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USRE45795E1 - Binding proteins for recognition of DNA - Google Patents

Binding proteins for recognition of DNA Download PDF

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USRE45795E1
USRE45795E1 US10/309,578 US30957802A USRE45795E US RE45795 E1 USRE45795 E1 US RE45795E1 US 30957802 A US30957802 A US 30957802A US RE45795 E USRE45795 E US RE45795E
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zinc finger
binding
sequence
library
zinc
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Yen Choo
Aaron Klug
Isidro Sanchez-Garcia
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Gendaq Ltd
United Kingdom Research and Innovation
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Gendaq Ltd
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Priority claimed from GB9422534A external-priority patent/GB9422534D0/en
Priority claimed from GBGB9514698.1A external-priority patent/GB9514698D0/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K19/00—Hybrid peptides, i.e. peptides covalently bound to nucleic acids, or non-covalently bound protein-protein complexes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity
    • C07K14/4705—Regulators; Modulating activity stimulating, promoting or activating activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1037—Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/02—Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/09—Fusion polypeptide containing a localisation/targetting motif containing a nuclear localisation signal
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/80—Fusion polypeptide containing a DNA binding domain, e.g. Lacl or Tet-repressor
    • C07K2319/81—Fusion polypeptide containing a DNA binding domain, e.g. Lacl or Tet-repressor containing a Zn-finger domain for DNA binding

Definitions

  • This invention relates inter alia to methods of selecting and designing polypeptides comprising zinc finger binding motifs, polypeptides made by the method(s) of the invention and to various applications thereof.
  • Zf zinc finger
  • DNA-binding protein domains are able to discriminate between different DNA sequences.
  • the zinc finger motif has been studied extensively, with a view to providing some insight into this problem, owing to its remarkable prevalence in the eukaryotic genome, and its important role in proteins which control gene expression in Drosophila (e.g. Harrison & Travers 1990 EMBO J. 9, 207-216), the mouse (Christy et al., 1988 Proc. Natl. Acad. Sci. USA 85, 7857-7861) and humans (Kinzler et al., 1988 Nature (London) 332, 371).
  • sequence-specific DNA-binding proteins bind to the DNA double helix by inserting an ⁇ -helix into the major groove (Pabo & Sauer 1992 Annu. Rev. Biochem. 61, 1053-1095; Harrison 1991 Nature (London) 353, 715-719; and Klug 1993 Gene 135, 83-92). Sequence specificity results from the geometrical and chemical complementarity between the amino acid side chains of the ⁇ -helix and the accessible groups exposed on the edges of base-pairs. In addition to this direct reading of the DNA sequence, interactions with the DNA backbone stabilise the complex and are sensitive to the conformation of the nucleic acid, which in turn depends on the base sequence (Dickerson & Drew 1981 J. Mol. Biol. 149, 761-786).
  • the zinc finger of the TFIIIA class is a good candidate for deriving a set of more generally applicable specificity rules owing to its great simplicity of structure and interaction with DNA.
  • the zinc finger is an independently folding domain which uses a zinc ion to stabilise the packing of an antiparallel ⁇ -sheet against an ⁇ -helix (Miller et al., 1985 EMBO J. 4, 1609-1614; Berg 1988 Proc. Natl. Acad. Sci. USA 85, 99-102; and Lee et al., 1989 Science 245, 635-637).
  • each finger is folded so that three amino acids are presented for binding to the DNA target sequence, although binding may be directly through only two of these positions.
  • the protein is made up of three fingers which contact a 9 base pair contiguous sequence of target DNA. A linker sequence is found between fingers which appears to make no direct contact with the nucleic acid.
  • Randomised mutagenesis (at the same postions as those selected by Rebar & Pabo) of finger 1 of Zif 268 with phage display has also been used by Jamieson et al., (1994 Biochemistry 33, 5689-5695) to create novel binding specificity and affinity.
