp [SEQ ID NO: 29] gaattcACAACGGTGAGCAAGTCACTGTTGGCAAGCCAGGATCTGAACAA TACCGTCTTGCGCTAGCTCTAGAACTAGTCCTCAGCCTAGGCCTAAGCTG TCTTTCGCTGCTGAGGGTGACGATCCCGCATAGGCGGCCTTTAACTCgga tcc >30 bp [SEQ ID NO: 30] gaattcACAACGGTGAGCAAGTCACTGTTGGCAAGCCAGGATCTGAACAA TACCGTCTTGCTAGCTCTAGAACTAGTCCTCAGCCTAGGAAGCTGTCTTT CGCTGCTGAGGGTGACGATCCCGCATAGGCGGCCTTTAACTCggatcc >25 bp [SEQ ID NO: 31] gaattcACAACGGTGAGCAAGTCACTGTTGGCAAGCCAGGATCTGAACAA TACCGTCTTCTCTAGAACTAGTCCTCAGCCTAGGAAGCTGTCTTTCGCTG CTGAGGGTGACGATCCCGCATAGGCGGCCTTTAACTCggatcc

[0153] Cleavage of the target plasmids was analysed on agarose gels, where negatively supercoiled (nSC) plasmid can be distinguished from linearized- or nicked plasmid. The cleavage site of the Cascade.sup.KKR/ELD pair in a target vector was determined by isolating linear cleavage products from an agarose gel and filling in the recessed 3' ends left by FokI cleavage with the Klenow fragment of E. coli DNA polymerase to create blunt ends. The linear vector was self-ligated, transformed, amplified, isolated and sequenced. Filling in of recessed 3' ends and re-ligation will lead to extra nucleotides in the sequence that represents the overhang left by FokI cleavage. By aligning the sequence reads to the original sequence, the cleavage sites can be found on a clonal level and mapped. Below, the additional bases incorporated into the sequence after filling in recessed 3' ends left by FokI cleavage are underlined:

##STR00001##

[0154] Reading from top to bottom, the 5'-3' sequences above are SEQ ID NOs: 32-35, respectively.

Cleavage of a Target Locus in Human Cells

[0155] The human CCR5 gene encodes the C--C chemokine receptor type 5 protein, which serves as the receptor for the human immunodeficiency virus (HIV) on the surface of white blood cells. The CCR5 gene is targeted using a pair of Cascade.sup.KKR/ELD nucleases in addition to an artificial GFP locus. A suitable binding site pair is selected on the coding region of CCR5. Two separate CRISPR arrays containing uniform spacers targeting each of the binding sites are constructed using DNA synthesis (Geneart).

[0156] The human CCR5 target gene selection and CRISPR designs used are as follows:

TABLE-US-00008 >Part of genomic human CCR5 sequence, containing whole ORF (position 347-1446). [SEQ ID NO: 36] GGTGGAACAAGATGGATTATCAAGTGTCAAGTCCAATCTATGACATCAAT TATTATACATCGGAGCCCTGCCAAAAAATCAATGTGAAGCAAATCGCAGC CCGCCTCCTGCCTCCGCTCTACTCACTGGTGTTCATCTTTGGTTTTGTGG GCAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAGGCTGAAGAGC ATGACTGACATCTACCTGCTCAACCTGGCCATCTCTGACCTGTTTTTCCT TCTTACTGTCCCCTTCTGGGCTCACTATGCTGCCGCCCAGTGGGACTTTG GAAATACAATGTGTCAACTCTTGACAGGGCTCTATTTTATAGGCTTCTTC TCTGGAATCTTCTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGT CGTCCATGCTGTGTTTGCTTTAAAAGCCAGGACGGTCACCTTTGGGGTGG TGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGA ATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTC TCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAA AGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTCATGGTCATCTGC TACTCGGGAATCCTAAAAACTCTGCTTCGGTGTCGAAATGAGAAGAAGAG GCACAGGGCTGTGAGGCTTATCTTCACCATCATGATTGTTTATTTTCTCT TCTGGGCTCCCTACAACATTGTCCTTCTCCTGAACACCTTCCAGGAATTC TTTGGCCTGAATAATTGCAGTAGCTCTAACAGGTTGGACCAAGCTATGCA GGTGACAGAGACTCTTGGGATGACGCACTGCTGCATCAACCCCATCATCT ATGCCTTTGTCGGGGAGAAGTTCAGAAACTACCTCTTAGTCTTCTTCCAA AAGCACATTGCCAAACGCTTCTGCAAATGCTGTTCTATTTTCCAGCAAGA GGCTCCCGAGCGAGCAAGCTCAGTTTACACCCGATCCACTGGGGAGCAGG AAATATCTGTGGGCTTGTGACACGGACTCAAGTGGGCTGGTGACCCAGTC

[0157] Red1/2: chosen target sites (distance: 34 bp, PAM 5'-CTT-3'). "Red 1 is first appearing underlined sequence in the above. Red2 is the second underlined sequence.

TABLE-US-00009 >CRISPR array red1 (italics = spacers, bold = repeats) [SEQ ID NO: 37] ccatggTAATACGACTCACTATAGGGAGAATTAGCTGATCTTTAATAATA AGGAAATGTTACATTAAGGTTGGTGGGTTGTTTTTATGGGAAAAAATGCT TTAAGAACAAATGTATACTTTTAGAGAGTTCCCCGCGCCAGCGGGGATAA ACCGCAAACACAGCATGGACGACAGCCAGGTACCTAGAGTTCCCCGCGCC AGCGGGGATAAACCGCAAACACAGCATGGACGACAGCCAGGTACCTAGAG TTCCCCGCGCCAGCGGGGATAAACCGCAAACACAGCATGGACGACAGCCA GGTACCTAGAGTTCCCCGCGCCAGCGGGGATAAACCGAAAACAAAAGGCT CAGTCGGAAGACTGGGCCTTTTGTTTTAACCCCTTGGGGCCTCTAAACGG GTCTTGAGGGGTTTTTTGggtacc >CRISPR array red2 (italics: spacers, bold: repeats) [SEQ ID NO: 38] ccatggTAATACGACTCACTATAGGGAGAATTAGCTGATCTTTAATAATA AGGAAATGTTACATTAAGGTTGGTGGGTTGTTTTTATGGGAAAAAATGCT TTAAGAACAAATGTATACTTTTAGAGAGTTCCCCGCGCCAGCGGGGATAA ACCGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTGAGTTCCCCGCGCC AGCGGGGATAAACCGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTGAG TTCCCCGCGCCAGCGGGGATAAACCGTGTGATCACTTGGGTGGTGGCTGT GTTTGCGTGAGTTCCCCGCGCCAGCGGGGATAAACCGAAAACAAAAGGCT CAGTCGGAAGACTGGGCCTTTTGTTTTAACCCCTTGGGGCCTCTAAACGG GTCTTGAGGGGTTTTTTGggtacc

Delivery of Cascade.sup.KKR/ELD into the Nucleus of Human Cells

[0158] Cascade is very stable as a multi-subunit protein-RNA complex and is easily produced in mg quantities in E. coli. Transfection or micro-injection of the complex in its intact form as purified from E. coli is used as methods of delivery (see FIG. 12). As shown in FIG. 12, Cascade-Fold nucleases are purified from E. coli and encapsulated in protein transfection vesicles. These are then fused with the cell membrane of human HepG2 cells releasing the nucleases in the cytoplasm (step 2). NLS sequences are then be recognized by importin proteins, which facilitate nucleopore passage (step 3). Cascade.sup.KKR (open rectangle) and Cascade.sup.ELD (filled rectangle) will then find and cleave their target site (step 4), inducing DNA repair pathways that will alter the target site leading to desired changes. Cascade.sup.KKR/ELD nucleases need to act only once and require no permanent presence in the cell encoded on DNA.

[0159] To deliver Cascade into human cells, protein transfection reagents are used from various sources including Pierce, NEB, Fermentas and Clontech. These reagents have recently been developed for the delivery of antibodies, and are useful to transfect a broad range of human cell lines with efficiencies up to 90%. Human HepG2 cells are transfected. Also, other cell lines including CHO-K1, COS-7, HeLa, and non-embryonic stem cells, are transfected.

[0160] To import the Cascade.sup.KKR/ELD nuclease pair into the nucleus, a tandem monopartite nuclear localisation signal (NLS) from the large T-antigen of simian virus 40 (SV40) is fused to the N-terminus of FokI. This ensures import of only intact Cascade.sup.ELD/KKR into the nucleus. (The nuclear pore complex translocates RNA polymerases (550 kDa) and other large protein complexes). As a check prior to transformations, the nuclease activity of the Cascade.sup.KKR/ELD nuclease pair is checked in vitro using purified complexes and CCR5PCR amplicons to exclude transfecting non-productive Cascade.sup.KKR/ELD nuclease pairs.

Surveyor Assay

[0161] Transfected cells are cultivated and passaged for several days. The efficiency of in vivo target DNA cleavage is then assessed by using the Surveyor assay of Guschin, D. Y., et al (2010) Methods Mol. Biol., 649: 247-256. Briefly, PCR amplicons of the target DNA locus will be mixed 1:1 with PCR amplicons from untreated cells. These are heated and allowed to anneal, giving rise to mismatches at target sites that have been erroneously repaired by NHEJ. A mismatch nuclease is then used to cleave only mismatched DNA molecules, giving a maximum of 50% of cleavage when target DNA cleavage by Cascade.sup.KKR/ELD is complete. This procedure was then followed up by sequencing of the target DNA amplicons of treated cells. The assay allows for rapid assessment and optimization of the delivery procedure.

Production of Cascade-Nuclease Pairs

[0162] The Cascade-nuclease complexes were constructed as explained above. Affinity purification from E. coli using the StrepII-tagged Cse2 subunit yields a complex with the expected stoichiometry when compared to native Cascade. Referring to FIG. 13, this shows the stoichiometry of native Cascade (1), Cascade.sup.KKR with P7 CrRNA and Cascade.sup.ELD with M13 CrRNA 24 h after purification using only Streptactin. Bands in native Cascade (1) are from top to bottom: Cse1, Cas7, Cas5, Cas6e, Cse2. Cascade.sup.KKR/ELD show the FokI-Cse1 fusion band and an additional band representing Cse1 with a small part of FokI as a result of proteolytic degradation.

[0163] Apart from an intact FokI-Cse1 fusion protein, we observed that a fraction of the FokI-Cse1-fusion protein is proteolytically cleaved, resulting in a Cse1 protein with only the linker and a small part of FokI attached to it (as confirmed by Mass Spectrometry, data not shown). In most protein isolations the fraction of degraded fusion protein is approximately 40%. The isolated protein is stably stored in the elution buffer (20 mM HEPES pH 7.5, 75 mM NaCl, 1 mM DTT, 4 mM desthiobiotin) with additional 0.1% Tween 20 and 50% glycerol at -20.degree. C. Under these storage conditions, integrity and activity of the complex have been found stable for at least three weeks (data not shown).

Introduction of a His.sub.6-Tag and NLS to the Cascade-Nuclease

[0164] The Cascade nuclease fusion design was modified to incorporate a Nucleolar Localization Signal (NLS) to enable transport into the nucleus of eukaryotic cells. For this a tandem monopartite NLS from the large T-antigen of Simian Virus SV40 (sequence: PKKKRKVDPKKKRKV) was translationally fused to the N-terminus of the FokI-Cse1 fusion protein, directly preceded by a His.sub.6-tag at the N-terminus. The His.sub.6-tag (sequence: MHHHHHH) allows for an additional Ni.sup.2+-resin affinity purification step after StrepII purification. This additional step ensures the isolation of only full-length Cascade-nuclease fusion complex, and increases the efficiency of cleavage by eliminating the binding of non-intact Cascade complexes to the target site forming an unproductive nuclease pair.

In Vitro Cleavage Assay

[0165] Cascade.sup.KKR/ELD activity and specificity was assayed in vitro as described above. FIG. 14A shows plasmids with distances between protospacers of 25-50 bp (5 bp increments, lanes 1-6) incubated with Cascade.sup.KKR/ELD for 30 minutes at 37.degree. C. Lane 10 contains the target plasmid in its three possible topologies: the lowest band represents the initial, negatively supercoiled (nSC) form of the plasmid, the middle band represents the linearized form (cleaved by XbaI), whilst the upper band represents the open circular (OC) form (after nicking with Nt.BbrCI). Lane 7 shows incubation of a plasmid with both binding sites removed (negative control). Therefore FIG. 14A shows a typical cleavage assay using various target plasmids in which the binding sites are separated by 25 to 50 base pairs in 5 bp increments (lanes 1 to 6). These plasmids with distances of 25-50 bp were incubated with Cascade.sup.KKR/ELD carrying anti P7 and M13 crRNA respectively. A plasmid containing no binding sites served as a control (lane 7). The original plasmid exists in negatively supercoiled form (nSC, control lane 8), and nicked or linearized products are clearly distinguishable. Upon incubation a linear cleavage product is formed when binding sites were separated by 30, 35 and 40 base pairs (lanes 2, 3, 4). At 25, 45 and 50 base pairs distance (lanes 1, 5, 6), the target plasmid appeared to be incompletely cleaved leading to the nicked form (OC). These results show the best cleavage in plasmids with distances between 30 and 40 bp, giving sufficient flexibility when designing a crRNA pair for any given locus. Both shorter and longer distances result in increased nicking activity while creating less DSBs. There is very little activity on a plasmid where the two protospacers have been removed, showing target specificity (lane 7).

Cleavage Conditions

[0166] To assess the optimal buffer conditions for cleavage assays, and to estimate whether activity of the complex is expected at physiological conditions, the following two buffers were selected: (1) NEB4 (New England Biolabs, 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 1 mM dithiothreitol, pH 7.9) and (2) Buffer 0 (Fermentas, 50 mM Tris-HCl, 10 mM MgCl.sub.2, 100 mM NaCl, 0.1 mg/mL BSA, pH 7.5). Of the two, NEB4 is recommended for optimal activity of the commercial intact FokI enzyme. Buffer 0 was chosen from a quick screen to give good activity and specificity (data not shown). FIG. 14B shows incubation with different buffers and different incubation times. Lanes 1-4 have been incubated with Fermentas Buffer 0 (lane 1, 2 for 15 minutes, lane 3, 4 for 30 minutes), lanes 5, 6 have been incubated with NEB4 (30 minutes). Lanes 1, 3, 5 used the target plasmid with 35 bp spacing, lanes 2, 4, 6 used the non-target plasmid (no binding sites). Lanes 7, 8 have been incubated with only Cascade.sup.KKR or Cascade.sup.ELD respectively (buffer 0). Lane 9 is the topology marker as in (A). Lane 10 and 11 show the target and non-target plasmid incubated without addition of Cascade. Therefore in FIG. 14B, activity was tested on the target plasmid with 35 base pairs distance (lane 1, 3, 5) and a non-target control plasmid (lane 2, 4, 6). There was a high amount of unspecific nicking and less cleavage in NEB4 (lane 5,6), whilst buffer 0 shows only activity in the target plasmid with a high amount of specific cleavage and little nicking (lane 1-4). The difference is likely caused by the NaCl concentration in buffer 0, higher ionic strength weakens protein-protein interactions, leading to less nonspecific activity. Incubation of 15 or 30 minutes shows little difference in both target and non-target plasmid (lane 1, 2 or 3,4 respectively). Addition of only one type of Cascade (P7.sup.KKR or M13.sup.ELD) does not result in cleavage activity (lane 7, 8) as expected. This experiment shows that specific Cascade nuclease activity by a designed pair occurs when the NaCl concentration is at least 100 mM, which is near the physiological saline concentration inside cells (137 mM NaCl). The Cascade nuclease pair is expected to be fully active in vivo, in eukaryotic cells, while displaying negligible off-target cleavage activity.

Cleavage Site

[0167] The site of cleavage in the target plasmid with a spacing of 35 bp (pTarget35) was determined. FIG. 15 shows how sequencing reveals up- and downstream cleavage sites by Cascade.sup.KKR/ELD in the target plasmid with 35 base pair spacing. In FIG. 15A) is shown the target region within pTarget35 with annotated potential cleavage sites. Parts of the protospacers are indicated in red and blue. B) The bar chart shows four different cleavage patterns and their relative abundance within sequenced clones. The blue bars represent the generated overhang, while the left and right border of each bar represents the left and right cleavage site (see B for annotation).

[0168] FIG. 15A shows the original sequence of pTarget35, with numbered cleavage sites from -7 to +7 where 0 lies in the middle between the two protospacers (indicated in red and blue). Seventeen clones were sequenced and these all show cleavage around position 0, creating varying overhangs between 3 and 5 bp (see FIG. 15B). Overhangs of 4 are most abundant (cumulatively 88%), while overhangs of 3 and 5 occur only once (6% each). The cleavage occurred exactly as expected with no clones showing off target cleavage.

Cleaving a Target Locus in Human Cells.

[0169] Cascade.sup.KKR/ELD nucleases were successfully modified to contain an N-terminal His.sub.6-tag followed by a dual mono-partite Nucleolar Localisation Signal. These modified Cascade nuclease fusion proteins were co-expressed with either one of two synthetically constructed CRISPR arrays, each targeting a binding site in the human CCR5 gene. First the activity of this new nuclease pair is validated in vitro by testing the activity on a plasmid containing this region of the CCR5 gene. The nuclease pair is transfected to a human cell line, e.g. HeLa cell line. Efficiency of target cleavage is assessed using the Surveyor assay as described above.