  • Zf protein motifs are widespread in DNA binding proteins and that binding is via three key amino acids, each one contacting a single base pair in the target DNA sequence.
  • Motifs are modular and may be linked together to form a set of fingers which recognise a contiguous DNA sequence (e.g. a three fingered protein will recognise a 9 mer etc).
  • the key residues involved in DNA binding have been identified through sequence data and from structural information. Directed and random mutagenesis has confirmed the role of these amino acids in determining specificity and affinity.
  • Phage display has been used to screen for new binding specificities of random mutants of fingers.
  • a recognition code, to aid design of new finger specificities, has been worked towards although it has been suggested that specificity may be difficult to predict.
  • the invention provides a library of DNA sequences, each sequence encoding at least one zinc finger binding motif for display on a viral particle, the sequences coding for zinc finger binding motifs having random allocation of amino acids at positions ⁇ 1, +2, +3, +6 and at least at one of positions +1, +5 and +8.
  • a zinc finger binding motif is the ⁇ -helical structural motif found in zinc finger binding proteins, well known to those skilled in the art. The above numbering is based on the first amino acid in the ⁇ -helix of the zinc finger binding motif being position +1. It will be apparent to those skilled in the art that the amino acid residue at position ⁇ 1 does not, strictly speaking, form part of the ⁇ -helix of the zinc binding finger motif. Nevertheless, the residue at ⁇ 1 is shown to be very important functionally and is therefore considered as part of the binding motif ⁇ -helix for the purposes of the present invention.
  • the sequences may code for zinc finger binding motifs having random allocation at all of positions +1, +5 and +8.
  • the sequences may also be randomised at other positions (e.g. at position +9, although it is generally preferred to retain an arginine or a lysine residue at this position).
  • allocation of amino acids at the designated “random” positions may be genuinely random, it is preferred to avoid a hydrophobic residue (Phe, Trp or Tyr) or a cysteine residue at such positions.
  • the zinc finger binding motif is present within the context of other amino acids (which may be present in zinc finger proteins), so as to form a zinc finger (which includes an antiparallel ⁇ -sheet).
  • the zinc finger is preferably displayed as part of a zinc finger polypeptide, which polypeptide comprises a plurality of zinc fingers joined by an intervening linker peptide.
  • the library of sequences is such that the zinc finger polypeptide will comprise two or more zinc fingers of defined amino acid sequence (generally the wild type sequence) and one zinc finger having a zinc finger binding motif randomised in the manner defined above. It is preferred that the randomised finger of the polypeptide is positioned between the two or more fingers having defined sequence. The defined fingers will establish the “phase” of binding of the polypeptide to DNA, which helps to increase the binding specificity of the randomised finger.
  • sequences encode the randomised binding motif of the middle finger of the Zif268 polypeptide.
  • sequences also encode those amino acids N-terminal and C-terminal of the middle finger in wild type Zif268, which encode the first and third zinc fingers respectively.
  • the sequence encodes the whole of the Zif268 polypeptide.
  • the invention provides a library of DNA sequences, each sequence encoding the zinc finger binding motif of at least a middle finger of a zinc finger binding polypeptide for display on a viral particle, the sequences coding for the binding motif having random allocation of amino acids at positions ⁇ 1, +2, +3 and +6.
  • the zinc finger polypeptide will be Zif268.
  • the sequences of either library are such that the zinc finger binding domain can be cloned as a fusion with the minor coat protein (pIII) of bacteriophage fd.
  • the encoded polypeptide includes the tripeptide sequence Met-Ala-Glu as the N terminal of the zinc finger domain, which is known to allow expression and display using the bacteriophage fd system.
  • the library comprises 10 6 or more different sequences (ideally, as many as is practicable).
  • the invention provides a method of designing a zinc finger polypeptide for binding to a particular target DNA sequence, comprising screening each of a plurality of zinc finger binding motifs against at least an effective portion of the target DNA sequence and selecting those motifs which bind to the target DNA sequence.
  • An effective portion of the target DNA sequence is a sufficient length of DNA to allow binding of the zinc binding motif to the DNA. This is the minimum sequence information (concerning the target DNA sequence) that is required. Desirably at least two, preferably three or more, rounds of screening are performed.
  • the invention also provides a method of designing a zinc finger polypeptide for binding to a particular target DNA sequence, comprising comparing the binding of each of a plurality of zinc finger binding motifs to one or more DNA triplets, and selecting those motifs exhibiting preferable binding characteristics.
  • the method defined immediately above is preceded by a screening step according to the method defined in the previous paragraph.
  • the first step comprising screening each of a plurality of zinc finger binding motifs (typically in the form of a display library), mainly or wholly on the basis of affinity for the target sequence; the second step comprising comparing binding characteristics of those motifs selected by the initial screening step, and selecting those having preferable binding characteristics for a particular DNA triplet.
  • the plurality of zinc finger binding motifs is screened against a single DNA triplet, it is preferred that the triplet is represented in the target DNA sequence at the appropriate postion. However, it is also desirable to compare the binding of the plurality of zinc binding motifs to one or more DNA triplets not represented in the target DNA sequence (e.g. differing by just one of the three base pairs) in order to compare the specificity of binding of the various binding motifs.
  • the plurality of zinc finger binding motifs may be screened against all 64 possible permutations of 3 DNA bases.
  • zinc finger binding motifs Once suitable zinc finger binding motifs have been identified and obtained, they will advantageously be combined in a single zinc finger polypeptide. Typically this will be accomplished by use of recombinant DNA technology; conveniently a phage display system may be used.
  • the invention provides a DNA library consisting of 64 sequences, each sequence comprising a different one of the 64 possible permutations of three DNA bases in a form suitable for use in the selection method defined above.
  • sequences are associated, or capable of being associated, with separation means.
  • the separation means is selected from one of the following: microtitre plate; magnetic beads; or affinity chromatography column.
  • the sequences are biotinylated.
  • sequences are contained within 12 mini-libraries, as explained elsewhere.
  • the invention provides a zinc finger polypeptide designed by one or both of the methods defined above.
  • the zinc finger polypeptide designed by the method comprises a combination of a plurality of zinc fingers (adjacent zinc fingers being joined by an intervening linker peptide), each finger comprising a zinc finger binding motif.
  • each zinc finger binding motif in the zinc finger polypeptide has been selected for preferable binding characteristics by the method defined above.
  • the intervening linker peptide may be the same between each adjacent zinc finger or, alternatively, the same zinc finger polypeptide may contain a number of different linker peptides.
  • the intervening linker peptide may be one that is present in naturally-occurring zinc finger polypeptides or may be an artificial sequence. In particular, the sequence of the intervening linker peptide may be varied, for example, to optimise binding of the zinc finger polypeptide to the target sequence.
  • each motif binds to those DNA triplets which represent contiguous or substantially contiguous DNA in the sequence of interest.
  • candidate binding motifs or candidate combinations of motifs may be screened against the actual target sequence to determine the optimum composition of the polypeptide. Competitor DNA may be included in the screening assay for comparison, as described below.
  • the non-specific component of all protein-DNA interactions which includes contacts to the sugar-phosphate backbone as well as ambiguous contacts to base-pairs, is a considerable driving force towards complex formation and can result in the selection of DNA-binding proteins with reasonable affinity but without specificity for a given DNA sequence. Therefore, in order to minimise these non-specific interactions when designing a polypeptide, selections should preferably be performed with low concentrations of specific binding site in a background of competitor DNA, and binding should desirably take place in solution to avoid local concentration effects and the avidity of multivalent phage for ligands immobilised on solid surfaces.
  • the known sequence is only 9 bases long then three zinc finger binding motifs can be included in the polypeptide. If the known sequence is 27 bases long then, in theory, up to nine binding motifs could be included in the polypeptide. The longer the target DNA sequence, the lower the probability of its occurrence in any given portion of DNA.