Sequence CWU 1

1

471502PRTEscherichia coli 1Met Asn Leu Leu Ile Asp Asn Trp Ile Pro Val Arg Pro Arg Asn Gly 1 5 10 15 Gly Lys Val Gln Ile Ile Asn Leu Gln Ser Leu Tyr Cys Ser Arg Asp 20 25 30 Gln Trp Arg Leu Ser Leu Pro Arg Asp Asp Met Glu Leu Ala Ala Leu 35 40 45 Ala Leu Leu Val Cys Ile Gly Gln Ile Ile Ala Pro Ala Lys Asp Asp 50 55 60 Val Glu Phe Arg His Arg Ile Met Asn Pro Leu Thr Glu Asp Glu Phe 65 70 75 80 Gln Gln Leu Ile Ala Pro Trp Ile Asp Met Phe Tyr Leu Asn His Ala 85 90 95 Glu His Pro Phe Met Gln Thr Lys Gly Val Lys Ala Asn Asp Val Thr 100 105 110 Pro Met Glu Lys Leu Leu Ala Gly Val Ser Gly Ala Thr Asn Cys Ala 115 120 125 Phe Val Asn Gln Pro Gly Gln Gly Glu Ala Leu Cys Gly Gly Cys Thr 130 135 140 Ala Ile Ala Leu Phe Asn Gln Ala Asn Gln Ala Pro Gly Phe Gly Gly 145 150 155 160 Gly Phe Lys Ser Gly Leu Arg Gly Gly Thr Pro Val Thr Thr Phe Val 165 170 175 Arg Gly Ile Asp Leu Arg Ser Thr Val Leu Leu Asn Val Leu Thr Leu 180 185 190 Pro Arg Leu Gln Lys Gln Phe Pro Asn Glu Ser His Thr Glu Asn Gln 195 200 205 Pro Thr Trp Ile Lys Pro Ile Lys Ser Asn Glu Ser Ile Pro Ala Ser 210 215 220 Ser Ile Gly Phe Val Arg Gly Leu Phe Trp Gln Pro Ala His Ile Glu 225 230 235 240 Leu Cys Asp Pro Ile Gly Ile Gly Lys Cys Ser Cys Cys Gly Gln Glu 245 250 255 Ser Asn Leu Arg Tyr Thr Gly Phe Leu Lys Glu Lys Phe Thr Phe Thr 260 265 270 Val Asn Gly Leu Trp Pro His Pro His Ser Pro Cys Leu Val Thr Val 275 280 285 Lys Lys Gly Glu Val Glu Glu Lys Phe Leu Ala Phe Thr Thr Ser Ala 290 295 300 Pro Ser Trp Thr Gln Ile Ser Arg Val Val Val Asp Lys Ile Ile Gln 305 310 315 320 Asn Glu Asn Gly Asn Arg Val Ala Ala Val Val Asn Gln Phe Arg Asn 325 330 335 Ile Ala Pro Gln Ser Pro Leu Glu Leu Ile Met Gly Gly Tyr Arg Asn 340 345 350 Asn Gln Ala Ser Ile Leu Glu Arg Arg His Asp Val Leu Met Phe Asn 355 360 365 Gln Gly Trp Gln Gln Tyr Gly Asn Val Ile Asn Glu Ile Val Thr Val 370 375 380 Gly Leu Gly Tyr Lys Thr Ala Leu Arg Lys Ala Leu Tyr Thr Phe Ala 385 390 395 400 Glu Gly Phe Lys Asn Lys Asp Phe Lys Gly Ala Gly Val Ser Val His 405 410 415 Glu Thr Ala Glu Arg His Phe Tyr Arg Gln Ser Glu Leu Leu Ile Pro 420 425 430 Asp Val Leu Ala Asn Val Asn Phe Ser Gln Ala Asp Glu Val Ile Ala 435 440 445 Asp Leu Arg Asp Lys Leu His Gln Leu Cys Glu Met Leu Phe Asn Gln 450 455 460 Ser Val Ala Pro Tyr Ala His His Pro Lys Leu Ile Ser Thr Leu Ala 465 470 475 480 Leu Ala Arg Ala Thr Leu Tyr Lys His Leu Arg Glu Leu Lys Pro Gln 485 490 495 Gly Gly Pro Ser Asn Gly 500 2160PRTEscherichia coli 2Met Ala Asp Glu Ile Asp Ala Met Ala Leu Tyr Arg Ala Trp Gln Gln 1 5 10 15 Leu Asp Asn Gly Ser Cys Ala Gln Ile Arg Arg Val Ser Glu Pro Asp 20 25 30 Glu Leu Arg Asp Ile Pro Ala Phe Tyr Arg Leu Val Gln Pro Phe Gly 35 40 45 Trp Glu Asn Pro Arg His Gln Gln Ala Leu Leu Arg Met Val Phe Cys 50 55 60 Leu Ser Ala Gly Lys Asn Val Ile Arg His Gln Asp Lys Lys Ser Glu 65 70 75 80 Gln Thr Thr Gly Ile Ser Leu Gly Arg Ala Leu Ala Asn Ser Gly Arg 85 90 95 Ile Asn Glu Arg Arg Ile Phe Gln Leu Ile Arg Ala Asp Arg Thr Ala 100 105 110 Asp Met Val Gln Leu Arg Arg Leu Leu Thr His Ala Glu Pro Val Leu 115 120 125 Asp Trp Pro Leu Met Ala Arg Met Leu Thr Trp Trp Gly Lys Arg Glu 130 135 140 Arg Gln Gln Leu Leu Glu Asp Phe Val Leu Thr Thr Asn Lys Asn Ala 145 150 155 160 3363PRTEscherichia coli 3Met Ser Asn Phe Ile Asn Ile His Val Leu Ile Ser His Ser Pro Ser 1 5 10 15 Cys Leu Asn Arg Asp Asp Met Asn Met Gln Lys Asp Ala Ile Phe Gly 20 25 30 Gly Lys Arg Arg Val Arg Ile Ser Ser Gln Ser Leu Lys Arg Ala Met 35 40 45 Arg Lys Ser Gly Tyr Tyr Ala Gln Asn Ile Gly Glu Ser Ser Leu Arg 50 55 60 Thr Ile His Leu Ala Gln Leu Arg Asp Val Leu Arg Gln Lys Leu Gly 65 70 75 80 Glu Arg Phe Asp Gln Lys Ile Ile Asp Lys Thr Leu Ala Leu Leu Ser 85 90 95 Gly Lys Ser Val Asp Glu Ala Glu Lys Ile Ser Ala Asp Ala Val Thr 100 105 110 Pro Trp Val Val Gly Glu Ile Ala Trp Phe Cys Glu Gln Val Ala Lys 115 120 125 Ala Glu Ala Asp Asn Leu Asp Asp Lys Lys Leu Leu Lys Val Leu Lys 130 135 140 Glu Asp Ile Ala Ala Ile Arg Val Asn Leu Gln Gln Gly Val Asp Ile 145 150 155 160 Ala Leu Ser Gly Arg Met Ala Thr Ser Gly Met Met Thr Glu Leu Gly 165 170 175 Lys Val Asp Gly Ala Met Ser Ile Ala His Ala Ile Thr Thr His Gln 180 185 190 Val Asp Ser Asp Ile Asp Trp Phe Thr Ala Val Asp Asp Leu Gln Glu 195 200 205 Gln Gly Ser Ala His Leu Gly Thr Gln Glu Phe Ser Ser Gly Val Phe 210 215 220 Tyr Arg Tyr Ala Asn Ile Asn Leu Ala Gln Leu Gln Glu Asn Leu Gly 225 230 235 240 Gly Ala Ser Arg Glu Gln Ala Leu Glu Ile Ala Thr His Val Val His 245 250 255 Met Leu Ala Thr Glu Val Pro Gly Ala Lys Gln Arg Thr Tyr Ala Ala 260 265 270 Phe Asn Pro Ala Asp Met Val Met Val Asn Phe Ser Asp Met Pro Leu 275 280 285 Ser Met Ala Asn Ala Phe Glu Lys Ala Val Lys Ala Lys Asp Gly Phe 290 295 300 Leu Gln Pro Ser Ile Gln Ala Phe Asn Gln Tyr Trp Asp Arg Val Ala 305 310 315 320 Asn Gly Tyr Gly Leu Asn Gly Ala Ala Ala Gln Phe Ser Leu Ser Asp 325 330 335 Val Asp Pro Ile Thr Ala Gln Val Lys Gln Met Pro Thr Leu Glu Gln 340 345 350 Leu Lys Ser Trp Val Arg Asn Asn Gly Glu Ala 355 360 4224PRTEscherichia coli 4Met Arg Ser Tyr Leu Ile Leu Arg Leu Ala Gly Pro Met Gln Ala Trp 1 5 10 15 Gly Gln Pro Thr Phe Glu Gly Thr Arg Pro Thr Gly Arg Phe Pro Thr 20 25 30 Arg Ser Gly Leu Leu Gly Leu Leu Gly Ala Cys Leu Gly Ile Gln Arg 35 40 45 Asp Asp Thr Ser Ser Leu Gln Ala Leu Ser Glu Ser Val Gln Phe Ala 50 55 60 Val Arg Cys Asp Glu Leu Ile Leu Asp Asp Arg Arg Val Ser Val Thr 65 70 75 80 Gly Leu Arg Asp Tyr His Thr Val Leu Gly Ala Arg Glu Asp Tyr Arg 85 90 95 Gly Leu Lys Ser His Glu Thr Ile Gln Thr Trp Arg Glu Tyr Leu Cys 100 105 110 Asp Ala Ser Phe Thr Val Ala Leu Trp Leu Thr Pro His Ala Thr Met 115 120 125 Val Ile Ser Glu Leu Glu Lys Ala Val Leu Lys Pro Arg Tyr Thr Pro 130 135 140 Tyr Leu Gly Arg Arg Ser Cys Pro Leu Thr His Pro Leu Phe Leu Gly 145 150 155 160 Thr Cys Gln Ala Ser Asp Pro Gln Lys Ala Leu Leu Asn Tyr Glu Pro 165 170 175 Val Gly Gly Asp Ile Tyr Ser Glu Glu Ser Val Thr Gly His His Leu 180 185 190 Lys Phe Thr Ala Arg Asp Glu Pro Met Ile Thr Leu Pro Arg Gln Phe 195 200 205 Ala Ser Arg Glu Trp Tyr Val Ile Lys Gly Gly Met Asp Val Ser Gln 210 215 220 5199PRTEscherichia coli 5Met Tyr Leu Ser Lys Val Ile Ile Ala Arg Ala Trp Ser Arg Asp Leu 1 5 10 15 Tyr Gln Leu His Gln Gly Leu Trp His Leu Phe Pro Asn Arg Pro Asp 20 25 30 Ala Ala Arg Asp Phe Leu Phe His Val Glu Lys Arg Asn Thr Pro Glu 35 40 45 Gly Cys His Val Leu Leu Gln Ser Ala Gln Met Pro Val Ser Thr Ala 50 55 60 Val Ala Thr Val Ile Lys Thr Lys Gln Val Glu Phe Gln Leu Gln Val 65 70 75 80 Gly Val Pro Leu Tyr Phe Arg Leu Arg Ala Asn Pro Ile Lys Thr Ile 85 90 95 Leu Asp Asn Gln Lys Arg Leu Asp Ser Lys Gly Asn Ile Lys Arg Cys 100 105 110 Arg Val Pro Leu Ile Lys Glu Ala Glu Gln Ile Ala Trp Leu Gln Arg 115 120 125 Lys Leu Gly Asn Ala Ala Arg Val Glu Asp Val His Pro Ile Ser Glu 130 135 140 Arg Pro Gln Tyr Phe Ser Gly Asp Gly Lys Ser Gly Lys Ile Gln Thr 145 150 155 160 Val Cys Phe Glu Gly Val Leu Thr Ile Asn Asp Ala Pro Ala Leu Ile 165 170 175 Asp Leu Val Gln Gln Gly Ile Gly Pro Ala Lys Ser Met Gly Cys Gly 180 185 190 Leu Leu Ser Leu Ala Pro Leu 195 6392DNAArtificial SequenceGA1070943 6actggaaagc gggcagtgaa aggaaggccc atgaggccag ttaattaagc ggatcctggc 60ggcggcagcg gcggcggcag cgacaagcag aagaacggca tcaaggcgaa cttcaagatc 120cgccacaaca tcgaggacgg cggcgtgcag ctcgccgacc actaccagca gaacaccccc 180atcggcgacg gccccgtgct gctgcccgac aaccactacc tgagctacca gtccgccctg 240agcaaagacc ccaacgagaa gcgcgatcac atggtcctgc tggagttcgt gaccgccgcc 300gggatcactc tcggcatgga cgagctgtac aagtaagcgg ccgcggcgcg cctaggcctt 360gacggccttc cttcaattcg ccctatagtg ag 3927603DNAArtificial SequenceGA1070941 7cactataggg cgaattggcg gaaggccgtc aaggccgcat ttaattaagc ggccgcaggc 60ggcggcagcg gcggcggcag catggtgagc aagggcgagg agctgttcac cggggtggtg 120cccatcctgg tcgagctgga cggcgacgta aacggccaca agttcagcgt gtccggcgag 180ggcgagggcg atgccaccta cggcaagctg accctgaagc tcatctgcac caccggcaag 240ctgcccgtgc cctggcccac cctcgtgacc accctcggct acggcctgca gtgcttcgcc 300cgctaccccg accacatgaa gcagcacgac ttcttcaagt ccgccatgcc cgaaggctac 360gtccaggagc gcaccatctt cttcaaggac gacggcaact acaagacccg cgccgaggtg 420aagttcgagg gcgacaccct ggtgaaccgc atcgagctga agggcatcga cttcaaggag 480gacggcaaca tcctggggca caagctggag tacaactaca acagccacaa cgtctatatc 540acggcctaac tcgagggcgc gccctgggcc tcatgggcct tccgctcact gcccgctttc 600cag 6038679DNAArtificial SequenceGA1068859 8cactataggg cgaattggcg gaaggccgtc aaggccgcat gagctccatg gaaacaaaga 60attagctgat ctttaataat aaggaaatgt tacattaagg ttggtgggtt gtttttatgg 120gaaaaaatgc tttaagaaca aatgtatact tttagagagt tccccgcgcc agcggggata 180aaccgggccg attgaaggtc cggtggatgg cttaaaagag ttccccgcgc cagcggggat 240aaaccgccgc aggtacagca ggtagcgcag atcatcaaga gttccccgcg ccagcgggga 300taaaccgact tctctccgaa aagtcaggac gctgtggcag agttccccgc gccagcgggg 360ataaaccgcc tacgcgctga acgccagcgg tgtggtgaat gagttccccg cgccagcggg 420gataaaccgg tgtggccatg cacgccttta acggtgaact ggagttcccc gcgccagcgg 480ggataaaccg cacgaactca gccagaacga caaacaaaag gcgagttccc cgcgccagcg 540gggataaacc ggcaccagta cgcgccccac gctgacggtt tctgagttcc ccgcgccagc 600ggggataaac cgcagctccc attttcaaac ccaggtaccc tgggcctcat gggccttccg 660ctcactgccc gctttccag 6799685DNAArtificial SequenceGA1047360 9gagctcccgg gctgacggta atagaggcac ctacaggctc cggtaaaacg gaaacagcgc 60tggcctatgc ttggaaactt attgatcaac aaattgcgga tagtgttatt tttgccctcc 120caacacaagc taccgcgaat gctatgctta cgagaatgga agcgagcgcg agccacttat 180tttcatcccc aaatcttatt cttgctcatg gcaattcacg gtttaaccac ctctttcaat 240caataaaatc acgcgcgatt actgaacagg ggcaagaaga agcgtgggtt cagtgttgtc 300agtggttgtc acaaagcaat aagaaagtgt ttcttgggca aatcggcgtt tgcacgattg 360atcaggtgtt gatttcggta ttgccagtta aacaccgctt tatccgtggt ttgggaattg 420gtagatctgt tttaattgtt aatgaagttc atgcttacga cacctatatg aacggcttgc 480tcgaggcagt gctcaaggct caggctgatg tgggagggag tgttattctt ctttccgcaa 540ccctaccaat gaaacaaaaa cagaagcttc tggatactta tggtctgcat acagatccag 600tggaaaataa ctccgcatat ccactcatta actggcgagg tgtgaatggt gcgcaacgtt 660ttgatctgct agcggatccg gtacc 6851037DNAArtificial SequencePrimer BG3186 10atagcgccat ggaacctttt aaatatatat gccatta 371141DNAArtificial SequencePrimer BG3213 11acagtgggat ccgctttggg atttgcaggg atgactctgg t 411243DNAArtificial SequencePrimer BG3303 12atagcgtcat gaatttgctt attgataact ggattcctgt acg 431344DNAArtificial SequencePrimer BG3212 13acagtggcgg ccgcgccatt tgatggccct ccttgcggtt ttaa 441445DNAArtificial SequencePrimer BG3076 14cgtatatcaa actttccaat agcatgaaga gcaatgaaaa ataac 451523DNAArtificial SequencePrimer BG3449 15atgataccgc gagacccacg ctc 231624DNAArtificial SequencePrimer BG3451 16cggataaagt tgcaggacca cttc 2417199PRTEscherichia coli 17Met Tyr Leu Ser Lys Val Ile Ile Ala Arg Ala Trp Ser Arg Asp Leu 1 5 10 15 Tyr Gln Leu His Gln Gly Leu Trp His Leu Phe Pro Asn Arg Pro Asp 20 25 30 Ala Ala Arg Asp Phe Leu Phe His Val Glu Lys Arg Asn Thr Pro Glu 35 40 45 Gly Cys His Val Leu Leu Gln Ser Ala Gln Met Pro Val Ser Thr Ala 50 55 60 Val Ala Thr Val Ile Lys Thr Lys Gln Val Glu Phe Gln Leu Gln Val 65 70 75 80 Gly Val Pro Leu Tyr Phe Arg Leu Arg Ala Asn Pro Ile Lys Thr Ile 85 90 95 Leu Asp Asn Gln Lys Arg Leu Asp Ser Lys Gly Asn Ile Lys Arg Cys 100 105 110 Arg Val Pro Leu Ile Lys Glu Ala Glu Gln Ile Ala Trp Leu Gln Arg 115 120 125 Lys Leu Gly Asn Ala Ala Arg Val Glu Asp Val His Pro Ile Ser Glu 130 135 140 Arg Pro Gln Tyr Phe Ser Gly Asp Gly Lys Ser Gly Lys Ile Gln Thr 145 150 155 160 Val Cys Phe Glu Gly Val Leu Thr Ile Asn Asp Ala Pro Ala Leu Ile 165 170 175 Asp Leu Val Gln Gln Gly Ile Gly Pro Ala Lys Ser Met Gly Cys Gly 180 185 190 Leu Leu Ser Leu Ala Pro Leu 195 182154DNAArtificial SequenceFusion protein 18atggctcaac tggttaaaag cgaactggaa gagaaaaaaa gtgaactgcg ccacaaactg 60aaatatgtgc cgcatgaata tatcgagctg attgaaattg cacgtaatcc gacccaggat 120cgtattctgg aaatgaaagt gatggaattt tttatgaaag tgtacggcta tcgcggtgaa 180catctgggtg gtagccgtaa accggatggt gcaatttata ccgttggtag cccgattgat 240tatggtgtta ttgttgatac caaagcctat agcggtggtt ataatctgcc gattggtcag 300gcagatgaaa tggaacgtta tgtggaagaa aatcagaccc gtgataaaca tctgaatccg 360aatgaatggt ggaaagttta tccgagcagc gttaccgagt ttaaattcct gtttgttagc 420ggtcacttca aaggcaacta taaagcacag ctgacccgtc tgaatcatat taccaattgt 480aatggtgcag ttctgagcgt tgaagaactg ctgattggtg gtgaaatgat taaagcaggc 540accctgaccc tggaagaagt tcgtcgcaaa tttaacaatg gcgaaatcaa ctttgcggat 600cccaccaacc gcgcgaaagg cctggaagcg gtgagcgtgg cgagcatgaa tttgcttatt 660gataactgga ttcctgtacg cccgcgaaac ggggggaaag tccaaatcat aaatctgcaa 720tcgctatact gcagtagaga tcagtggcga ttaagtttgc cccgtgacga tatggaactg 780gccgctttag cactgctggt

ttgcattggg caaattatcg ccccggcaaa agatgacgtt 840gaatttcgac atcgcataat gaatccgctc actgaagatg agtttcaaca actcatcgcg 900ccgtggatag atatgttcta ccttaatcac gcagaacatc cctttatgca gaccaaaggt 960gtcaaagcaa atgatgtgac tccaatggaa aaactgttgg ctggggtaag cggcgcgacg 1020aattgtgcat ttgtcaatca accggggcag ggtgaagcat tatgtggtgg atgcactgcg 1080attgcgttat tcaaccaggc gaatcaggca ccaggttttg gtggtggttt taaaagcggt 1140ttacgtggag gaacacctgt aacaacgttc gtacgtggga tcgatcttcg ttcaacggtg 1200ttactcaatg tcctcacatt acctcgtctt caaaaacaat ttcctaatga atcacatacg 1260gaaaaccaac ctacctggat taaacctatc aagtccaatg agtctatacc tgcttcgtca 1320attgggtttg tccgtggtct attctggcaa ccagcgcata ttgaattatg cgatcccatt 1380gggattggta aatgttcttg ctgtggacag gaaagcaatt tgcgttatac cggttttctt 1440aaggaaaaat ttacctttac agttaatggg ctatggcccc atccgcattc cccttgtctg 1500gtaacagtca agaaagggga ggttgaggaa aaatttcttg ctttcaccac ctccgcacca 1560tcatggacac aaatcagccg agttgtggta gataagatta ttcaaaatga aaatggaaat 1620cgcgtggcgg cggttgtgaa tcaattcaga aatattgcgc cgcaaagtcc tcttgaattg 1680attatggggg gatatcgtaa taatcaagca tctattcttg aacggcgtca tgatgtgttg 1740atgtttaatc aggggtggca acaatacggc aatgtgataa acgaaatagt gactgttggt 1800ttgggatata aaacagcctt acgcaaggcg ttatatacct ttgcagaagg gtttaaaaat 1860aaagacttca aaggggccgg agtctctgtt catgagactg cagaaaggca tttctatcga 1920cagagtgaat tattaattcc cgatgtactg gcgaatgtta atttttccca ggctgatgag 1980gtaatagctg atttacgaga caaacttcat caattgtgtg aaatgctatt taatcaatct 2040gtagctccct atgcacatca tcctaaatta ataagcacat tagcgcttgc ccgcgccacg 2100ctatacaaac atttacggga gttaaaaccg caaggagggc catcaaatgg ctga 215419717PRTArtificial SequenceFusion protein 19Met Ala Gln Leu Val Lys Ser Glu Leu Glu Glu Lys Lys Ser Glu Leu 1 5 10 15 Arg His Lys Leu Lys Tyr Val Pro His Glu Tyr Ile Glu Leu Ile Glu 20 25 30 Ile Ala Arg Asn Pro Thr Gln Asp Arg Ile Leu Glu Met Lys Val Met 35 40 45 Glu Phe Phe Met Lys Val Tyr Gly Tyr Arg Gly Glu His Leu Gly Gly 50 55 60 Ser Arg Lys Pro Asp Gly Ala Ile Tyr Thr Val Gly Ser Pro Ile Asp 65 70 75 80 Tyr Gly Val Ile Val Asp Thr Lys Ala Tyr Ser Gly Gly Tyr Asn Leu 85 90 95 Pro Ile Gly Gln Ala Asp Glu Met Glu Arg Tyr Val Glu Glu Asn Gln 100 105 110 Thr Arg Asp Lys His Leu Asn Pro Asn Glu Trp Trp Lys Val Tyr Pro 115 120 125 Ser Ser Val Thr Glu Phe Lys Phe Leu Phe Val Ser Gly His Phe Lys 130 135 140 Gly Asn Tyr Lys Ala Gln Leu Thr Arg Leu Asn His Ile Thr Asn Cys 145 150 155 160 Asn Gly Ala Val Leu Ser Val Glu Glu Leu Leu Ile Gly Gly Glu Met 165 170 175 Ile Lys Ala Gly Thr Leu Thr Leu Glu Glu Val Arg Arg Lys Phe Asn 180 185 190 Asn Gly Glu Ile Asn Phe Ala Asp Pro Thr Asn Arg Ala Lys Gly Leu 195 200 205 Glu Ala Val Ser Val Ala Ser Met Asn Leu Leu Ile Asp Asn Trp Ile 210 215 220 Pro Val Arg Pro Arg Asn Gly Gly Lys Val Gln Ile Ile Asn Leu Gln 225 230 235 240 Ser Leu Tyr Cys Ser Arg Asp Gln Trp Arg Leu Ser Leu Pro Arg Asp 245 250 255 Asp Met Glu Leu Ala Ala Leu Ala Leu Leu Val Cys Ile Gly Gln Ile 260 265 270 Ile Ala Pro Ala Lys Asp Asp Val Glu Phe Arg His Arg Ile Met Asn 275 280 285 Pro Leu Thr Glu Asp Glu Phe Gln Gln Leu Ile Ala Pro Trp Ile Asp 290 295 300 Met Phe Tyr Leu Asn His Ala Glu His Pro Phe Met Gln Thr Lys Gly 305 310 315 320 Val Lys Ala Asn Asp Val Thr Pro Met Glu Lys Leu Leu Ala Gly Val 325 330 335 Ser Gly Ala Thr Asn Cys Ala Phe Val Asn Gln Pro Gly Gln Gly Glu 340 345 350 Ala Leu Cys Gly Gly Cys Thr Ala Ile Ala Leu Phe Asn Gln Ala Asn 355 360 365 Gln Ala Pro Gly Phe Gly Gly Gly Phe Lys Ser Gly Leu Arg Gly Gly 370 375 380 Thr Pro Val Thr Thr Phe Val Arg Gly Ile Asp Leu Arg Ser Thr Val 385 390 395 400 Leu Leu Asn Val Leu Thr Leu Pro Arg Leu Gln Lys Gln Phe Pro Asn 405 410 415 Glu Ser His Thr Glu Asn Gln Pro Thr Trp Ile Lys Pro Ile Lys Ser 420 425 430 Asn Glu Ser Ile Pro Ala Ser Ser Ile Gly Phe Val Arg Gly Leu Phe 435 440 445 Trp Gln Pro Ala His Ile Glu Leu Cys Asp Pro Ile Gly Ile Gly Lys 450 455 460 Cys Ser Cys Cys Gly Gln Glu Ser Asn Leu Arg Tyr Thr Gly Phe Leu 465 470 475 480 Lys Glu Lys Phe Thr Phe Thr Val Asn Gly Leu Trp Pro His Pro His 485 490 495 Ser Pro Cys Leu Val Thr Val Lys Lys Gly Glu Val Glu Glu Lys Phe 500 505 510 Leu Ala Phe Thr Thr Ser Ala Pro Ser Trp Thr Gln Ile Ser Arg Val 515 520 525 Val Val Asp Lys Ile Ile Gln Asn Glu Asn Gly Asn Arg Val Ala Ala 530 535 540 Val Val Asn Gln Phe Arg Asn Ile Ala Pro Gln Ser Pro Leu Glu Leu 545 550 555 560 Ile Met Gly Gly Tyr Arg Asn Asn Gln Ala Ser Ile Leu Glu Arg Arg 565 570 575 His Asp Val Leu Met Phe Asn Gln Gly Trp Gln Gln Tyr Gly Asn Val 580 585 590 Ile Asn Glu Ile Val Thr Val Gly Leu Gly Tyr Lys Thr Ala Leu Arg 595 600 605 Lys Ala Leu Tyr Thr Phe Ala Glu Gly Phe Lys Asn Lys Asp Phe Lys 610 615 620 Gly Ala Gly Val Ser Val His Glu Thr Ala Glu Arg His Phe Tyr Arg 625 630 635 640 Gln Ser Glu Leu Leu Ile Pro Asp Val Leu Ala Asn Val Asn Phe Ser 645 650 655 Gln Ala Asp Glu Val Ile Ala Asp Leu Arg Asp Lys Leu His Gln Leu 660 665 670 Cys Glu Met Leu Phe Asn Gln Ser Val Ala Pro Tyr Ala His His Pro 675 680 685 Lys Leu Ile Ser Thr Leu Ala Leu Ala Arg Ala Thr Leu Tyr Lys His 690 695 700 Leu Arg Glu Leu Lys Pro Gln Gly Gly Pro Ser Asn Gly 705 710 715 202154DNAArtificial SequenceFusion protein 20atggctcaac tggttaaaag cgaactggaa gagaaaaaaa gtgaactgcg ccacaaactg 60aaatatgtgc cgcatgaata tatcgagctg attgaaattg cacgtaatcc gacccaggat 120cgtattctgg aaatgaaagt gatggaattt tttatgaaag tgtacggcta tcgcggtgaa 180catctgggtg gtagccgtaa accggatggt gcaatttata ccgttggtag cccgattgat 240tatggtgtta ttgttgatac caaagcctat agcggtggtt ataatctgcc gattggtcag 300gcagatgaaa tgcagcgtta tgtgaaagaa aatcagaccc gcaacaaaca tattaacccg 360aatgaatggt ggaaagttta tccgagcagc gttaccgagt ttaaattcct gtttgttagc 420ggtcacttca aaggcaacta taaagcacag ctgacccgtc tgaatcgtaa aaccaattgt 480aatggtgcag ttctgagcgt tgaagaactg ctgattggtg gtgaaatgat taaagcaggc 540accctgaccc tggaagaagt tcgtcgcaaa tttaacaatg gcgaaatcaa ctttgcggat 600cccaccaacc gcgcgaaagg cctggaagcg gtgagcgtgg cgagcatgaa tttgcttatt 660gataactgga ttcctgtacg cccgcgaaac ggggggaaag tccaaatcat aaatctgcaa 720tcgctatact gcagtagaga tcagtggcga ttaagtttgc cccgtgacga tatggaactg 780gccgctttag cactgctggt ttgcattggg caaattatcg ccccggcaaa agatgacgtt 840gaatttcgac atcgcataat gaatccgctc actgaagatg agtttcaaca actcatcgcg 900ccgtggatag atatgttcta ccttaatcac gcagaacatc cctttatgca gaccaaaggt 960gtcaaagcaa atgatgtgac tccaatggaa aaactgttgg ctggggtaag cggcgcgacg 1020aattgtgcat ttgtcaatca accggggcag ggtgaagcat tatgtggtgg atgcactgcg 1080attgcgttat tcaaccaggc gaatcaggca ccaggttttg gtggtggttt taaaagcggt 1140ttacgtggag gaacacctgt aacaacgttc gtacgtggga tcgatcttcg ttcaacggtg 1200ttactcaatg tcctcacatt acctcgtctt caaaaacaat ttcctaatga atcacatacg 1260gaaaaccaac ctacctggat taaacctatc aagtccaatg agtctatacc tgcttcgtca 1320attgggtttg tccgtggtct attctggcaa ccagcgcata ttgaattatg cgatcccatt 1380gggattggta aatgttcttg ctgtggacag gaaagcaatt tgcgttatac cggttttctt 1440aaggaaaaat ttacctttac agttaatggg ctatggcccc atccgcattc cccttgtctg 1500gtaacagtca agaaagggga ggttgaggaa aaatttcttg ctttcaccac ctccgcacca 1560tcatggacac aaatcagccg agttgtggta gataagatta ttcaaaatga aaatggaaat 1620cgcgtggcgg cggttgtgaa tcaattcaga aatattgcgc cgcaaagtcc tcttgaattg 1680attatggggg gatatcgtaa taatcaagca tctattcttg aacggcgtca tgatgtgttg 1740atgtttaatc aggggtggca acaatacggc aatgtgataa acgaaatagt gactgttggt 1800ttgggatata aaacagcctt acgcaaggcg ttatatacct ttgcagaagg gtttaaaaat 1860aaagacttca aaggggccgg agtctctgtt catgagactg cagaaaggca tttctatcga 1920cagagtgaat tattaattcc cgatgtactg gcgaatgtta atttttccca ggctgatgag 1980gtaatagctg atttacgaga caaacttcat caattgtgtg aaatgctatt taatcaatct 2040gtagctccct atgcacatca tcctaaatta ataagcacat tagcgcttgc ccgcgccacg 2100ctatacaaac atttacggga gttaaaaccg caaggagggc catcaaatgg ctga 215421717PRTArtificial SequenceFusion protein 21Met Ala Gln Leu Val Lys Ser Glu Leu Glu Glu Lys Lys Ser Glu Leu 1 5 10 15 Arg His Lys Leu Lys Tyr Val Pro His Glu Tyr Ile Glu Leu Ile Glu 20 25 30 Ile Ala Arg Asn Pro Thr Gln Asp Arg Ile Leu Glu Met Lys Val Met 35 40 45 Glu Phe Phe Met Lys Val Tyr Gly Tyr Arg Gly Glu His Leu Gly Gly 50 55 60 Ser Arg Lys Pro Asp Gly Ala Ile Tyr Thr Val Gly Ser Pro Ile Asp 65 70 75 80 Tyr Gly Val Ile Val Asp Thr Lys Ala Tyr Ser Gly Gly Tyr Asn Leu 85 90 95 Pro Ile Gly Gln Ala Asp Glu Met Gln Arg Tyr Val Lys Glu Asn Gln 100 105 110 Thr Arg Asn Lys His Ile Asn Pro Asn Glu Trp Trp Lys Val Tyr Pro 115 120 125 Ser Ser Val Thr Glu Phe Lys Phe Leu Phe Val Ser Gly His Phe Lys 130 135 140 Gly Asn Tyr Lys Ala Gln Leu Thr Arg Leu Asn Arg Lys Thr Asn Cys 145 150 155 160 Asn Gly Ala Val Leu Ser Val Glu Glu Leu Leu Ile Gly Gly Glu Met 165 170 175 Ile Lys Ala Gly Thr Leu Thr Leu Glu Glu Val Arg Arg Lys Phe Asn 180 185 190 Asn Gly Glu Ile Asn Phe Ala Asp Pro Thr Asn Arg Ala Lys Gly Leu 195 200 205 Glu Ala Val Ser Val Ala Ser Met Asn Leu Leu Ile Asp Asn Trp Ile 210 215 220 Pro Val Arg Pro Arg Asn Gly Gly Lys Val Gln Ile Ile Asn Leu Gln 225 230 235 240 Ser Leu Tyr Cys Ser Arg Asp Gln Trp Arg Leu Ser Leu Pro Arg Asp 245 250 255 Asp Met Glu Leu Ala Ala Leu Ala Leu Leu Val Cys Ile Gly Gln Ile 260 265 270 Ile Ala Pro Ala Lys Asp Asp Val Glu Phe Arg His Arg Ile Met Asn 275 280 285 Pro Leu Thr Glu Asp Glu Phe Gln Gln Leu Ile Ala Pro Trp Ile Asp 290 295 300 Met Phe Tyr Leu Asn His Ala Glu His Pro Phe Met Gln Thr Lys Gly 305 310 315 320 Val Lys Ala Asn Asp Val Thr Pro Met Glu Lys Leu Leu Ala Gly Val 325 330 335 Ser Gly Ala Thr Asn Cys Ala Phe Val Asn Gln Pro Gly Gln Gly Glu 340 345 350 Ala Leu Cys Gly Gly Cys Thr Ala Ile Ala Leu Phe Asn Gln Ala Asn 355 360 365 Gln Ala Pro Gly Phe Gly Gly Gly Phe Lys Ser Gly Leu Arg Gly Gly 370 375 380 Thr Pro Val Thr Thr Phe Val Arg Gly Ile Asp Leu Arg Ser Thr Val 385 390 395 400 Leu Leu Asn Val Leu Thr Leu Pro Arg Leu Gln Lys Gln Phe Pro Asn 405 410 415 Glu Ser His Thr Glu Asn Gln Pro Thr Trp Ile Lys Pro Ile Lys Ser 420 425 430 Asn Glu Ser Ile Pro Ala Ser Ser Ile Gly Phe Val Arg Gly Leu Phe 435 440 445 Trp Gln Pro Ala His Ile Glu Leu Cys Asp Pro Ile Gly Ile Gly Lys 450 455 460 Cys Ser Cys Cys Gly Gln Glu Ser Asn Leu Arg Tyr Thr Gly Phe Leu 465 470 475 480 Lys Glu Lys Phe Thr Phe Thr Val Asn Gly Leu Trp Pro His Pro His 485 490 495 Ser Pro Cys Leu Val Thr Val Lys Lys Gly Glu Val Glu Glu Lys Phe 500 505 510 Leu Ala Phe Thr Thr Ser Ala Pro Ser Trp Thr Gln Ile Ser Arg Val 515 520 525 Val Val Asp Lys Ile Ile Gln Asn Glu Asn Gly Asn Arg Val Ala Ala 530 535 540 Val Val Asn Gln Phe Arg Asn Ile Ala Pro Gln Ser Pro Leu Glu Leu 545 550 555 560 Ile Met Gly Gly Tyr Arg Asn Asn Gln Ala Ser Ile Leu Glu Arg Arg 565 570 575 His Asp Val Leu Met Phe Asn Gln Gly Trp Gln Gln Tyr Gly Asn Val 580 585 590 Ile Asn Glu Ile Val Thr Val Gly Leu Gly Tyr Lys Thr Ala Leu Arg 595 600 605 Lys Ala Leu Tyr Thr Phe Ala Glu Gly Phe Lys Asn Lys Asp Phe Lys 610 615 620 Gly Ala Gly Val Ser Val His Glu Thr Ala Glu Arg His Phe Tyr Arg 625 630 635 640 Gln Ser Glu Leu Leu Ile Pro Asp Val Leu Ala Asn Val Asn Phe Ser 645 650 655 Gln Ala Asp Glu Val Ile Ala Asp Leu Arg Asp Lys Leu His Gln Leu 660 665 670 Cys Glu Met Leu Phe Asn Gln Ser Val Ala Pro Tyr Ala His His Pro 675 680 685 Lys Leu Ile Ser Thr Leu Ala Leu Ala Arg Ala Thr Leu Tyr Lys His 690 695 700 Leu Arg Glu Leu Lys Pro Gln Gly Gly Pro Ser Asn Gly 705 710 715 222235DNAArtificial SequenceFusion protein 22atgcatcacc atcatcacca cccgaaaaaa aagcgcaaag tggatccgaa gaaaaaacgt 60aaagttgaag atccgaaaga catggctcaa ctggttaaaa gcgaactgga agagaaaaaa 120agtgaactgc gccacaaact gaaatatgtg ccgcatgaat atatcgagct gattgaaatt 180gcacgtaatc cgacccagga tcgtattctg gaaatgaaag tgatggaatt ttttatgaaa 240gtgtacggct atcgcggtga acatctgggt ggtagccgta aaccggatgg tgcaatttat 300accgttggta gcccgattga ttatggtgtt attgttgata ccaaagccta tagcggtggt 360tataatctgc cgattggtca ggcagatgaa atgcagcgtt atgtgaaaga aaatcagacc 420cgcaacaaac atattaaccc gaatgaatgg tggaaagttt atccgagcag cgttaccgag 480tttaaattcc tgtttgttag cggtcacttc aaaggcaact ataaagcaca gctgacccgt 540ctgaatcgta aaaccaattg taatggtgca gttctgagcg ttgaagaact gctgattggt 600ggtgaaatga ttaaagcagg caccctgacc ctggaagaag ttcgtcgcaa atttaacaat 660ggcgaaatca actttgcgga tcccaccaac cgcgcgaaag gcctggaagc ggtgagcgtg 720gcgagcatga atttgcttat tgataactgg attcctgtac gcccgcgaaa cggggggaaa 780gtccaaatca taaatctgca atcgctatac tgcagtagag atcagtggcg attaagtttg 840ccccgtgacg atatggaact ggccgcttta gcactgctgg tttgcattgg gcaaattatc 900gccccggcaa aagatgacgt tgaatttcga catcgcataa tgaatccgct cactgaagat 960gagtttcaac aactcatcgc gccgtggata gatatgttct accttaatca cgcagaacat 1020ccctttatgc agaccaaagg tgtcaaagca aatgatgtga ctccaatgga aaaactgttg 1080gctggggtaa gcggcgcgac gaattgtgca tttgtcaatc aaccggggca gggtgaagca 1140ttatgtggtg gatgcactgc gattgcgtta ttcaaccagg cgaatcaggc accaggtttt 1200ggtggtggtt ttaaaagcgg tttacgtgga ggaacacctg taacaacgtt cgtacgtggg 1260atcgatcttc gttcaacggt gttactcaat gtcctcacat tacctcgtct tcaaaaacaa 1320tttcctaatg aatcacatac ggaaaaccaa cctacctgga ttaaacctat caagtccaat 1380gagtctatac ctgcttcgtc aattgggttt gtccgtggtc tattctggca accagcgcat 1440attgaattat gcgatcccat tgggattggt aaatgttctt gctgtggaca ggaaagcaat 1500ttgcgttata ccggttttct taaggaaaaa tttaccttta cagttaatgg gctatggccc 1560catccgcatt ccccttgtct ggtaacagtc aagaaagggg aggttgagga aaaatttctt 1620gctttcacca cctccgcacc atcatggaca caaatcagcc gagttgtggt agataagatt 1680attcaaaatg aaaatggaaa tcgcgtggcg gcggttgtga atcaattcag aaatattgcg 1740ccgcaaagtc ctcttgaatt gattatgggg ggatatcgta ataatcaagc atctattctt 1800gaacggcgtc atgatgtgtt gatgtttaat caggggtggc aacaatacgg caatgtgata 1860aacgaaatag tgactgttgg tttgggatat aaaacagcct tacgcaaggc gttatatacc 1920tttgcagaag ggtttaaaaa taaagacttc aaaggggccg gagtctctgt tcatgagact 1980gcagaaaggc atttctatcg acagagtgaa ttattaattc