  • those motifs selected for inclusion in the polypeptide could be artificially modified (e.g. by directed mutagenesis) in order to optimise further their binding characteristics.
  • the length and amino acid sequence of the linker peptide joining adjacent zinc binding fingers could be varied, as outlined above. This may have the effect of altering the position of the zinc finger binding motif relative to the DNA sequence of interest, and thereby exert a further influence on binding characteristics.
  • the invention provides a kit for making a zinc finger polypeptide for binding to a nucleic acid sequence of interest, comprising: a library of DNA sequences encoding zinc finger binding motifs of known binding characteristics in a form suitable for cloning into a vector; a vector molecule suitable for accepting one or more sequences from the library; and instructions for use.
  • the vector is capable of directing the expression of the cloned sequences as a single zinc finger polypeptide.
  • the vector is capable of directing the expression of the cloned sequences as a single zinc finger polypeptide displayed on the surface of a viral particle, typically of the sort of viral display particle which are known to those skilled in the art.
  • the DNA sequences are preferably in such a form that the expressed polypeptides are capable of self-assembling into a number of zinc finger polypeptides.
  • the kit defined above will be of particular use in designing a zinc finger polypeptide comprising a plurality of zinc finger binding motifs, the binding characteristics of which are already known.
  • the invention provides a kit for use when zinc finger binding motifs with suitable binding characteristics have not yet been identified, such that the invention provides a kit for making a zinc finger polypeptide for binding to a nucleic acid sequence of interest, comprising: a library of DNA sequences, each encoding a zinc finger binding motif in a form suitable for screening and/or selecting according to the methods defined above; and instructions for use.
  • the library of DNA sequences in the kit will be a library in accordance with the first aspect of the invention.
  • the kit may also comprise a library of 64 DNA sequences, each sequence comprising a different one of the 64 possible permutations of three DNA bases, in a form suitable for use in the selection method defined previously.
  • the 64 sequences are present in 12 separate mini-libraries, each mini-library having one postion in the relevant triplet fixed and two portions randomised.
  • the kit will also comprise appropriate buffer solutions, and/or reagents for use in the detection of bound zinc fingers.
  • the kit may also usefully include a vector suitable for accepting one or more sequences selected from the library of DNA sequences encoding zinc finger binding motifs.
  • the present teaching will be used for isolating the genes for the middle zinc fingers which, having been previously selected by one of the 64 triplets, are thought to have specific DNA binding activity.
  • the mixture of genes specifying fingers which bind to a given triplet will be amplified by PCR using three sets of primers. The sets will have unique restriction sites, which will define the assembly of zinc fingers into three finger polypeptides.
  • the appropriate reagents are preferably provided in kit form.
  • the first set of primers might have SfiI and AgeI sites, the second set AgeI and EagI sites and third set EagI and NotI sites.
  • the “first” site will preferably be SfiI, and the “last” site NotI, so as to facilitate cloning into the SfiI and NotI sites of the phage vector.
  • the fingers selected by the triplet GGG are amplified using the first two sets of primers and ligated to the fingers selected by the triplet AAA amplified using the third set of primers.
  • the combinatorial library is cloned on the surface of phage and a nine base-pair site can be used to select the best combination of fingers en bloc.
  • genes for fingers which bind to each of the 64 triplets can be amplified by each set of primers and cut using the appropriate restriction enzymes.
  • These building blocks for three-finger proteins can be sold as components of a kit for use as described above. The same could be done for the library amplified with different primers so that 4- or 5-finger proteins could be built.
  • a large (pre-assembled) library of all combinations of the fingers selected by all triplets can also be developed for single-step selection of DNA-binding proteins using 9 bp, or much longer. DNA fragments.
  • methods of selection other than phage display for example stalled polysomes (developed by Affimax) where protein and mRNA become linked.
  • the invention provides a method of altering the expression of a gene of interest in a target cell, comprising: determining (if necessary) at least part of the DNA sequence of the structural region and/or a regulatory region of the gene of interest; designing a zinc finger polypeptide to bind to the DNA of known sequence, and causing said zinc finger polypeptide to be present in the target cell, (preferably in the nucleus thereof). (It will be apparent that the DNA sequence need not be determined if it is already known.)
  • the regulatory region could be quite remote from the structural region of the gene of interest (e.g. a distant enhancer sequence or similar).
  • the zinc finger polypeptide is designed by one or both of the methods of the invention defined above.
  • Binding of the zinc finger polypeptide to the target sequence may result in increased or reduced expression of the gene of interest depending, for example, on the nature of the target sequence (e.g. structural or regulatory) to which the polypeptide binds.
  • the zinc finger polypeptide may advantageously comprise functional domains from other proteins (e.g. catalytic domains from restriction enzymes, recombinases, replicases, integrases and the like) or even “synthetic” effector domains.
  • the polypeptide may also comprise activation or processing signals, such as nuclear localisation signals. These are of particular usefulness in targtetting the polypeptide to the nucleus of the cell in order to enhance the binding of the polypeptide to an intranuclear target (such as genomic DNA).
  • a particular example of such a localisation signal is that from the large T antigen of SV40.
  • Such other functional domains/signals and the like are conveniently present as a fusion with the zinc finger polypeptide.
  • Other desirable fusion partners comprise immunoglobulins or fragments thereof (eg. Fab, scFv) having binding activity.
  • the zinc finger polypeptide may be synthesised in situ in the cell as a result of delivery to the cell of DNA directing expression of the polypeptide.
  • Methods of facilitating delivery of DNA include, for example, recombinant viral vectors (e.g. retroviruses, adenoviruses), liposomes and the like.
  • the zinc finger polypeptide could be made outside the cell and then delivered thereto. Delivery could be facilitated by incorporating the polypeptide into liposomes etc. or by attaching the polypeptide to a targetting moiety (such as the binding portion of an antibody or hormone molecule).
  • Media e.g. microtitre wells, resins etc.
  • NIP nanoparticles
  • the invention provides a method of inhibiting cell division by causing the presence in a cell of a zinc finger polypeptide which inhibits the expression of a gene enabling the cell to divide.
  • the invention provides a method of treating a cancer, comprising delivering to a patient, or causing to be present therein, a zinc finger polypeptide which inhibits the expression of a gene enabling the cancer cells to divide.
  • the target could be. for example, an oncogene or a normal gene which is overexpressed in the cancer cells.
  • zinc finger polypeptides could be designed for therapeutic and/or prophylactic use in regulating the expression of disease-associated genes.
  • zinc finger polypeptides could be used to inhibit the expression of foreign genes (e.g,. the genes of bacterial or viral pathogens) in man or animals, or to modify the expression of mutated host genes (such as oncogenes).
  • the invention therefore provides a zinc finger polypeptide capable of inhibiting the expression of a disease-associated gene.
  • the zinc finger polypeptide will not be a naturally-occurring polypeptide but will be specifically designed to inhibit the expression of the disease-associated gene.
  • the polypeptide will be designed by one or both of the methods of the invention defined above.
  • the disease-associated gene will be an oncogene, typically the BCR-ABL fusion oncogene or a ras oncogene.
  • the invention provides a zinc finger polypeptide designed to bind to the DNA sequence GCAGAAGCC and capable of inihibting the expression of the BCR-ABL fusion oncogene.
  • the invention provides a method of modifying a nucleic acid sequence of interest present in a sample mixture by binding thereto a zinc finger polypeptide, comprising contacting the sample mixture with a zinc finger polypeptide having affinity for at least a portion of the sequence of interest, so as to allow the zinc finger polypeptide to bind specifically to the sequence of interest.