ccgatgtact ggcgaatgtt 2040aatttttccc aggctgatga ggtaatagct gatttacgag acaaacttca tcaattgtgt 2100gaaatgctat ttaatcaatc tgtagctccc tatgcacatc atcctaaatt aataagcaca 2160ttagcgcttg cccgcgccac gctatacaaa catttacggg agttaaaacc gcaaggaggg 2220ccatcaaatg gctga 223523744PRTArtificial SequenceFusion protein 23Met His His His His His His Pro Lys Lys Lys Arg Lys Val Asp Pro 1 5 10 15 Lys Lys Lys Arg Lys Val Glu Asp Pro Lys Asp Met Ala Gln Leu Val 20 25 30 Lys Ser Glu Leu Glu Glu Lys Lys Ser Glu Leu Arg His Lys Leu Lys 35 40 45 Tyr Val Pro His Glu Tyr Ile Glu Leu Ile Glu Ile Ala Arg Asn Pro 50 55 60 Thr Gln Asp Arg Ile Leu Glu Met Lys Val Met Glu Phe Phe Met Lys 65 70 75 80 Val Tyr Gly Tyr Arg Gly Glu His Leu Gly Gly Ser Arg Lys Pro Asp 85 90 95 Gly Ala Ile Tyr Thr Val Gly Ser Pro Ile Asp Tyr Gly Val Ile Val 100 105 110 Asp Thr Lys Ala Tyr Ser Gly Gly Tyr Asn Leu Pro Ile Gly Gln Ala 115 120 125 Asp Glu Met Gln Arg Tyr Val Lys Glu Asn Gln Thr Arg Asn Lys His 130 135 140 Ile Asn Pro Asn Glu Trp Trp Lys Val Tyr Pro Ser Ser Val Thr Glu 145 150 155 160 Phe Lys Phe Leu Phe Val Ser Gly His Phe Lys Gly Asn Tyr Lys Ala 165 170 175 Gln Leu Thr Arg Leu Asn Arg Lys Thr Asn Cys Asn Gly Ala Val Leu 180 185 190 Ser Val Glu Glu Leu Leu Ile Gly Gly Glu Met Ile Lys Ala Gly Thr 195 200 205 Leu Thr Leu Glu Glu Val Arg Arg Lys Phe Asn Asn Gly Glu Ile Asn 210 215 220 Phe Ala Asp Pro Thr Asn Arg Ala Lys Gly Leu Glu Ala Val Ser Val 225 230 235 240 Ala Ser Met Asn Leu Leu Ile Asp Asn Trp Ile Pro Val Arg Pro Arg 245 250 255 Asn Gly Gly Lys Val Gln Ile Ile Asn Leu Gln Ser Leu Tyr Cys Ser 260 265 270 Arg Asp Gln Trp Arg Leu Ser Leu Pro Arg Asp Asp Met Glu Leu Ala 275 280 285 Ala Leu Ala Leu Leu Val Cys Ile Gly Gln Ile Ile Ala Pro Ala Lys 290 295 300 Asp Asp Val Glu Phe Arg His Arg Ile Met Asn Pro Leu Thr Glu Asp 305 310 315 320 Glu Phe Gln Gln Leu Ile Ala Pro Trp Ile Asp Met Phe Tyr Leu Asn 325 330 335 His Ala Glu His Pro Phe Met Gln Thr Lys Gly Val Lys Ala Asn Asp 340 345 350 Val Thr Pro Met Glu Lys Leu Leu Ala Gly Val Ser Gly Ala Thr Asn 355 360 365 Cys Ala Phe Val Asn Gln Pro Gly Gln Gly Glu Ala Leu Cys Gly Gly 370 375 380 Cys Thr Ala Ile Ala Leu Phe Asn Gln Ala Asn Gln Ala Pro Gly Phe 385 390 395 400 Gly Gly Gly Phe Lys Ser Gly Leu Arg Gly Gly Thr Pro Val Thr Thr 405 410 415 Phe Val Arg Gly Ile Asp Leu Arg Ser Thr Val Leu Leu Asn Val Leu 420 425 430 Thr Leu Pro Arg Leu Gln Lys Gln Phe Pro Asn Glu Ser His Thr Glu 435 440 445 Asn Gln Pro Thr Trp Ile Lys Pro Ile Lys Ser Asn Glu Ser Ile Pro 450 455 460 Ala Ser Ser Ile Gly Phe Val Arg Gly Leu Phe Trp Gln Pro Ala His 465 470 475 480 Ile Glu Leu Cys Asp Pro Ile Gly Ile Gly Lys Cys Ser Cys Cys Gly 485 490 495 Gln Glu Ser Asn Leu Arg Tyr Thr Gly Phe Leu Lys Glu Lys Phe Thr 500 505 510 Phe Thr Val Asn Gly Leu Trp Pro His Pro His Ser Pro Cys Leu Val 515 520 525 Thr Val Lys Lys Gly Glu Val Glu Glu Lys Phe Leu Ala Phe Thr Thr 530 535 540 Ser Ala Pro Ser Trp Thr Gln Ile Ser Arg Val Val Val Asp Lys Ile 545 550 555 560 Ile Gln Asn Glu Asn Gly Asn Arg Val Ala Ala Val Val Asn Gln Phe 565 570 575 Arg Asn Ile Ala Pro Gln Ser Pro Leu Glu Leu Ile Met Gly Gly Tyr 580 585 590 Arg Asn Asn Gln Ala Ser Ile Leu Glu Arg Arg His Asp Val Leu Met 595 600 605 Phe Asn Gln Gly Trp Gln Gln Tyr Gly Asn Val Ile Asn Glu Ile Val 610 615 620 Thr Val Gly Leu Gly Tyr Lys Thr Ala Leu Arg Lys Ala Leu Tyr Thr 625 630 635 640 Phe Ala Glu Gly Phe Lys Asn Lys Asp Phe Lys Gly Ala Gly Val Ser 645 650 655 Val His Glu Thr Ala Glu Arg His Phe Tyr Arg Gln Ser Glu Leu Leu 660 665 670 Ile Pro Asp Val Leu Ala Asn Val Asn Phe Ser Gln Ala Asp Glu Val 675 680 685 Ile Ala Asp Leu Arg Asp Lys Leu His Gln Leu Cys Glu Met Leu Phe 690 695 700 Asn Gln Ser Val Ala Pro Tyr Ala His His Pro Lys Leu Ile Ser Thr 705 710 715 720 Leu Ala Leu Ala Arg Ala Thr Leu Tyr Lys His Leu Arg Glu Leu Lys 725 730 735 Pro Gln Gly Gly Pro Ser Asn Gly 740 242235DNAArtificial SequenceFusion protein 24atgcatcacc atcatcacca cccgaaaaaa aagcgcaaag tggatccgaa gaaaaaacgt 60aaagttgaag atccgaaaga catggctcaa ctggttaaaa gcgaactgga agagaaaaaa 120agtgaactgc gccacaaact gaaatatgtg ccgcatgaat atatcgagct gattgaaatt 180gcacgtaatc cgacccagga tcgtattctg gaaatgaaag tgatggaatt ttttatgaaa 240gtgtacggct atcgcggtga acatctgggt ggtagccgta aaccggatgg tgcaatttat 300accgttggta gcccgattga ttatggtgtt attgttgata ccaaagccta tagcggtggt 360tataatctgc cgattggtca ggcagatgaa atggaacgtt atgtggaaga aaatcagacc 420cgtgataaac atctgaatcc gaatgaatgg tggaaagttt atccgagcag cgttaccgag 480tttaaattcc tgtttgttag cggtcacttc aaaggcaact ataaagcaca gctgacccgt 540ctgaatcata ttaccaattg taatggtgca gttctgagcg ttgaagaact gctgattggt 600ggtgaaatga ttaaagcagg caccctgacc ctggaagaag ttcgtcgcaa atttaacaat 660ggcgaaatca actttgcgga tcccaccaac cgcgcgaaag gcctggaagc ggtgagcgtg 720gcgagcatga atttgcttat tgataactgg attcctgtac gcccgcgaaa cggggggaaa 780gtccaaatca taaatctgca atcgctatac tgcagtagag atcagtggcg attaagtttg 840ccccgtgacg atatggaact ggccgcttta gcactgctgg tttgcattgg gcaaattatc 900gccccggcaa aagatgacgt tgaatttcga catcgcataa tgaatccgct cactgaagat 960gagtttcaac aactcatcgc gccgtggata gatatgttct accttaatca cgcagaacat 1020ccctttatgc agaccaaagg tgtcaaagca aatgatgtga ctccaatgga aaaactgttg 1080gctggggtaa gcggcgcgac gaattgtgca tttgtcaatc aaccggggca gggtgaagca 1140ttatgtggtg gatgcactgc gattgcgtta ttcaaccagg cgaatcaggc accaggtttt 1200ggtggtggtt ttaaaagcgg tttacgtgga ggaacacctg taacaacgtt cgtacgtggg 1260atcgatcttc gttcaacggt gttactcaat gtcctcacat tacctcgtct tcaaaaacaa 1320tttcctaatg aatcacatac ggaaaaccaa cctacctgga ttaaacctat caagtccaat 1380gagtctatac ctgcttcgtc aattgggttt gtccgtggtc tattctggca accagcgcat 1440attgaattat gcgatcccat tgggattggt aaatgttctt gctgtggaca ggaaagcaat 1500ttgcgttata ccggttttct taaggaaaaa tttaccttta cagttaatgg gctatggccc 1560catccgcatt ccccttgtct ggtaacagtc aagaaagggg aggttgagga aaaatttctt 1620gctttcacca cctccgcacc atcatggaca caaatcagcc gagttgtggt agataagatt 1680attcaaaatg aaaatggaaa tcgcgtggcg gcggttgtga atcaattcag aaatattgcg 1740ccgcaaagtc ctcttgaatt gattatgggg ggatatcgta ataatcaagc atctattctt 1800gaacggcgtc atgatgtgtt gatgtttaat caggggtggc aacaatacgg caatgtgata 1860aacgaaatag tgactgttgg tttgggatat aaaacagcct tacgcaaggc gttatatacc 1920tttgcagaag ggtttaaaaa taaagacttc aaaggggccg gagtctctgt tcatgagact 1980gcagaaaggc atttctatcg acagagtgaa ttattaattc ccgatgtact ggcgaatgtt 2040aatttttccc aggctgatga ggtaatagct gatttacgag acaaacttca tcaattgtgt 2100gaaatgctat ttaatcaatc tgtagctccc tatgcacatc atcctaaatt aataagcaca 2160ttagcgcttg cccgcgccac gctatacaaa catttacggg agttaaaacc gcaaggaggg 2220ccatcaaatg gctga 223525744PRTArtificial SequenceFusion protein 25Met His His His His His His Pro Lys Lys Lys Arg Lys Val Asp Pro 1 5 10 15 Lys Lys Lys Arg Lys Val Glu Asp Pro Lys Asp Met Ala Gln Leu Val 20 25 30 Lys Ser Glu Leu Glu Glu Lys Lys Ser Glu Leu Arg His Lys Leu Lys 35 40 45 Tyr Val Pro His Glu Tyr Ile Glu Leu Ile Glu Ile Ala Arg Asn Pro 50 55 60 Thr Gln Asp Arg Ile Leu Glu Met Lys Val Met Glu Phe Phe Met Lys 65 70 75 80 Val Tyr Gly Tyr Arg Gly Glu His Leu Gly Gly Ser Arg Lys Pro Asp 85 90 95 Gly Ala Ile Tyr Thr Val Gly Ser Pro Ile Asp Tyr Gly Val Ile Val 100 105 110 Asp Thr Lys Ala Tyr Ser Gly Gly Tyr Asn Leu Pro Ile Gly Gln Ala 115 120 125 Asp Glu Met Glu Arg Tyr Val Glu Glu Asn Gln Thr Arg Asp Lys His 130 135 140 Leu Asn Pro Asn Glu Trp Trp Lys Val Tyr Pro Ser Ser Val Thr Glu 145 150 155 160 Phe Lys Phe Leu Phe Val Ser Gly His Phe Lys Gly Asn Tyr Lys Ala 165 170 175 Gln Leu Thr Arg Leu Asn His Ile Thr Asn Cys Asn Gly Ala Val Leu 180 185 190 Ser Val Glu Glu Leu Leu Ile Gly Gly Glu Met Ile Lys Ala Gly Thr 195 200 205 Leu Thr Leu Glu Glu Val Arg Arg Lys Phe Asn Asn Gly Glu Ile Asn 210 215 220 Phe Ala Asp Pro Thr Asn Arg Ala Lys Gly Leu Glu Ala Val Ser Val 225 230 235 240 Ala Ser Met Asn Leu Leu Ile Asp Asn Trp Ile Pro Val Arg Pro Arg 245 250 255 Asn Gly Gly Lys Val Gln Ile Ile Asn Leu Gln Ser Leu Tyr Cys Ser 260 265 270 Arg Asp Gln Trp Arg Leu Ser Leu Pro Arg Asp Asp Met Glu Leu Ala 275 280 285 Ala Leu Ala Leu Leu Val Cys Ile Gly Gln Ile Ile Ala Pro Ala Lys 290 295 300 Asp Asp Val Glu Phe Arg His Arg Ile Met Asn Pro Leu Thr Glu Asp 305 310 315 320 Glu Phe Gln Gln Leu Ile Ala Pro Trp Ile Asp Met Phe Tyr Leu Asn 325 330 335 His Ala Glu His Pro Phe Met Gln Thr Lys Gly Val Lys Ala Asn Asp 340 345 350 Val Thr Pro Met Glu Lys Leu Leu Ala Gly Val Ser Gly Ala Thr Asn 355 360 365 Cys Ala Phe Val Asn Gln Pro Gly Gln Gly Glu Ala Leu Cys Gly Gly 370 375 380 Cys Thr Ala Ile Ala Leu Phe Asn Gln Ala Asn Gln Ala Pro Gly Phe 385 390 395 400 Gly Gly Gly Phe Lys Ser Gly Leu Arg Gly Gly Thr Pro Val Thr Thr 405 410 415 Phe Val Arg Gly Ile Asp Leu Arg Ser Thr Val Leu Leu Asn Val Leu 420 425 430 Thr Leu Pro Arg Leu Gln Lys Gln Phe Pro Asn Glu Ser His Thr Glu 435 440 445 Asn Gln Pro Thr Trp Ile Lys Pro Ile Lys Ser Asn Glu Ser Ile Pro 450 455 460 Ala Ser Ser Ile Gly Phe Val Arg Gly Leu Phe Trp Gln Pro Ala His 465 470 475 480 Ile Glu Leu Cys Asp Pro Ile Gly Ile Gly Lys Cys Ser Cys Cys Gly 485 490 495 Gln Glu Ser Asn Leu Arg Tyr Thr Gly Phe Leu Lys Glu Lys Phe Thr 500 505 510 Phe Thr Val Asn Gly Leu Trp Pro His Pro His Ser Pro Cys Leu Val 515 520 525 Thr Val Lys Lys Gly Glu Val Glu Glu Lys Phe Leu Ala Phe Thr Thr 530 535 540 Ser Ala Pro Ser Trp Thr Gln Ile Ser Arg Val Val Val Asp Lys Ile 545 550 555 560 Ile Gln Asn Glu Asn Gly Asn Arg Val Ala Ala Val Val Asn Gln Phe 565 570 575 Arg Asn Ile Ala Pro Gln Ser Pro Leu Glu Leu Ile Met Gly Gly Tyr 580 585 590 Arg Asn Asn Gln Ala Ser Ile Leu Glu Arg Arg His Asp Val Leu Met 595 600 605 Phe Asn Gln Gly Trp Gln Gln Tyr Gly Asn Val Ile Asn Glu Ile Val 610 615 620 Thr Val Gly Leu Gly Tyr Lys Thr Ala Leu Arg Lys Ala Leu Tyr Thr 625 630 635 640 Phe Ala Glu Gly Phe Lys Asn Lys Asp Phe Lys Gly Ala Gly Val Ser 645 650 655 Val His Glu Thr Ala Glu Arg His Phe Tyr Arg Gln Ser Glu Leu Leu 660 665 670 Ile Pro Asp Val Leu Ala Asn Val Asn Phe Ser Gln Ala Asp Glu Val 675 680 685 Ile Ala Asp Leu Arg Asp Lys Leu His Gln Leu Cys Glu Met Leu Phe 690 695 700 Asn Gln Ser Val Ala Pro Tyr Ala His His Pro Lys Leu Ile Ser Thr 705 710 715 720 Leu Ala Leu Ala Arg Ala Thr Leu Tyr Lys His Leu Arg Glu Leu Lys 725 730 735 Pro Gln Gly Gly Pro Ser Asn Gly 740 26168DNAArtificial SequenceTarget plasmid 26gaattcacaa cggtgagcaa gtcactgttg gcaagccagg atctgaacaa taccgtcttg 60ctttcgagcg ctagctctag aactagtcct cagcctaggc ctcgttccga agctgtcttt 120cgctgctgag ggtgacgatc ccgcataggc ggcctttaac tcggatcc 16827163DNAArtificial SequenceTarget plasmid 27gaattcacaa cggtgagcaa gtcactgttg gcaagccagg atctgaacaa taccgtcttt 60tcgagcgcta gctctagaac tagtcctcag cctaggcctc gttcaagctg tctttcgctg 120ctgagggtga cgatcccgca taggcggcct ttaactcgga tcc 16328158DNAArtificial SequenceTarget plasmid 28gaattcacaa cggtgagcaa gtcactgttg gcaagccagg atctgaacaa taccgtcttc 60gagcgctagc tctagaacta gtcctcagcc taggcctcga agctgtcttt cgctgctgag 120ggtgacgatc ccgcataggc ggcctttaac tcggatcc 15829153DNAArtificial SequenceTarget plasmid 29gaattcacaa cggtgagcaa gtcactgttg gcaagccagg atctgaacaa taccgtcttg 60cgctagctct agaactagtc ctcagcctag gcctaagctg tctttcgctg ctgagggtga 120cgatcccgca taggcggcct ttaactcgga tcc 15330148DNAArtificial SequenceTarget plasmid 30gaattcacaa cggtgagcaa gtcactgttg gcaagccagg atctgaacaa taccgtcttg 60ctagctctag aactagtcct cagcctagga agctgtcttt cgctgctgag ggtgacgatc 120ccgcataggc ggcctttaac tcggatcc 14831143DNAArtificial SequenceTarget plasmid 31gaattcacaa cggtgagcaa gtcactgttg gcaagccagg atctgaacaa taccgtcttc 60tctagaacta gtcctcagcc taggaagctg tctttcgctg ctgagggtga cgatcccgca 120taggcggcct ttaactcgga tcc 1433241DNAArtificial SequenceCleavage product 32cttgcgctag ctctagaact agtcctcagc ctaggcctaa g 413341DNAArtificial SequenceCleavage product 33cttaggccta ggctgaggac tagttctaga gctagcgcaa g 413445DNAArtificial SequenceFill-in ligation 34cttgcgctag ctctagaact agctagtcct cagcctaggc ctaag 453545DNAArtificial SequenceFill-in ligation 35cttaggccta ggctgaggac tagctagttc tagagctagc gcaag 45361100DNAHomo sapiens 36ggtggaacaa gatggattat caagtgtcaa gtccaatcta tgacatcaat tattatacat 60cggagccctg ccaaaaaatc aatgtgaagc aaatcgcagc ccgcctcctg cctccgctct 120actcactggt gttcatcttt ggttttgtgg gcaacatgct ggtcatcctc atcctgataa 180actgcaaaag gctgaagagc atgactgaca tctacctgct caacctggcc atctctgacc 240tgtttttcct tcttactgtc cccttctggg ctcactatgc tgccgcccag tgggactttg 300gaaatacaat gtgtcaactc ttgacagggc tctattttat aggcttcttc tctggaatct 360tcttcatcat cctcctgaca atcgataggt acctggctgt cgtccatgct gtgtttgctt 420taaaagccag gacggtcacc tttggggtgg tgacaagtgt gatcacttgg gtggtggctg 480tgtttgcgtc tctcccagga atcatcttta ccagatctca aaaagaaggt cttcattaca 540cctgcagctc tcattttcca tacagtcagt atcaattctg gaagaatttc cagacattaa 600agatagtcat cttggggctg gtcctgccgc tgcttgtcat ggtcatctgc tactcgggaa 660tcctaaaaac tctgcttcgg tgtcgaaatg agaagaagag gcacagggct gtgaggctta 720tcttcaccat catgattgtt tattttctct tctgggctcc ctacaacatt gtccttctcc 780tgaacacctt ccaggaattc tttggcctga ataattgcag tagctctaac aggttggacc 840aagctatgca ggtgacagag actcttggga tgacgcactg ctgcatcaac cccatcatct 900atgcctttgt cggggagaag ttcagaaact acctcttagt cttcttccaa aagcacattg

960ccaaacgctt ctgcaaatgc tgttctattt tccagcaaga ggctcccgag cgagcaagct 1020cagtttacac ccgatccact ggggagcagg aaatatctgt gggcttgtga cacggactca 1080agtgggctgg tgacccagtc 110037424DNAArtificial SequenceCRISPR array red1 37ccatggtaat acgactcact atagggagaa ttagctgatc tttaataata aggaaatgtt 60acattaaggt tggtgggttg tttttatggg aaaaaatgct ttaagaacaa atgtatactt 120ttagagagtt ccccgcgcca gcggggataa accgcaaaca cagcatggac gacagccagg 180tacctagagt tccccgcgcc agcggggata aaccgcaaac acagcatgga cgacagccag 240gtacctagag ttccccgcgc cagcggggat aaaccgcaaa cacagcatgg acgacagcca 300ggtacctaga gttccccgcg ccagcgggga taaaccgaaa acaaaaggct cagtcggaag 360actgggcctt ttgttttaac cccttggggc ctctaaacgg gtcttgaggg gttttttggg 420tacc 42438424DNAArtificial SequenceCRISPR array red2 38ccatggtaat acgactcact atagggagaa ttagctgatc tttaataata aggaaatgtt 60acattaaggt tggtgggttg tttttatggg aaaaaatgct ttaagaacaa atgtatactt 120ttagagagtt ccccgcgcca gcggggataa accgtgtgat cacttgggtg gtggctgtgt 180ttgcgtgagt tccccgcgcc agcggggata aaccgtgtga tcacttgggt ggtggctgtg 240tttgcgtgag ttccccgcgc cagcggggat aaaccgtgtg atcacttggg tggtggctgt 300gtttgcgtga gttccccgcg ccagcgggga taaaccgaaa acaaaaggct cagtcggaag 360actgggcctt ttgttttaac cccttggggc ctctaaacgg gtcttgaggg gttttttggg 420tacc 4243943DNAArtificial Sequenceplasmid 39aaggatgcca gtgataagtg gaatgccatg tgggctgtca aaa 434043DNAArtificial Sequenceplasmid mutant 1 40aaggatgcga gtgataagtg gaatgccatg tgggctgtca aaa 434119DNAArtificial Sequenceplasmid mutant 2 41gccatgtggg ctgtcaaaa 194223DNAArtificial Sequenceplasmid mutant 3 42gaatgccatg tgggctgtca aaa 23431604PRTStreptomyces sp. SPB78 43Met Pro Asp Gln Leu Asn Ala Pro Thr Pro Leu Gly Asp Arg Leu Thr 1 5 10 15 Gly Ala Val Arg Thr Val Trp Ala Lys His Asp Arg Asp Thr Gly Lys 20 25 30 Trp Leu Pro Leu Trp Arg His Met Thr Asp Ser Ala Ala Val Ala Gly 35 40 45 Leu Leu Trp Asp His Trp Leu Pro Arg Asn Ile Lys Asp Leu Ile Ala 50 55 60 Glu Pro Leu Pro Gly Gly Val Ala Asp Ala Arg Ser Leu Cys Val Trp 65 70 75 80 Leu Ala Gly Thr His Asp Ile Gly Lys Ala Thr Pro Ala Phe Ala Cys 85 90 95 Gln Val Asp Glu Leu Ala Gly Val Met Thr Ala Ala Gly Leu Asp Met 100 105 110 Arg Thr Ser Lys Gln Leu Gly Glu Asp Arg Arg Met Ala Pro His Gly 115 120 125 Leu Ala Gly Gln Val Leu Leu Gln Glu Trp Leu Glu Glu Arg Arg Gly 130 135 140 Trp Thr His Arg Ala Ser Ala Gln Phe Ala Val Val Ala Gly Gly His 145 150 155 160 His Gly Val Pro Pro Asp His Met Gln Leu His Asn Leu Asp Ala His 165 170 175 Pro Glu Leu Leu Arg Thr Gln Gly Leu Ala Glu Ala Gln Trp Arg Ala 180 185 190 Val Gln Asp Glu Leu Leu Asp Ala Cys Ala Leu Val Phe Gly Val Glu 195 200 205 Glu Arg Leu Asp Ala Trp Arg Thr Val Lys Leu Pro Gln Thr Val Gln 210 215 220 Val Leu Leu Thr Ala Thr Val Ile Val Ser Asp Trp Ile Ala Ser Asn 225 230 235 240 Pro Asp Leu Phe Pro Tyr Phe Pro Glu Glu His Pro Arg Glu Glu Ala 245 250 255 Glu Arg Val Ala Ala Ala Trp Gln Gly Leu Leu Leu Pro Ala Pro Trp 260 265 270 Glu Pro Glu Glu Pro Ser Ala Pro Ala Ala Glu Phe Tyr Ala Ser Arg 275 280 285 Phe Ala Leu Pro Pro Gly Ala Val Val Arg Pro Val Gln Glu Gln Ala 290 295 300 Leu Ala Met Ala Arg Asp Met Glu Arg Pro Gly Met Leu Ile Ile Glu 305 310 315 320 Ala Pro Met Gly Glu Gly Lys Thr Glu Ala Ala Leu Ala Val Ala Glu 325 330 335 Val Phe Ala Ala Arg Ser Gly Ala Gly Gly Cys Tyr Val Ala Leu Pro 340 345 350 Thr Met Ala Thr Ser Asn Ala Met Phe Pro Arg Leu Leu Arg Trp Leu 355 360 365 Asp Arg Leu Pro Arg Ala Asp Val Ser Gly Gly Arg Asp His Glu Gln 370 375 380 Arg Ser Val Leu Leu Ala His Ala Lys Ser Ala Leu Gln Glu Asp Tyr 385 390 395 400 Ala Thr Leu Met Arg Glu Ser His Arg Thr Ile Ala Ala Val Asp Ala 405 410 415 Tyr Gly Asp Asp Ser Arg Pro Arg Lys Gly Arg Pro Ala Ala Asp Gly 420 425 430 Val Arg Arg Lys Ala Pro Ala Glu Leu Val Ala His Gln Trp Leu Arg 435 440 445 Gly Arg Lys Lys Gly Leu Leu Ala Ser Phe Ala Val Gly Thr Ile Asp 450 455 460 Gln Leu Leu Met Ala Gly Leu Lys Ser Arg His Leu Ala Leu Arg His 465 470 475 480 Leu Ala Met Ala Gly Lys Val Val Val Ile Asp Glu Val His Ala Tyr 485 490 495 Asp Thr Tyr Met Asn Ala Tyr Leu Asp Arg Val Leu Ala Trp Leu Gly 500 505 510 Glu Tyr Arg Val Pro Val Val Val Leu Ser Ala Thr Leu Pro Ala Arg 515 520 525 Arg Arg Gly Glu Leu Ala Ala Ala Tyr Thr Gly Glu Asp Ala Gln Ala 530 535 540 Leu Thr Glu Ala Thr Gly Tyr Pro Leu Leu Thr Ala Val Val Pro Gly 545 550 555 560 Arg Glu Ala Val Gln Phe Val Ala Ala Ala Ser Gly Arg Gly Ser Asp 565 570 575 Val Leu Leu Glu Lys Leu Asp Asp Asp Asp Glu Ala Leu Ala Asp Arg 580 585 590 Leu Asp Thr Asp Leu Ala Asp Gly Gly Cys Ala Leu Val Val Arg Asn 595 600 605 Thr Val Asp Arg Val Met Asp Thr Ala Ser Val Leu Arg Glu Arg Phe 610 615 620 Gly Ala Asp His Val Thr Val Ala His Ala Arg Phe Val Asp Leu Asp 625 630 635 640 Arg Ala Arg Lys Asp Ser Glu Leu Leu Ala Arg Phe Gly Pro Pro Asp 645 650 655 Pro Asp Gly Gly Ser Pro Gln Arg Pro Arg Asn Ala His Ile Val Val 660 665 670 Ala Ser Gln Val Ala Glu Gln Ser Leu Asp Val Asp Phe Asp Leu Leu 675 680 685 Val Ser Asp Leu Cys Pro Val Asp Leu Leu Leu Gln Arg Met Gly Arg 690 695 700 Leu His Arg His Pro Arg Gly Arg Asp Gln Glu Arg Arg Pro Ala Arg 705 710 715 720 Leu Arg Gln Ala Arg Cys Leu Val Thr Gly Val Gly Trp Asp Thr Ser 725 730 735 Pro Ala Pro Glu Ala Asp Glu Gly Ser Arg Ala Ile Tyr Gly Ala Tyr 740 745 750 Ser Leu Leu Arg Ser Leu Ala Val Leu Ala Pro His Leu Gly Thr Ala 755 760 765 Gly Ala Ala Gly His Pro Leu Arg Leu Pro Glu Asp Ile Ser Pro Leu 770 775 780 Val Arg Arg Ala Tyr Gly Glu Glu Asp Pro Cys Pro Pro Glu Trp Glu 785 790 795 800 Pro Val Leu Ala Pro Ala Arg Asp Lys Tyr Arg Thr Ala Arg Glu Arg 805 810 815 Gln Ser Gln Lys Ala Glu Val Phe Arg Leu Asp Glu Val Arg Lys Ala 820 825 830 Gly Arg Pro Leu Ile Gly Trp Ile Asp Ala Gly Val Gly Asp Ala Asp 835 840 845 Asp Thr Pro Val Gly Arg Ala Gln Val Arg Asp Thr Lys Glu Gly Leu 850 855 860 Glu Val Leu Val Val Arg Arg Arg Ala Asp Gly Ser Leu Cys Thr Leu 865 870 875 880 Pro Trp Leu Asp Lys Gly Arg Gly Gly Leu Glu Leu Pro Val Asp Ala 885 890 895 Val Pro Ser Ala Leu Ala Ala Arg Ala Val Ala Ala Ser Gly Leu Arg 900 905 910 Leu Pro Tyr His Phe Thr Ser Ser Pro Gln Thr Leu Asp Arg Thr Leu 915 920 925 Ala Glu Leu Glu Glu Leu Tyr Val Pro Ala Trp Gln Glu Lys Glu Ser 930 935 940 His Trp Ile Ala Gly Glu Leu Ile Leu Ala Leu Asp Glu Glu Gly Arg 945 950 955 960 Ala Ala Leu Ala Gly Gln Gln Leu Val Tyr Asn Pro Glu Glu Gly Leu 965 970 975 Leu Val Ala Ser Ala Asp Ala Asn Thr Glu Ala Thr Ser Gly Arg Val 980 985 990 Met Asp Gly Lys Pro Ser Ser Ala Gly Asp Gly Lys Pro Gly His Ala 995 1000 1005 Ala Asp Gly Asn Arg Ala Arg Thr Thr Val Gly Gln Ser Pro Ala 1010 1015 1020 Asp Arg Gln Thr His Gln Pro Pro Glu Gly Glu Arg His Pro Val 1025 1030 1035 Pro Pro Ser Ala Ala Pro Pro Pro Ala Arg Pro Ser Phe Asp Leu 1040 1045 1050 Thr Ser Arg Pro Trp Leu Pro Val Leu Leu Lys Asp Gly Ser Glu 1055 1060 1065 Arg Glu Leu Ser Leu Pro Glu Val Phe Asp Gln Ala Arg Asp Ile 1070 1075 1080 Arg Arg Leu Val Gly Asp Leu Pro Thr Gln Asp Phe Ala Leu Thr 1085 1090 1095 Arg Met Leu Leu Ala Leu Leu Tyr Asp Ala Leu Ser Glu Pro Gly 1100 1105 1110 Gly Asp Met Ala Pro Ala Asp Thr Asp Ala Trp Glu Glu Leu Trp 1115 1120 1125 Leu Ser Gln Ser Ala Tyr Ala Ala Pro Val Ala Ala Tyr Leu His 1130 1135 1140 Arg Tyr Arg Glu Arg Phe Asp Leu Leu His Pro Glu Ser Pro Phe 1145 1150 1155 Phe Gln Thr Pro Gly Leu Arg Thr Ala Lys Asn Glu Val Phe Ser 1160 1165 1170 Leu Asn Arg Leu Val Ala Asp Val Pro Asn Gly Asp Pro Phe Phe 1175 1180 1185 Ser Met Arg Arg Pro Gly Val Asp Arg Leu Gly Phe Ala Glu Ala 1190 1195 1200 Ala Arg Trp Leu Val His Ala Gln Ala Tyr Asp Thr Ser Gly Ile 1205 1210 1215 Lys Thr Gly Ala Val Gly Asp Pro Arg Val Lys Ala Gly Lys Gly 1220 1225 1230 Tyr Pro Gln Gly Pro Ala Trp Ala Gly Asn Leu Gly Gly Val Leu 1235 1240 1245 Leu Glu Gly Asp Asn Leu His Glu Thr Leu Leu Leu Asn Leu Ile 1250 1255 1260 Ala Gly Asp Thr Pro Gly Val His Ala Ala Glu Val Asp Arg Pro 1265 1270 1275 Ala Trp Arg Ala Glu Pro Ser Gly Pro Ala Pro Ala Pro Asp Leu 1280 1285 1290 Gly Leu Arg Pro Tyr Gly Leu Arg Asp Leu Tyr Thr Trp Gln Ser 1295 1300 1305 Arg Arg Ile Arg Leu His His Asp Ala Asp Gly Val His Gly Val 1310 1315 1320 Val Leu Ala Tyr Gly Asp Ser Leu Glu Pro His Asn Arg His Gly 1325 1330 1335 His Glu Pro Met Thr Ser Trp Arg Arg Ser Pro Thr Gln Glu Lys 1340 1345 1350 Lys Arg Gln Glu Asn Leu Val Tyr Leu Pro Arg Glu His Asp Pro 1355 1360 1365 Ser Arg Leu Ala Trp Arg Gly Met Asp Gly Leu Leu Ala Gly Arg 1370 1375 1380 Glu Thr Gly Ser Ala Gln Gly Pro Asp Gly Ala Asp Arg Leu Ala 1385 1390 1395 Pro Lys Val Val Gln Trp Ala Ala Gln Leu Thr Thr Glu Gly Leu 1400 1405 1410 Leu Pro Arg Gly Tyr Leu Ile Arg Thr Arg Val Ile Gly Ala Arg 1415 1420 1425 Tyr Gly Thr Gln Gln Ser Val Ile Asp Glu Val Val Asp Asp Gly 1430 1435 1440 Val Leu Met Pro Ala Val Leu Leu His Glu Ala Asp Arg Arg Tyr 1445 1450 1455 Gly Asp Lys Ala Val Asp Ala Leu His Asp Ala Glu Lys Ala Val 1460 1465 1470 Gly Ala Leu Ala Gln Leu Ala Ala Asp Leu Ala Leu Ala Val Gly 1475 1480 1485 Thr Asp Pro Glu Pro Gly Arg Asn Thr Ala Arg Asp Leu Gly Phe 1490 1495 1500 Gly Thr Leu Asp Thr His Tyr Arg Arg Trp Leu Arg Glu Leu Gly 1505 1510 1515 Gly Thr Ser Asp Pro Glu Glu His Arg Asp Arg Trp Lys Gln Glu 1520 1525 1530 Val Arg Arg Leu Val Ala Glu Leu Gly Glu Arg Leu Leu Asp Gly 1535 1540 1545 Ala Gly Pro Ala Ala Trp Glu Gly Arg Leu Val Glu Thr Gly Lys 1550 1555 1560 Gly Thr Arg Trp Leu Asn Asp Ala Ala Ala Glu Leu Arg Phe Arg 1565 1570 1575 Thr Arg Leu Arg Glu Phe Leu Thr Thr Ala Pro Asp Thr Pro Thr 1580 1585 1590 Ser Pro Arg Pro Ala Pro Val Glu Ser Pro Ala 1595 1600 441559PRTStreptomyces griseus 44Met Ser Asn Thr Pro Met Ser Arg Asp His Pro Glu Ser Leu Ser Ala 1 5 10 15 Tyr Ala Arg Leu Ser Pro Val Ser Arg Thr Ala Trp Gly Lys His Asp 20 25 30 Arg Gln Thr Glu Gln Trp Leu Pro Leu Trp Arg His Met Ala Asp Ser 35 40 45 Ala Ala Val Ala Glu Arg Leu Trp Asp Gln Trp Val Pro Asp Asn Val 50 55 60 Lys Ala Leu Ile Ala Asp Ala Phe Pro Gln Gly Ala Gln Asp Ala Arg 65 70 75 80 Arg Val Ala Val Phe Leu Ala Cys Val His Asp Ile Gly Lys Ala Thr 85 90 95 Pro Ala Phe Ala Cys Gln Val Asp Gly Leu Ala Asp Arg Met Arg Ala 100 105 110 Ala Gly Leu Ser Met Pro Tyr Leu Lys Gln Phe Gly Leu Asp Arg Arg 115 120 125 Met Ala Pro His Gly Leu Ala Gly Gln Leu Leu Leu Gln Glu Trp Leu 130 135 140 Ala Glu Arg Phe Gly Trp Ser Glu Arg Ala Ser Gly Gln Phe Ala Val 145 150 155 160 Val Ala Gly Gly His His Gly Thr Pro Pro Asp His Gln His Ile His 165 170 175 Asp Leu Gly Leu Arg Pro His Leu Leu Arg Thr Ala Gly Glu Ser Gln 180 185 190 Asp Thr Trp Arg Ser Val Gln Asp Glu Leu Met Asp Ala Cys Ala Val 195 200 205 Arg Ala Gly Val Gly Gly Arg Phe Gly Ala Trp Arg Ser Val Arg Leu 210 215 220 Pro Gln Pro Val Gln Val Val Leu Thr Ala Ile Val Ile Val Ser Asp 225 230 235 240 Trp Ile Ala Ser Ser Ser Glu Leu Phe Pro Tyr Asp Pro Ala Ser Trp 245 250 255 Ser Pro Val Gly Pro Glu Gly Glu Gly Arg Arg Leu Thr Ala Ala Trp 260 265 270 Gly Gly Leu Asp Leu Pro Gly Pro Trp Arg Ala Asp Gln Pro Asp Cys 275 280 285 Thr Ala Ala Glu Leu Phe Gly Lys Arg Phe Asp Leu Pro Glu Gly Ala 290 295 300 Gly Val Arg Pro Val Gln Glu Glu Ala Val Arg Val Ala Gln Glu Leu 305 310 315 320 Pro Gly Pro Gly Leu Leu Ile Ile Glu Ala Pro Met Gly Glu Gly Lys 325 330 335 Thr Glu Ala Ala Phe Ala Ala Ala Glu Ile Leu Ala Ala Arg Thr Gly 340 345 350 Ala Gly Gly Cys Leu Val Ala Leu Pro Thr Arg Ala Thr Gly Asp Ala 355 360 365 Met Phe Pro Arg Leu Leu Arg Trp Leu Glu Arg Leu Pro Ser Asp Gly 370 375 380 Pro Arg Ser Val Val Leu Ala His Ala Lys Ala Ala Leu Asn Glu Val 385 390 395 400 Trp Ala Gly Met Thr Lys Ala Asp Arg Arg Lys Ile Thr Ala Val Asp 405 410