  • modifying as used herein is intended to mean that the sequence is considered modified simply by the binding of the zinc finger polypeptide. It is not intended to suggest that the sequence of nucleotides is changed, although such changes (and others) could ensue following binding of the zinc finger polypeptide to the nucleic acid of interest. Conveniently the nucleic acid sequence is DNA.
  • Modification of the nucleic acid of interest could be detected in any of a number of methods (e.g. gel mobility shift assays, use of labelled zinc finger polypeptides—labels could include radioactive, fluorescent, enzyme or biotin/streptavidin labels).
  • Modification of the nucleic acid sequence of interest may be all that is required (e.g. in diagnosis of disease). Desirably however, further processing of the sample is performed. Conveniently the zinc finger polypeptide (and nucleic acid sequences specifically bound thereto) are separated from the rest of the sample.
  • the zinc finger polypeptide is bound to a solid phase support, to facilitate such separation.
  • the zinc finger polypeptide may be present in an acrylamide or agarose gel matrix or, more preferably, is immobilised on the surface of a membrane or in the wells of a microtitre place.
  • a) Therapy e.g. targetting to double stranded DNA
  • Diagnosis e.g. detecting mutations in gene sequences: the present work has shown that “tailor made” zinc finger polypeptides can distinguish DNA sequences differing by one base pair).
  • DNA purification the zinc finger polypeptide could be used to purify restriction fragments from solution, or to visualise DNA fragments on a gel [for example, where the polypeptide is linked to an appropriate fusion partner, or is detected by probing with an antibody ]).
  • zinc finger polypeptides could even be targeted to other nucleic acids such as ss or ds RNA (e.g. self-complementary RNA such as is present in many RNA molecules) or to RNA-DNA hybrids, which would present another possible mechanism of affecting cellular events at the molecular level.
  • nucleic acids such as ss or ds RNA (e.g. self-complementary RNA such as is present in many RNA molecules) or to RNA-DNA hybrids, which would present another possible mechanism of affecting cellular events at the molecular level.
  • Example 1 the inventors describe and successfully demonstrate the use of the phage display technique to construct and screen a random zinc finger binding motif library, using a defined oligonucleotide target sequence.
  • Example 2 is disclosed the analysis of zinc finger binding motif sequences selected by the screening procedure of Example 1, the DNA-specificity of the motifs being studied by binding to a mini-library of randomised DNA target sequences to reveal a pattern of acceptable bases at each position in the target triplet—a “binding site signature”.
  • Example 3 the findings of the first two sections are used to select and modify rationally a zinc finger binding polypeptide in order to bind to a particular DNA target with high affinity: it is convincingly shown that the peptide binds to the target sequence and can modify gene expression in cells cultured in vitro.
  • Example 4 describes the development of an alternative zinc finger binding motif library.
  • Example 5 describes the design of a zinc finger binding polypeptide which binds to a DNA sequence of special clinical significance.
  • FIG. 1 is a schematic representation of affinity purification of phage particles displaying zinc finger binding motifs fused to phage coat proteins
  • FIG. 2 shows an alignment of the three zinc fingers of a single zinc finger protein (Seq ID No. 2) used in the phage display library;
  • FIG. 3 shows the DNA sequences of three oligonucleotides (Seq ID Nos. 3-8) used in the affinity purification of phage display particles;
  • FIG. 4 is a “checker board” of binding site signatures determined for various zinc finger binding motifs (Seq ID Nos. 19-51);
  • FIG. 5A-5F show graphs fractional saturation against concentration of DNA (nM) for various binding motifs and target DNA triplets
  • FIG. 6 shows the nucleotide sequence of the fusion between BCR and ABL sequences in p190 cDNA (Seq ID No. 9) and the corresponding exon boundaries in the BCR and ABL genes (Seq ID Nos. 10-11),
  • FIG. 7 shows the amino acid sequences of various zinc finger binding motifs (Seq ID Nos. 12-17) designed to test for binding to the BCR/ABL fusion;
  • FIG. 8 is a graph of peptide binding (as measured by A 450-460 nm) against DNA concentration ( ⁇ M) of target or control DNA sequences;
  • FIG. 9 is a graph showing percentage viability against time for various transfected cells.