415 Leu Asp Ser Gln Val Glu Asp Val Ser Ser Ala Gly Gly Ala Arg Arg 420 425 430 Ala Asn Pro Ala Ser Leu His Ala His Gln Trp Leu Arg Gly Arg Lys 435 440 445 Lys Ala Leu Leu Ser Ser Phe Ala Val Gly Thr Val Asp Gln Val Leu 450 455 460 Phe Ala Gly Leu Lys Ser Arg His Leu Ala Leu Arg His Leu Ala Val 465 470 475 480 Ala Gly Lys Val Val Ile Val Asp Glu Val His Ala Tyr Asp Ala Tyr 485 490 495 Met Ser Ala Tyr Leu Asp Arg Val Leu Glu Trp Leu Ala Ala Tyr Arg 500 505 510 Val Pro Val Val Met Leu Ser Ala Thr Leu Pro Ala His Arg Arg Arg 515 520 525 Glu Leu Ala Ala Ala Tyr Ala Gly Glu Glu Thr Pro Glu Leu Ala Asp 530 535 540 Ala Leu Ala Leu Pro Asp Asp Ala Tyr Pro Leu Ile Thr Ala Val Ala 545 550 555 560 Pro Gly Gly Leu Val Leu Thr Ala Arg Pro Glu Pro Ala Ser Gly Arg 565 570 575 Arg Thr Glu Val Val Leu Glu Arg Leu Gly Asp Gly Pro Ala Leu Leu 580 585 590 Ala Ala Arg Leu Asp Glu Glu Leu Arg Asp Gly Gly Cys Ala Leu Val 595 600 605 Val Arg Asn Thr Val Asp Arg Val Leu Glu Ala Ala Glu His Leu Arg 610 615 620 Ala His Phe Gly Ala Glu Ala Val Thr Val Ala His Ser Arg Phe Val 625 630 635 640 Ala Ala Asp Arg Ala Arg Asn Asp Thr Val Leu Arg Glu Arg Phe Gly 645 650 655 Pro Gly Gly Asp Arg Pro Ala Gly Pro His Ile Val Val Ala Ser Gln 660 665 670 Val Val Glu Gln Ser Leu Asp Ile Asp Phe Asp Leu Leu Val Thr Asp 675 680 685 Leu Ala Pro Val Asp Leu Val Leu Gln Arg Met Gly Arg Leu His Arg 690 695 700 His Pro Arg Thr Arg Pro Pro Arg Leu Ser Arg Ala Arg Cys Leu Ile 705 710 715 720 Thr Gly Val Glu Asp Trp His Ala Glu Arg Pro Val Pro Val Arg Gly 725 730 735 Ser Leu Ala Val Tyr Gln Gly Pro His Thr Leu Leu Arg Ala Leu Ala 740 745 750 Val Leu Gly Pro His Leu Asp Gly Val Pro Leu Val Leu Pro Asp His 755 760 765 Ile Ser Pro Leu Val Gln Ala Ala Tyr Asp Glu Arg Pro Val Gly Pro 770 775 780 Ala His Trp Ala Pro Val Leu Asp Glu Ala Arg Arg Gln Tyr Leu Thr 785 790 795 800 Arg Leu Ala Glu Lys Arg Glu Arg Ala Asp Val Phe Arg Leu Gly Pro 805 810 815 Val Arg Arg Pro Gly Arg Pro Leu Phe Gly Trp Leu Asp Gly Asn Ala 820 825 830 Gly Asp Ala Asp Asp Ser Arg Thr Gly Arg Ala Gln Val Arg Asp Ser 835 840 845 Glu Glu Ser Leu Glu Val Leu Val Val Gln Arg Arg Ala Asp Gly Arg 850 855 860 Leu Thr Thr Val Ser Trp Leu Asp Gly Gly Arg Gly Gly Leu Asp Leu 865 870 875 880 Pro Glu His Ala Pro Pro Pro Pro Arg Ala Ala Glu Val Val Ala Ala 885 890 895 Cys Ala Leu Thr Leu Pro Arg Ser Leu Thr His Pro Gly Val Ile Asp 900 905 910 Arg Thr Ile Ala Glu Leu Glu Arg Phe Val Val Pro Ala Trp Gln Val 915 920 925 Lys Glu Cys Pro Trp Leu Ala Gly Glu Leu Leu Leu Val Leu Asp Glu 930 935 940 Asp Cys Gln Thr Arg Leu Ser Gly Leu Glu Val His Tyr Ser Thr Asp 945 950 955 960 Gln Gly Leu Arg Val Gly Ser Val Gly Thr Arg Ser Thr Asn Arg Ala 965 970 975 Lys Gly Leu Glu Ala Val Ser Val Ala Ser Phe Asp Leu Val Ser Arg 980 985 990 Pro Trp Leu Pro Val Gln Tyr Glu Asp Gly Ala Thr Gly Glu Leu Ser 995 1000 1005 Leu Arg Glu Val Phe Ala Arg Ala Gly Glu Val Arg Arg Leu Val 1010 1015 1020 Gly Asp Leu Pro Thr Gln Glu Leu Ala Leu Leu Arg Leu Leu Leu 1025 1030 1035 Ala Ile Leu Tyr Asp Ala Tyr Asp Glu Ala Pro Gly Arg Ser Gly 1040 1045 1050 Gly Ala Pro Ala Gln Leu Glu Asp Trp Glu Ala Leu Trp Asp Glu 1055 1060 1065 Pro Asp Ser Phe Ala Val Val Ala Gly Tyr Leu Asp Arg His Arg 1070 1075 1080 Asp Arg Phe Asp Leu Leu His Pro Glu Arg Pro Phe Phe Gln Val 1085 1090 1095 Ala Gly Leu His Thr Gln Lys His Glu Val Ala Ser Leu Asn Arg 1100 1105 1110 Ile Val Ala Asp Val Pro Asn Gly Glu Ala Phe Phe Ser Met Arg 1115 1120 1125 Arg Pro Gly Val His Arg Leu Gly Leu Ala Glu Ala Ala Arg Trp 1130 1135 1140 Leu Val His Thr His Ala Tyr Asp Ala Ser Gly Ile Lys Ser Gly 1145 1150 1155 Met Glu Gly Asp Ala Arg Val Lys Gly Gly Lys Val Tyr Pro Gln 1160 1165 1170 Gly Val Gly Trp Val Gly Gly Leu Gly Gly Val Phe Ala Glu Gly 1175 1180 1185 Ala Ser Leu Arg Glu Thr Leu Leu Leu Asn Leu Ile Pro Thr Asp 1190 1195 1200 Glu Asp Ile Leu Thr Ser Glu Pro Lys Ala Asp Leu Pro Val Trp 1205 1210 1215 Arg Arg Glu Thr Pro Pro Gly Pro Gly Val Val Glu Gly Asp Pro 1220 1225 1230 Ser Ala Pro Arg Pro Ala Gly Pro Arg Asp Leu Tyr Thr Trp Gln 1235 1240 1245 Ser Arg Arg Leu Leu Leu His Thr Glu Gly Ser Asp Ala Ile Gly 1250 1255 1260 Val Val Leu Gly Tyr Gly Asp Pro Leu Ser Pro Ala Asn Arg Gln 1265 1270 1275 Lys Thr Glu Pro Met Thr Gly Trp Arg Arg Ser Pro Ala Gln Glu 1280 1285 1290 Lys Lys Leu Gly Arg Pro Leu Val Tyr Leu Pro Arg Gln His Asp 1295 1300 1305 Pro Gly Arg Ala Ala Trp Arg Gly Leu Ala Ser Leu Leu Tyr Pro 1310 1315 1320 Gln Gly Glu Asp Gly Asp Thr Thr Gly Arg Gly Thr Asp Arg Ser 1325 1330 1335 Arg Pro Ala Gly Ile Val Arg Trp Leu Ala Leu Leu Ser Thr Glu 1340 1345 1350 Gly Val Leu Pro Lys Gly Ser Leu Ile Arg Thr Arg Leu Val Gly 1355 1360 1365 Ala Val Tyr Gly Thr Gln Gln Ser Val Val Asp Asp Val Val Asp 1370 1375 1380 Asp Ser Ile Ala Leu Pro Val Val Leu Leu His Gln Asp Arg Arg 1385 1390 1395 Leu His Gly Ala Val Ala Val Asp Ala Val Ala Asp Ala Glu Arg 1400 1405 1410 Ala Val Ser Ala Leu Gly His Leu Ala Gly Asn Leu Ala Arg Ala 1415 1420 1425 Ser Gly Ser Glu Ala Gly Pro Ala Thr Ala Thr Ala Arg Asp Gln 1430 1435 1440 Gly Phe Gly Ala Leu Asp Gly Pro Tyr Arg Arg Trp Leu Val Asp 1445 1450 1455 Leu Ala Glu Asp Thr Asp Leu Glu Arg Ala Arg Ala Ala Trp Arg 1460 1465 1470 Asp Thr Val Arg Leu Val Val Leu Gly Ile Gly Arg Glu Leu Leu 1475 1480 1485 Asp Ala Ala Gly Arg Ala Ala Ala Glu Gly Arg Val Ile Glu Leu 1490 1495 1500 Pro Gly Val Gly Lys Arg Trp Ile Asp Ser Ser Arg Ala Asp Leu 1505 1510 1515 Trp Phe Arg Thr Arg Ile Asn Arg Val Leu Pro Arg Pro Leu Pro 1520 1525 1530 Glu Ala His Ala Pro Thr Ala Asp Ile His Ala Gly His Ala Val 1535 1540 1545 Arg Ala Asp Glu Ala Leu Ser Glu Glu Thr Val 1550 1555 451540PRTCatenulispora acidiphila 45Met Phe Asn Val Gly Ser Thr Arg Cys Trp Gly Asp Gly Gly Leu Arg 1 5 10 15 Asn Ala Ala Glu Asp Leu Ser Ala Ala Thr Arg Ser Ala Trp Ala Lys 20 25 30 Ser Asp Pro Asp Ser Gly Gln Ser Leu Ser Leu Ile Arg His Leu Ala 35 40 45 Asp Ser Ala Ala Ile Ala Glu His Leu Trp Asp Gln Trp Leu Pro Asp 50 55 60 His Val Lys Ser Leu Ile Ala Glu Gly Leu Pro Glu Gly Leu Val Asp 65 70 75 80 Gly Arg Thr Leu Ala Val Trp Leu Ala Gly Thr His Asp Ile Gly Lys 85 90 95 Leu Thr Pro Ala Phe Ala Cys Gln Cys Glu Pro Leu Ala Gln Ala Met 100 105 110 Arg Glu Cys Gly Leu Asp Met Pro Thr Arg Thr Gln Phe Gly Asp Asp 115 120 125 Arg Arg Val Ala Pro His Gly Leu Ala Gly Gln Val Leu Leu Arg Glu 130 135 140 Trp Leu Met Glu Arg His Gly Trp Ser Gly Arg Ser Ala Asp Ala Phe 145 150 155 160 Thr Val Ile Ala Gly Gly His His Gly Val Pro Pro Ser Tyr Ser Gln 165 170 175 Leu His Asp Leu Asp Ala Tyr Pro Glu Leu Leu Arg Thr Pro Gly Ala 180 185 190 Ser Glu Gly Ile Trp Lys Ser Ser Gln His Glu Leu Leu Asp Ala Cys 195 200 205 Ala Val Met Thr Gly Ala Ser Ser Arg Leu Ala His Trp Arg Gly Leu 210 215 220 Arg Leu Ser Gln Gln Ala Gln Val Leu Leu Thr Gly Leu Val Ile Val 225 230 235 240 Ala Asp Trp Ile Ala Ser Asn Thr Asp Leu Phe Pro Tyr Pro Ala Leu 245 250 255 Gly Thr Gly Glu Ala Ala Ile Asp Pro Gly Lys Arg Val Glu Leu Ala 260 265 270 Trp Arg Gly Leu Glu Leu Pro Ala Pro Trp Ala Pro Lys Tyr Leu Met 275 280 285 Pro Gly Met Gln Gly Leu Leu Ala Ser Arg Phe Gly Leu Pro Ala Asp 290 295 300 Ala Gln Leu Arg Pro Val Gln Gln Met Ala Val Gln Leu Ala Ser Ala 305 310 315 320 Asn Ala Ala Pro Gly Leu Leu Val Ile Glu Ala Pro Met Gly Glu Gly 325 330 335 Lys Thr Glu Ala Ala Leu Leu Ala Ala Glu Ile Leu Ala Ala Arg Ser 340 345 350 Gly Ala Gly Gly Val Phe Leu Ala Leu Pro Thr Gln Ala Thr Ser Asn 355 360 365 Ala Met Phe Ala Arg Val Val Asn Trp Leu Arg Gln Val Pro Arg Glu 370 375 380 Gly Val Ala Ser Val His Leu Ala His Gly Lys Ala Ala Leu Asp Asp 385 390 395 400 Ala Phe Ala Ser Phe Leu Arg Ala Ala Pro Arg Leu Thr Ser Ile Asp 405 410 415 Ala Asp Gly Tyr Ala Gly Glu Ala Asn Val Arg Arg Asp Arg Arg Ala 420 425 430 Gly Ser Ala Asp Met Val Ala His Gln Trp Leu Arg Gly Arg Lys Lys 435 440 445 Gly Ile Leu Ser Pro Phe Val Val Gly Thr Ile Asp Gln Leu Leu Phe 450 455 460 Thr Gly Leu Lys Ser Arg His Leu Ala Leu Arg His Leu Ala Val Ala 465 470 475 480 Gly Lys Val Val Val Ile Asp Glu Val His Ala Tyr Asp Ala Tyr Met 485 490 495 Ser Val Tyr Leu Glu Arg Val Leu Ser Trp Leu Gly Ala Tyr Arg Val 500 505 510 Pro Val Val Leu Leu Ser Ala Thr Leu Pro Ala Asp Arg Arg Gln Ala 515 520 525 Leu Val Glu Ala Tyr Gly Gly Ile Thr Ser Glu Ala Leu Arg Asp Ala 530 535 540 Arg Glu Ala Tyr Pro Val Leu Thr Ala Val Thr Ile Gly Ala Pro Ala 545 550 555 560 Gln Ala Val Gly Thr Glu Pro Ala Glu Gly Arg Arg Val Asp Val Asn 565 570 575 Val Glu Ala Phe Asp Asp Asp Leu Gly Arg Leu Ala Asp Arg Leu Glu 580 585 590 Ala Glu Leu Val Asp Gly Gly Cys Ala Leu Ile Ile Arg Asn Thr Val 595 600 605 Gly Arg Val Leu Gln Thr Ala Gln Gln Leu Arg Glu Arg Phe Gly Ala 610 615 620 Gly Gln Val Thr Val Ala His Ser Arg Phe Ile Asp Leu Asp Arg Ala 625 630 635 640 Arg Lys Asp Ala Asp Leu Leu Ala Arg Phe Gly His Asp Gly Ala Arg 645 650 655 Pro Arg Arg His Ile Val Val Ala Ser Gln Val Ala Glu Gln Ser Leu 660 665 670 Asp Ile Asp Phe Asp Leu Leu Val Thr Asp Leu Ala Pro Ile Asp Leu 675 680 685 Val Leu Gln Arg Met Gly Arg Val His Arg His His Arg Gly Gly Pro 690 695 700 Glu Gln Ser Glu Arg Pro Pro Ser Leu Arg Thr Ala Arg Cys Leu Val 705 710 715 720 Thr Gly Val Asp Trp Ala Gly Ile Pro Ser Ala Pro Ile Ala Gly Ser 725 730 735 Val Ala Val Tyr Gly Leu His Pro Leu Leu Arg Ser Leu Ala Val Leu 740 745 750 Gln Pro Tyr Leu Thr Gly Ser Ala Leu Thr Leu Pro Gly Asp Ile Asn 755 760 765 Pro Leu Val Gln Cys Ala Tyr Ala Gln Ser Phe Val Ala Pro Thr Gly 770 775 780 Trp Gly Glu Ala Met Asp Ala Ala Gln Ala Glu His Met Ala His Ile 785 790 795 800 Val Gln Gln Arg Glu Gly Ala Met Ala Phe Cys Leu Asp Glu Val Arg 805 810 815 Gly Pro Gly Arg Ser Leu Ile Gly Trp Ile Asp Gly Gly Val Gly Asp 820 825 830 Ala Asp Asp Thr Arg Ala Gly Arg Ala Gln Val Arg Asp Ser Pro Glu 835 840 845 Thr Ile Glu Val Leu Val Val Gln Arg Gly Ser Asp Gly Val Leu Arg 850 855 860 Thr Leu Pro Trp Leu Asp Arg Gly Arg Gly Gly Leu Glu Leu Pro Thr 865 870 875 880 Glu Ala Val Pro Pro Pro Arg Ala Ala Arg Ala Ala Ala Ala Ser Ala 885 890 895 Leu Arg Leu Pro Gly Leu Phe Ala Lys Pro Trp Met Phe Asp Arg Val 900 905 910 Leu Arg Glu Leu Glu Arg Glu Tyr His Glu Ala Trp Gln Ala Lys Glu 915 920 925 Ser Ser Trp Leu Gln Gly Glu Leu Leu Leu Val Leu Asp Glu Glu Cys 930 935 940 Arg Thr Val Leu Ala Gly Tyr Glu Leu Ser Tyr Asn Pro Asp Asp Gly 945 950 955 960 Leu Glu Met Val Met Pro Gly Glu Pro His Ala Ala Val Val Arg Asp 965 970 975 Lys Glu Ala Ser Asp Asp Lys Thr Ala Ser Phe Asp Leu Thr Ser Ala 980 985 990 Pro Trp Leu Pro Val Leu Tyr Ala Asp Gly Met Gln Gly Val Leu Ser 995 1000 1005 Leu Arg Asp Val Phe Ala Gln Ser Asn Leu Ile Arg Arg Leu Val 1010 1015 1020 Gly Asp Leu Pro Thr Gln Asp Phe Ala Leu Leu Arg Leu Leu Leu 1025 1030 1035 Ala Val Leu Tyr Asp Ala Val Asp Gly Pro Arg Asp Gly Gln Asp 1040 1045 1050 Trp Glu Asp Leu Trp Thr Ser Asp Asp Pro Phe Ala Ala Val Pro 1055 1060 1065 Ala Tyr Leu Asp Ser His Arg Glu Arg Phe Asp Leu Leu His Pro 1070 1075 1080 Ala Thr Pro Phe Tyr Gln Val Pro Gly Leu Gln Thr Ala Lys Gly 1085 1090 1095 Glu Val Gly Pro Leu Asn Lys Ile Val Ala Asp Val Pro Asp Gly 1100 1105 1110 Asp Pro Phe Leu Thr Met Arg Met Pro Gly Val Glu Gln Leu Ser 1115

1120 1125 Phe Ala Glu Ala Ala Arg Trp Leu Val His Thr Gln Ala Phe Asp 1130 1135 1140 Thr Ser Gly Ile Lys Ser Gly Val Val Gly Asp Pro Lys Ala Val 1145 1150 1155 Asn Gly Lys Arg Tyr Pro Gln Gly Val Ala Trp Leu Gly Asn Leu 1160 1165 1170 Gly Gly Val Phe Ala Glu Gly Asp Thr Leu Arg Gln Thr Leu Leu 1175 1180 1185 Leu Asn Leu Ile Pro Ala Asp Thr Thr Asn Leu Gln Val Thr Ser 1190 1195 1200 Ala Gln Asp Val Pro Ala Trp Arg Gly Thr Asn Gly Arg Ala Gly 1205 1210 1215 Ser Asp His Ala Asp Ala Glu Pro Arg Val Pro Ala Gly Leu Arg 1220 1225 1230 Asp Leu Tyr Thr Trp Gln Ser Arg Arg Ile Arg Leu Glu Tyr Asp 1235 1240 1245 Thr Arg Gly Val Thr Gly Ala Val Leu Thr Tyr Gly Asp Glu Leu 1250 1255 1260 Thr Ala His Asn Lys His Gly Val Glu Pro Met Thr Gly Trp Arg 1265 1270 1275 Arg Ser Lys Pro Gln Glu Lys Lys Leu Gly Leu Ser Thr Val Tyr 1280 1285 1290 Met Pro Gln Gln His Asp Pro Thr Arg Ala Ala Trp Arg Gly Ile 1295 1300 1305 Glu Ser Leu Leu Ala Gly Ser Ala Gly Ser Gly Ser Ser Gln Thr 1310 1315 1320 Gly Glu Pro Ala Ser His Tyr Arg Pro Lys Ile Val Asp Trp Leu 1325 1330 1335 Gly Glu Leu Ala His His Gly Asn Leu Pro Ser Arg Gly Leu Ile 1340 1345 1350 Arg Val Arg Thr Ser Gly Ala Val Tyr Gly Thr Gln Gln Ser Ile 1355 1360 1365 Ile Asp Glu Val Val Ser Asp Glu Leu Thr Met Ala Val Val Leu 1370 1375 1380 Leu His Glu Asp Asp Pro Arg Phe Gly Lys Ala Ala Val Thr Ala 1385 1390 1395 Val Lys Asp Ala Asp Ser Ala Val Ala Ala Leu Gly Asp Leu Ala 1400 1405 1410 Ser Asp Leu Ala Arg Ala Ala Gly Leu Asp Pro Glu Pro Glu Arg 1415 1420 1425 Val Thr Ala Arg Asp Arg Ala Phe Gly Ala Leu Asp Gly Pro Tyr 1430 1435 1440 Arg Arg Trp Leu Leu Asp Leu Gly Asn Ser Thr Asp Pro Ala Ala 1445 1450 1455 Met Arg Ala Val Trp Gln Gly Arg Val Tyr Asp Ile Ile Ala Val 1460 1465 1470 Gln Gly Gln Met Leu Leu Asp Ser Ala Gly Ser Ala Ala Ala Gln 1475 1480 1485 Gly Arg Met Val Lys Thr Thr Arg Gly Glu Arg Trp Met Asp Asp 1490 1495 1500 Ser Leu Ala Asp Leu Tyr Phe Lys Gly Arg Ile Ala Lys Ala Leu 1505 1510 1515 Ser Ser Arg Leu Gly Lys Lys Pro Thr Asp Pro Gly Glu Pro Val 1520 1525 1530 Gly Ile Gln Glu Asp Pro Ala 1535 1540 461407PRTArtificial SequenceFusion Cas3-Cse1 46Met Glu Pro Phe Lys Tyr Ile Cys His Tyr Trp Gly Lys Ser Ser Lys 1 5 10 15 Ser Leu Thr Lys Gly Asn Asp Ile His Leu Leu Ile Tyr His Cys Leu 20 25 30 Asp Val Ala Ala Val Ala Asp Cys Trp Trp Asp Gln Ser Val Val Leu 35 40 45 Gln Asn Thr Phe Cys Arg Asn Glu Met Leu Ser Lys Gln Arg Val Lys 50 55 60 Ala Trp Leu Leu Phe Phe Ile Ala Leu His Asp Ile Gly Lys Phe Asp 65 70 75 80 Ile Arg Phe Gln Tyr Lys Ser Ala Glu Ser Trp Leu Lys Leu Asn Pro 85 90 95 Ala Thr Pro Ser Leu Asn Gly Pro Ser Thr Gln Met Cys Arg Lys Phe 100 105 110 Asn His Gly Ala Ala Gly Leu Tyr Trp Phe Asn Gln Asp Ser Leu Ser 115 120 125 Glu Gln Ser Leu Gly Asp Phe Phe Ser Phe Phe Asp Ala Ala Pro His 130 135 140 Pro Tyr Glu Ser Trp Phe Pro Trp Val Glu Ala Val Thr Gly His His 145 150 155 160 Gly Phe Ile Leu His Ser Gln Asp Gln Asp Lys Ser Arg Trp Glu Met 165 170 175 Pro Ala Ser Leu Ala Ser Tyr Ala Ala Gln Asp Lys Gln Ala Arg Glu 180 185 190 Glu Trp Ile Ser Val Leu Glu Ala Leu Phe Leu Thr Pro Ala Gly Leu 195 200 205 Ser Ile Asn Asp Ile Pro Pro Asp Cys Ser Ser Leu Leu Ala Gly Phe 210 215 220 Cys Ser Leu Ala Asp Trp Leu Gly Ser Trp Thr Thr Thr Asn Thr Phe 225 230 235 240 Leu Phe Asn Glu Asp Ala Pro Ser Asp Ile Asn Ala Leu Arg Thr Tyr 245 250 255 Phe Gln Asp Arg Gln Gln Asp Ala Ser Arg Val Leu Glu Leu Ser Gly 260 265 270 Leu Val Ser Asn Lys Arg Cys Tyr Glu Gly Val His Ala Leu Leu Asp 275 280 285 Asn Gly Tyr Gln Pro Arg Gln Leu Gln Val Leu Val Asp Ala Leu Pro 290 295 300 Val Ala Pro Gly Leu Thr Val Ile Glu Ala Pro Thr Gly Ser Gly Lys 305 310 315 320 Thr Glu Thr Ala Leu Ala Tyr Ala Trp Lys Leu Ile Asp Gln Gln Ile 325 330 335 Ala Asp Ser Val Ile Phe Ala Leu Pro Thr Gln Ala Thr Ala Asn Ala 340 345 350 Met Leu Thr Arg Met Glu Ala Ser Ala Ser His Leu Phe Ser Ser Pro 355 360 365 Asn Leu Ile Leu Ala His Gly Asn Ser Arg Phe Asn His Leu Phe Gln 370 375 380 Ser Ile Lys Ser Arg Ala Ile Thr Glu Gln Gly Gln Glu Glu Ala Trp 385 390 395 400 Val Gln Cys Cys Gln Trp Leu Ser Gln Ser Asn Lys Lys Val Phe Leu 405 410 415 Gly Gln Ile Gly Val Cys Thr Ile Asp Gln Val Leu Ile Ser Val Leu 420 425 430 Pro Val Lys His Arg Phe Ile Arg Gly Leu Gly Ile Gly Arg Ser Val 435 440 445 Leu Ile Val Asp Glu Val His Ala Tyr Asp Thr Tyr Met Asn Gly Leu 450 455 460 Leu Glu Ala Val Leu Lys Ala Gln Ala Asp Val Gly Gly Ser Val Ile 465 470 475 480 Leu Leu Ser Ala Thr Leu Pro Met Lys Gln Lys Gln Lys Leu Leu Asp 485 490 495 Thr Tyr Gly Leu His Thr Asp Pro Val Glu Asn Asn Ser Ala Tyr Pro 500 505 510 Leu Ile Asn Trp Arg Gly Val Asn Gly Ala Gln Arg Phe Asp Leu Leu 515 520 525 Ala His Pro Glu Gln Leu Pro Pro Arg Phe Ser Ile Gln Pro Glu Pro 530 535 540 Ile Cys Leu Ala Asp Met Leu Pro Asp Leu Thr Met Leu Glu Arg Met 545 550 555 560 Ile Ala Ala Ala Asn Ala Gly Ala Gln Val Cys Leu Ile Cys Asn Leu 565 570 575 Val Asp Val Ala Gln Val Cys Tyr Gln Arg Leu Lys Glu Leu Asn Asn 580 585 590 Thr Gln Val Asp Ile Asp Leu Phe His Ala Arg Phe Thr Leu Asn Asp 595 600 605 Arg Arg Glu Lys Glu Asn Arg Val Ile Ser Asn Phe Gly Lys Asn Gly 610 615 620 Lys Arg Asn Val Gly Arg Ile Leu Val Ala Thr Gln Val Val Glu Gln 625 630 635 640 Ser Leu Asp Val Asp Phe Asp Trp Leu Ile Thr Gln His Cys Pro Ala 645 650 655 Asp Leu Leu Phe Gln Arg Leu Gly Arg Leu His Arg His His Arg Lys 660 665 670 Tyr Arg Pro Ala Gly Phe Glu Ile Pro Val Ala Thr Ile Leu Leu Pro 675 680 685 Asp Gly Glu Gly Tyr Gly Arg His Glu His Ile Tyr Ser Asn Val Arg 690 695 700 Val Met Trp Arg Thr Gln Gln His Ile Glu Glu Leu Asn Gly Ala Ser 705 710 715 720 Leu Phe Phe Pro Asp Ala Tyr Arg Gln Trp Leu Asp Ser Ile Tyr Asp 725 730 735 Asp Ala Glu Met Asp Glu Pro Glu Trp Val Gly Asn Gly Met Asp Lys 740 745 750 Phe Glu Ser Ala Glu Cys Glu Lys Arg Phe Lys Ala Arg Lys Val Leu 755 760 765 Gln Trp Ala Glu Glu Tyr Ser Leu Gln Asp Asn Asp Glu Thr Ile Leu 770 775 780 Ala Val Thr Arg Asp Gly Glu Met Ser Leu Pro Leu Leu Pro Tyr Val 785 790 795 800 Gln Thr Ser Ser Gly Lys Gln Leu Leu Asp Gly Gln Val Tyr Glu Asp 805 810 815 Leu Ser His Glu Gln Gln Tyr Glu Ala Leu Ala Leu Asn Arg Val Asn 820 825 830 Val Pro Phe Thr Trp Lys Arg Ser Phe Ser Glu Val Val Asp Glu Asp 835 840 845 Gly Leu Leu Trp Leu Glu Gly Lys Gln Asn Leu Asp Gly Trp Val Trp 850 855 860 Gln Gly Asn Ser Ile Val Ile Thr Tyr Thr Gly Asp Glu Gly Met Thr 865 870 875 880 Arg Val Ile Pro Ala Asn Pro Lys Gly Asp Pro Thr Asn Arg Ala Lys 885 890 895 Gly Leu Glu Ala Val Ser Val Ala Ser Met Asn Leu Leu Ile Asp Asn 900 905 910 Trp Ile Pro Val Arg Pro Arg Asn Gly Gly Lys Val Gln Ile Ile Asn 915 920 925 Leu Gln Ser Leu Tyr Cys Ser Arg Asp Gln Trp Arg Leu Ser Leu Pro 930 935 940 Arg Asp Asp Met Glu Leu Ala Ala Leu Ala Leu Leu Val Cys Ile Gly 945 950 955 960 Gln Ile Ile Ala Pro Ala Lys Asp Asp Val Glu Phe Arg His Arg Ile 965 970 975 Met Asn Pro Leu Thr Glu Asp Glu Phe Gln Gln Leu Ile Ala Pro Trp 980 985 990 Ile Asp Met Phe Tyr Leu Asn His Ala Glu His Pro Phe Met Gln Thr 995 1000 1005 Lys Gly Val Lys Ala Asn Asp Val Thr Pro Met Glu Lys Leu Leu 1010 1015 1020 Ala Gly Val Ser Gly Ala Thr Asn Cys Ala Phe Val Asn Gln Pro 1025 1030 1035 Gly Gln Gly Glu Ala Leu Cys Gly Gly Cys Thr Ala Ile Ala Leu 1040 1045 1050 Phe Asn Gln Ala Asn Gln Ala Pro Gly Phe Gly Gly Gly Phe Lys 1055 1060 1065 Ser Gly Leu Arg Gly Gly Thr Pro Val Thr Thr Phe Val Arg Gly 1070 1075 1080 Ile Asp Leu Arg Ser Thr Val Leu Leu Asn Val Leu Thr Leu Pro 1085 1090 1095 Arg Leu Gln Lys Gln Phe Pro Asn Glu Ser His Thr Glu Asn Gln 1100 1105 1110 Pro Thr Trp Ile Lys Pro Ile Lys Ser Asn Glu Ser Ile Pro Ala 1115 1120 1125 Ser Ser Ile Gly Phe Val Arg Gly Leu Phe Trp Gln Pro Ala His 1130 1135 1140 Ile Glu Leu Cys Asp Pro Ile Gly Ile Gly Lys Cys Ser Cys Cys 1145 1150 1155 Gly Gln Glu Ser Asn Leu Arg Tyr Thr Gly Phe Leu Lys Glu Lys 1160 1165 1170 Phe Thr Phe Thr Val Asn Gly Leu Trp Pro His Pro His Ser Pro 1175 1180 1185 Cys Leu Val Thr Val Lys Lys Gly Glu Val Glu Glu Lys Phe Leu 1190 1195 1200 Ala Phe Thr Thr Ser Ala Pro Ser Trp Thr Gln Ile Ser Arg Val 1205 1210 1215 Val Val Asp Lys Ile Ile Gln Asn Glu Asn Gly Asn Arg Val Ala 1220 1225 1230 Ala Val Val Asn Gln Phe Arg Asn Ile Ala Pro Gln Ser Pro Leu 1235 1240 1245 Glu Leu Ile Met Gly Gly Tyr Arg Asn Asn Gln Ala Ser Ile Leu 1250 1255 1260 Glu Arg Arg His Asp Val Leu Met Phe Asn Gln Gly Trp Gln Gln 1265 1270 1275 Tyr Gly Asn Val Ile Asn Glu Ile Val Thr Val Gly Leu Gly Tyr 1280 1285 1290 Lys Thr Ala Leu Arg Lys Ala Leu Tyr Thr Phe Ala Glu Gly Phe 1295 1300 1305 Lys Asn Lys Asp Phe Lys Gly Ala Gly Val Ser Val His Glu Thr 1310 1315 1320 Ala Glu Arg His Phe Tyr Arg Gln Ser Glu Leu Leu Ile Pro Asp 1325 1330 1335 Val Leu Ala Asn Val Asn Phe Ser Gln Ala Asp Glu Val Ile Ala 1340 1345 1350 Asp Leu Arg Asp Lys Leu His Gln Leu Cys Glu Met Leu Phe Asn 1355 1360 1365 Gln Ser Val Ala Pro Tyr Ala His His Pro Lys Leu Ile Ser Thr 1370 1375 1380 Leu Ala Leu Ala Arg Ala Thr Leu Tyr Lys His Leu Arg Glu Leu 1385 1390 1395 Lys Pro Gln Gly Gly Pro Ser Asn Gly 1400 1405 4749DNAArtificial SequenceCASCADE sequence cleavage 47ccgtcttgcg ctagctctag aactagtcct cagcctaggc ctaagctgt 49

Claims

1.-46. (canceled)

47. A composition comprising: (a) a double-stranded target nucleic acid comprising a protospacer adjacent motif; and (b) a synthetically constructed non-natural nucleic acid comprising a CRISPR RNA, wherein a spacer portion of said CRISPR RNA is hybridized with one strand of said double-stranded target nucleic acid.

48. The composition of claim 47, wherein said synthetically constructed non-natural nucleic acid comprising a CRISPR RNA is a designed non-natural nucleic acid comprising a CRISPR RNA.

49. The composition of claim 47, wherein said spacer portion of said CRISPR RNA is hybridized adjacent to said protospacer adjacent motif.

50. The composition of claim 47, further comprising a CRISPR associated polypeptide.

51. The composition of claim 50, wherein said CRISPR associated polypeptide is a nuclease.

52. The composition of claim 50, wherein said CRISPR associated polypeptide forms a complex with said double-stranded target nucleic acid.

53. The composition of claim 50, wherein said CRISPR associated polypeptide forms a complex with said CRISPR RNA.

54. The composition of claim 47, wherein said protospacer adjacent motif is located at the 5' end of said double-stranded target nucleic acid.

55. The composition of claim 47, wherein said protospacer adjacent motif is located at the 3' end of said double-stranded target nucleic acid.

56. The composition of claim 47, wherein said protospacer adjacent motif comprises 5'-CTT-3'.

57. The composition of claim 47, wherein said protospacer adjacent motif comprises 5'-CAT-3'.

58. The composition of claim 47, wherein said protospacer adjacent motif comprises 5'-CTC-3'.

59. The composition of claim 47, wherein said protospacer adjacent motif comprises 5'-CCT-3'.

60. The composition of claim 47, wherein one strand of said protospacer adjacent motif comprises a CC dinucleotide.

61. The composition of claim 47, wherein one strand said protospacer adjacent motif comprises a CC dinucleotide, wherein said CC dinucleotide is hybridized with a GG dinucleotide on the other strand of said protospacer adjacent motif.

62. The composition of claim 47, wherein said double-stranded target nucleic acid is DNA.

63. The composition of claim 47, wherein said double-stranded target nucleic acid is a target for genetic modification.

64. The composition of claim 47, wherein said spacer portion of said CRISPR RNA hybridizes to said double-stranded target nucleic acid with a dissociation constant from 1 picomolar to 1 micromolar.

65. The composition of claim 47, wherein said spacer portion of said CRISPR RNA hybridizes to said double-stranded target nucleic acid with a dissociation constant from 1 nanomolar to 100 nanomolar.

66. The composition of claim 47, wherein said spacer portion of said CRISPR RNA is synthetically constructed to hybridize to a sequence of said double-stranded target nucleic acid comprising at least 50% identity to said spacer portion.

67. The composition of claim 47, wherein said CRISPR RNA comprises a handle region.

68. The composition of claim 47, wherein said CRISPR RNA comprises a seed region.

69. The composition of claim 47, wherein said CRISPR RNA comprises a 3' hairpin region.

70. The composition of claim 47, wherein said CRISPR RNA comprises a handle region, a seed region, and 3' hairpin region, or any combination thereof.

71. The composition of claim 70, wherein said handle region is located 5' to said seed region which is located 5' to said spacer portion which is located 5' to said 3' hairpin region.

72. The composition of claim 50, wherein said CRISPR associated polypeptide is adapted to induce a modification in said double-stranded target nucleic acid.

73. The composition of claim 50, wherein said CRISPR associated polypeptide further comprises a polypeptide selected from the group consisting of: helicase, nuclease, methyltransferase, demethylase, acetylase, deacetylase, phosphatase, kinase, transcription activator, RNA polymerase subunit, transcription repressor, DNA binding polypeptide, DNA structuring polypeptide, marker polypeptide, reporter polypeptide, fluorescent polypeptide, ligand binding polypeptide, signal polypeptide, subcellular localization polypeptide, and antibody epitope, or any combination thereof.

74. The composition of claim 50, wherein said CRISPR associated polypeptide further comprises a nuclease.

75. The composition of claim 50, wherein said CRISPR associated polypeptide further comprises a helicase.

76. The composition of claim 50, wherein said CRISPR associated polypeptide further comprises a transcription activator.

77. The composition of claim 50, wherein said CRISPR associated polypeptide further comprises a transcription repressor.

78. The composition of claim 47, wherein said double-stranded target nucleic acid is bound to a solid support.

79. A method of synthesizing a synthetically constructed non-natural CRISPR RNA comprising: synthesizing the synthetically constructed non-natural nucleic acid of claim 47.

80. A composition comprising: a nucleic acid-targeting nucleic acid comprising: (a) a synthetically constructed non-natural spacer region adapted to hybridize to one strand of a double-stranded target nucleic acid comprising a protospacer adjacent motif; (b) a nucleic acid duplex; (c) a linker linking both strands of said duplex, wherein at least one strand of said duplex is adapted to form a complex with a CRISPR associated polypeptide.

81. The composition of claim 80, wherein said duplex comprises a hairpin.

82. The composition of claim 81, wherein said duplex is 3' to said synthetically constructed non-natural spacer region.

83. The composition of claim 80, wherein said linker comprises a tetranucleotide loop.

84. The composition of claim 80, wherein said synthetically constructed non-natural spacer region is 5' to said duplex.

85. The composition of claim 80, wherein said synthetically constructed non-natural spacer region hybridizes adjacent to said protospacer adajcent motif of said one strand of said double-stranded target nucleic acid.

86. The composition of claim 80, wherein said spacer region comprises a seed region.

87. The composition of claim 80, wherein said CRISPR associated polypeptide is a nuclease.

88. The composition of claim 80, wherein said protospacer adjacent motif is located at the 5' end of said double-stranded target nucleic acid.

89. The composition of claim 80, wherein said protospacer adjacent motif is located at the 3' end of said double-stranded target nucleic acid.

90. The composition of claim 80, wherein said protospacer adjacent motif comprises 5'-CTT-3'.

91. The composition of claim 80, wherein said protospacer adjacent motif comprises 5'-CAT-3'.

92. The composition of claim 80, wherein said protospacer adjacent motif comprises 5'-CTC-3'.

93. The composition of claim 80, wherein said protospacer adjacent motif comprises 5'-CCT-3'.

94. The composition of claim 80, wherein one strand of said protospacer adjacent motif comprises a CC dinucleotide.

95. The composition of claim 80, wherein one strand said protospacer adjacent motif comprises a CC dinucleotide, wherein said CC dinucleotide is hybridized with a GG dinucleotide on the other strand of said protospacer adjacent motif.

96. The composition of claim 80, wherein said double-stranded target nucleic acid is DNA.

97. The composition of claim 80, wherein said double-stranded target nucleic acid is a target for genetic modification.

98. The composition of claim 80, wherein said synthetically constructed spacer region hybridizes to said double-stranded target nucleic acid with a dissociation constant from 1 picomolar to 1 micromolar.

99. The composition of claim 80, wherein said synthetically constructed spacer region hybridizes to said double-stranded target nucleic acid with a dissociation constant from 1 nanomolar to 100 nanomolar.

100. The composition of claim 80, wherein said synthetically constructed spacer region is synthetically constructed to hybridize to a sequence of said double-stranded target nucleic acid comprising at least 50% identity to said synthetically constructed spacer region.

101. The composition of claim 80, wherein said nucleic acid-targeting nucleic acid is from 35-75 nucleotides in length.

102. The composition of claim 80, further comprising a delivery vehicle.

103. The composition of claim 102, wherein said delivery vehicle comprises a virus.

104. The composition of claim 102, wherein said delivery vehicle comprises adenovirus.

105. The composition of claim 102, wherein said delivery vehicle comprises an Agrobacterium.

106. A pharmaceutical composition comprising the composition of claim 80.

107. A method of synthesizing a synthetically constructed non-natural CRISPR RNA comprising: synthesizing the synthetically constructed non-natural nucleic acid of claim 80.

108. The composition of claim 80 for use as a medicament.

109. A composition comprising: a delivery vehicle comprising a CRISPR RNA, wherein a portion of said CRISPR RNA is adapted to hybridize to a region of one strand of a double-stranded target nucleic acid, wherein said region is adjacent to a protospacer adjacent motif.

110. The composition of claim 109, wherein said delivery vehicle is selected from the group consisting of: cationic polymers, lipids, and cell-penetrating peptide, or any combination thereof.

111. The composition of claim 109, wherein said delivery vehicle comprises a virus.

112. The composition of claim 109, wherein said delivery vehicle comprises adenovirus.

113. The composition of claim 109, wherein said delivery vehicle comprises an Agrobacterium.

114. A pharmaceutical composition comprising the composition of claim 109.

115. The composition of claim 109 for use as a medicament.

116. A vector comprising: (a) a first polynucleotide sequence encoding a CRISPR associated polypeptide; and (b) a second polynucleotide sequence encoding a visualizing polypeptide.

117. The vector of claim 116, wherein said CRISPR associated polypeptide comprises nuclease activity.

118. The vector of claim 116, wherein said vector comprises a third polynucleotide sequence encoding for a linker, wherein said third polynucleotide sequence is between said first and second polynucleotide sequences.

119. The vector of claim 116, wherein said vector further comprises a polynucleotide sequence encoding for a CRISPR RNA.

120. The vector of claim 116, wherein said visualizing polypeptide comprises a fluorescent protein.

121. The vector of claim 116, wherein said visualizing polypeptide comprises green fluorescent protein.

122. The vector of claim 116, wherein said visualizing polypeptide comprises yellow fluorescent protein.

123. A pharmaceutical composition comprising: the vector of claim 116.

124. A delivery vehicle comprising: the vector of claim 116.

125. The delivery vehicle of claim 124, wherein said delivery vehicle is selected from the group consisting of: cationic polymers, lipids, and cell-penetrating peptide, or any combination thereof.

126. The delivery vehicle of claim 124, wherein said delivery vehicle comprises a virus.

127. The delivery vehicle of claim 124, wherein said delivery vehicle comprises adenovirus.

128. The delivery vehicle of claim 124, wherein said delivery vehicle comprises an Agrobacterium.

129. A method for modifying a genomic target nucleic acid in a eukaryotic cell comprising: (a) contacting a nucleic acid-targeting nucleic acid with a target nucleic acid, wherein said nucleic acid-targeting nucleic acid comprises a CRISPR RNA; and (b) modifying said target nucleic acid in said eukaryotic cell.

130. The method of claim 129, wherein said target nucleic acid is adjacent to a protospacer adjacent motif.

131. The method of claim 129, wherein a spacer of said nucleic acid-targeting nucleic acid is synthetically constructed.

132. The method of claim 129, wherein said target nucleic acid is single stranded DNA.

133. The method of claim 129, wherein said target nucleic acid is double stranded DNA.

134. The method of claim 129, wherein said target nucleic acid is RNA.

135. The method of claim 129, wherein said target nucleic acid is genomic DNA.

136. The method of claim 129, wherein said contacting comprises hybridizing a portion of said nucleic acid-targeting nucleic acid to said target nucleic acid.

137. The method of claim 129, wherein said contacting comprises binding said nucleic acid-targeting nucleic acid to said target nucleic acid with a dissociation constant of at least 1 micromolar.

138. The method of claim 129, wherein said nucleic acid-targeting nucleic acid is introduced into said eukaryotic cell by a delivery method selected from the group consisting of: microinjection, transfection, electroporation, calcium co-precipitation, cationic polymer and lipid delivery, and cell-penetrating particles, or any combination thereof.

139. The method of claim 129, wherein said contacting comprises hybridizing a synthetically constructed spacer portion of said CRISPR RNA to a sequence of said target nucleic acid comprising at least 50% identity to said synthetically constructed spacer portion.

140. The method of claim 129, wherein said nucleic acid-targeting nucleic acid is RNA.

141. The method of claim 129, wherein said nucleic acid-targeting nucleic acid comprises a handle region.

142. The method of claim 129, wherein said nucleic acid-targeting nucleic acid comprises a seed region.

143. The method of claim 129, wherein said nucleic acid-targeting nucleic acid comprises a spacer region.

144. The method of claim 129, wherein said nucleic acid-targeting nucleic acid comprises a 3' hairpin region.

145. The method of claim 129, wherein said nucleic acid-targeting nucleic acid comprises a handle region, a seed region, a spacer region, and 3' hairpin region, or any combination thereof.

146. The method of claim 145, wherein said handle region is located 5' to said seed region which is located 5' to said spacer region which is located 5' to said 3' hairpin region.

147. The method of claim 129, wherein said modifying comprises cleaving said target nucleic acid.

148. The method of claim 129, wherein said modifying comprises introducing a single-stranded break in said target nucleic acid.

149. The method of claim 129, wherein said modifying comprises introducing a double-stranded break in said target nucleic acid.

150. The method of claim 129, wherein said modifying comprises allowing said target nucleic acid to be visualized.

151. The method of claim 129, wherein said modifying comprises introducing a modification selected from the group consisting of: an organic dye, a radiolabel, and a spin label, or any combination thereof.

152. The method of claim 129, wherein said modifying comprises deleting a portion of said target nucleic acid.

153. The method of claim 129, wherein said modifying is selected from the group consisting of: activating trancription of said target nucleic acid, repressing transcription of said target nucleic acid, or both activating and repressing transcription of said target nucleic acid.

154. The method of claim 129, wherein said modifying comprises inserting a nucleic acid into said target nucleic acid.

155. The method of claim 129, wherein said modifying is performed by a CRISPR associated polypeptide.

156. The method of claim 155, wherein said CRISPR associated polypeptide is a nuclease.

157. The method of claim 129, wherein said cell is an insect cell.

158. The method of claim 129, wherein said cell is a cell of a multicellular organism.

159. The method of claim 129, wherein said cell is a mammalian cell.

160. The method of claim 129, wherein said cell is a mammalian stem cell.

161. The method of claim 129, wherein said cell is a human cell.

162. The method of claim 129, wherein said cell is a human stem cell.

163. The method of claim 129, wherein said cell is a plant cell.

164. The method of claim 129, wherein said cell is an isolated cell.

165. The method of claim 164, wherein said cell is a yeast cell.

166. The method of claim 164, wherein said cell is a fungal cell.

167. A composition comprising: (a) a eukaryotic cell; (b) a double-stranded target nucleic acid in said eukaryotic cell comprising a protospacer adjacent motif; and (c) a non-natural nucleic acid comprising a CRISPR RNA, wherein a spacer portion of said CRISPR RNA is hybridized with one strand of said double-stranded target nucleic acid in said eukaryotic cell.

168. The eukaryotic cell of claim 167, wherein a portion of said CRISPR RNA hybridizes to one strand of a double-stranded target nucleic acid in said eukaryotic cell.

169. The eukaryotic cell of claim 167, wherein said cell is an insect cell.

170. The eukaryotic cell of claim 167, wherein said cell is a cell of a multicellular organism.

171. The eukaryotic cell of claim 167, wherein said cell is a mammalian cell.

172. The eukaryotic cell of claim 167, wherein said cell is a mammalian stem cell.

173. The eukaryotic cell of claim 167, wherein said cell is a human cell.

174. The eukaryotic cell of claim 167, wherein said cell is a human stem cell.

175. The eukaryotic cell of claim 167, wherein said cell is a plant cell.

176. The eukaryotic cell of claim 167, wherein said cell is a cell of a multicellular tissue.

177. The eukaryotic cell of claim 167, wherein said cell is an isolated cell.

178. The eukaryotic cell of claim 167, wherein said cell is a cell of an organ.

179. The eukaryotic cell of claim 167, wherein said cell is a cell of an organism.

180. A method for using a eukaryotic cell comprising: (a) isolating said eukaryotic cell; (b) contacting a target nucleic acid in said cell with a complex comprising: (i) a CRISPR RNA; and (ii) a CRISPR associated polypeptide; (c) modifying said target nucleic acid; and (d) relocating said eukaryotic cell.

181. The method of claim 180, wherein said isolating comprises isolating from a whole tissue.

182. The method of claim 180, wherein said isolating comprises isolating from an organ.

183. The method of claim 180, wherein said isolating comprises isolating from an organism.

184. The method of claim 180, wherein said relocating comprises transplanting said cell to a different location from which said cell originated.

185. The method of claim 180, wherein said relocating comprises transplanting said cell to a different organism from which said cell originated.

186. The method of claim 180, wherein said relocating comprises transplanting said cell to a same location from which said cell originated.

187. The method of claim 180, wherein said relocating comprises transplanting said cell to a same organism from which said cell originated.

188. The method of claim 180, wherein said relocating comprises a transplanting method selected from the group consisting of: allograft transplant, autograft transplant, isograft transplant, and xenograft transplant, or any combination thereof.

189. The method of claim 180, wherein said contacting comprises hybridizing a portion of said nucleic acid-targeting nucleic acid to said target nucleic acid.

190. The method of claim 180, wherein said contacting comprises hybridizing a portion of said CRISPR RNA to said target nucleic acid with a dissociation constant from 1 picomolar to 1 micromolar.

191. The method of claim 180, wherein said contacting comprises hybridizing a portion of said CRISPR RNA to said target nucleic acid with a dissociation constant from 1 nanomolar to 100 nanomolar.

192. The method of claim 180, wherein said contacting comprises introducing said nucleic acid-targeting nucleic acid by a delivery method selected from the group consisting of: microinjection, transfection, electroporation, calcium co-precipitation, cationic polymer and lipid delivery, and cell-penetrating particles, or any combination thereof.

193. The method of claim 180, wherein said contacting comprises contacting said complex to said target nucleic acid at a site adjacent to a protospacer adjacent motif.

194. The method of claim 193, wherein said protospacer adjacent motif is located 5' to said target nucleic acid.

195. The method of claim 193, wherein said protospacer adjacent motif is located 3' to said target nucleic acid.

196. The method of claim 193, wherein said protospacer adjacent motif comprises 5'-CTT-3'.

197. The method of claim 193, wherein said protospacer adjacent motif comprises 5'-CAT-3'.

198. The method of claim 193, wherein said protospacer adjacent motif comprises 5'-CTC-3'.

199. The method of claim 193, wherein said protospacer adjacent motif comprises 5'-CCT-3'.

200. The method of claim 180, wherein said target nucleic acid is selected from the group consisting of ssDNA, dsDNA, and RNA.

201. The method of claim 180, wherein said target nucleic acid is DNA.

202. The method of claim 180, wherein said CRISPR associated polypeptide is a nuclease.

203. The method of claim 180, wherein said CRISPR associated polypeptide further comprises a polypeptide selected from the group consisting of: helicase, nuclease, methyltransferase, demthylase, acetylase, deacetylase, phosphatase, kinase, transcription activator, RNA polymerase subunit, transcription repressor, DNA binding polypeptide, DNA structuring polypeptide, marker polypeptide, reporter polypeptide, fluorescent polypeptide, ligand binding polypeptide, signal polypeptide, subcellular localization polypeptide, and antibody epitope, or any combination thereof.

204. The method of claim 180, wherein said CRISPR RNA comprises a handle region.

205. The method of claim 180, wherein said CRISPR RNA comprises a seed region.

206. The method of claim 180, wherein said CRISPR RNA comprises a 3' hairpin region.

207. The method of claim 180, wherein said CRISPR RNA comprises a handle region, a seed region, a spacer region and 3' hairpin region, or any combination thereof.

208. The method of claim 207, wherein said handle region is located 5' to said seed region which is located 5' to said spacer region, which is located 5' to said 3' hairpin region.

209. The method of claim 180, wherein said contacting comprises hybridizing a synthetically constructed spacer portion of said CRISPR RNA to a sequence of said target nucleic acid comprising at least 50% identity to said synthetically constructed spacer portion.

210. The method of claim 180, wherein said nucleic acid-targeting nucleic acid is RNA.

211. The method of claim 180, wherein said modifying comprises cleaving said target nucleic acid.

212. The method of claim 180, wherein said modifying comprises introducing a single-stranded break in said target nucleic acid.

213. The method of claim 180, wherein said modifying comprises introducing a double-stranded break in said target nucleic acid.

214. The method of claim 180, wherein said modifying comprises allowing said target nucleic acid to be visualized.

215. The method of claim 180, wherein said modifying comprises introducing a modification selected from the group consisting of: an organic dye, a radiolabel, and a spin label, or any combination thereof.

216. The method of claim 180, wherein said modifying comprises deleting a portion of said target nucleic acid.

217. The method of claim 180, wherein said modifying is selected from the group consisting of: activating transcription of said target nucleic acid, and repressing transcription of said target nucleic acid, or any combination thereof.

218. The method of claim 180, wherein said modifying comprises inserting a nucleic acid into said target nucleic acid.

219. The method of claim 180, wherein said eukaryotic cell is an insect cell.

220. The method of claim 180, wherein said eukaryotic cell is a mammalian cell.

221. The method of claim 180, wherein said eukaryotic cell is a mammalian stem cell.

222. The method of claim 180, wherein said eukaryotic cell is a human cell.

223. The method of claim 180, wherein said eukaryotic cell is a human stem cell.

224. The method of claim 180, wherein said eukaryotic cell is a plant cell.

225. A CRISPR associated polypeptide comprising: an amino acid sequence comprising XXXNHXNNHXXHH, wherein: (a) "X" signifies an amino acid identical to an amino acid at the same position in SEQ ID NO: 3, "H" signifies an amino acid similar to an amino acid at the same position in SEQ ID NO: 3, and "N" is an any amino acid; and (b) said polypeptide comprises an activity selected from the group consisting of: visualizing activity, nuclease activity, or both visualizing and nuclease activity.

226. The polypeptide of claim 225, further comprising at least 18% identity to SEQ ID NO: 3.

227. The polypeptide of claim 225, further comprising at least 17% identity to SEQ ID NO: 4.

228. The polypeptide of claim 225 further comprising at least 16% identity to SEQ ID NO: 5.

229. The polypeptide of claim 225, wherein said CRISPR associated polypeptide is adapted to induce a modification in said double-stranded target nucleic acid.

230. The polypeptide of claim 229, wherein said modification is adapted to cleave said double-stranded target nucleic acid.

231. The polypeptide of claim 229, wherein said modification comprises introduction of a single-stranded break in said double-stranded target nucleic acid.

232. The polypeptide of claim 229, wherein said modification comprises introduction of a double-stranded break in said double-stranded target nucleic acid.

233. The polypeptide of claim 229, wherein said modification comprises deletion of a portion of said double-stranded target nucleic acid.

234. The polypeptide of claim 229, wherein said modification comprises introduction of a nucleic acid into said double-stranded target nucleic acid.

235. The polypeptide of claim 229, wherein said modification is selected from the group consisting of: a modification to visualize said double-stranded target nucleic acid, a modification to activate trancription of said double-stranded target nucleic acid, and a modification to repress transcription of said double-stranded target nucleic acid, or any combination thereof.

236. The polypeptide of claim 229, wherein said CRISPR associated polypeptide further comprises a polypeptide selected from the group consisting of: helicase, nuclease, methyltransferase, demthylase, acetylase, deacetylase, phosphatase, kinase, transcription activator, RNA polymerase subunit, transcription repressor, DNA binding polypeptide, DNA structuring polypeptide, marker polypeptide, reporter polypeptide, fluorescent polypeptide, ligand binding polypeptide, signal polypeptide, subcellular localization polypeptide, and antibody epitope, or any combination thereof.

237. A pharmaceutical composition comprising: the polypeptide of claim 225.

238. A delivery vehicle comprising: the polypeptide of claim 225.

239. The delivery vehicle of claim 238, wherein said delivery vehicle is selected from the group consisting of: cationic polymers, lipids, cell-penetrating peptide, and viruses, or any combination thereof.

240. A kit comprising: the composition of claim 80.

241. A kit comprising: the composition of claim 109.

242. A kit comprising: the vector of claim 116.

243. A kit comprising: the composition of claim 167.

244. A kit comprising: the polypeptide of claim 225.