  • FIGS. 10A-10C and 11 illustrate schematically different methods of designing zinc finger binding polypeptides.
  • FIG. 12 shows an alignment of the amino acid sequence of zinc fingers in a single zinc finger polypeptide (Seq ID No. 18) designed to bind to a particular DNA sequence (a ras oncogene).
  • the inventors have used a screening technique to study sequence-specific DNA recognition by zinc finger binding motifs.
  • the example describes how a library of zinc finger binding motifs displayed on the surface of bacteriophage enables selection of fingers capable of binding to given DNA triplets.
  • the amino acid sequences of selected fingers which bind the same triplet were compared to examine how sequence-specific DNA recognition occurs.
  • the results can be rationalised in terms of coded interactions between zinc fingers and DNA, involving base contacts from a few ⁇ -helical positions.
  • the inventors applied this technology to the study of zinc finger-DNA interactions after demonstrating that functional zinc finger proteins can be displayed on the surface of fd phage, and that the engineered phage can be captured on a solid support coated with specific DNA.
  • a phage display library was created comprising variants of the middle finger from the DNA binding domain of Zif268 (a mouse transcription factor containing 3 zinc fingers—Christy et al., 1988). DNA of fixed sequence was used to purify phage from this library over several rounds of selection, returning a number of different but related zinc fingers which bind the given DNA. By comparing similarities in the amino acid sequences of functionally equivalent fingers we deduce the likely mode of interaction of these fingers with DNA.
  • TFIIIA Transcription Factor IIIA
  • the gene for the first three fingers (residues 3-101) of Transcription Factor IIIA (TFIIIA) was amplified by PCR from the cDNA clone of TFIIIA using forward and backward primers which contain restriction sites for L NotI and SfiI respectively.
  • the gene for the Zif268 fingers (residues 333-420) was assembled from 8 overlapping synthetic oligonucleotides, giving SfiI and NotI overhangs.
  • the genes for fingers of the phage library were synthesised from 4 oligonucleotides by directional end to end ligation using 3 short complementary linkers, and amplified by PCR from the single strand using forward and backward primers which contained sites for NotI and SfiI respectively.
  • Backward PCR primers in addition introduced Met-Ala-Glu as the first three amino acids of the zinc finger peptides, and these were followed by the residues of the wild type or library fingers as discussed in the text. Cloning overhangs were produced by digestion with SfiI and NotI where necessary. Fragments were ligated to 1 ⁇ g similarly prepared Fd-Tet-SN vector.
  • Electrocompetent DH5 ⁇ cells were transformed with recombinant vector in 200 ng aliquots, grown for 1 hour in 2xTY medium with 1% glucose, and plated on TYE containing 15 ⁇ g/ml tetracycline and 1% glucose.
  • FIG. 2 shows the amino acid sequence (Seq ID No. 2) of the three zinc fingers from Zif268 used in the phage display library.
  • the top and bottom rows represent the sequence of the first and third fingers respectively.
  • the middle row represents the sequence of the middle finger.
  • the randomised positions in the ⁇ -helix of the middle finger have residues marked ‘X’.
  • the amino acid positions are numbered relative to the first helical residue (position 1).
  • codons are equal mixtures of (G,A,C)NN: T in the first base position is omitted in order to avoid stop codons, but this has the unfortunate effect that the codons for Trp, Phe, Tyr and Cys are not represented.
  • Position +9 is specified by the codon A(G,A)G, allowing either Arg or Lys. Residues of the hydrophobic core are circled, whereas the zinc ligands are written as white letters on black circles. The positions forming the ⁇ -sheets and the ⁇ -helix of the zinc fingers are marked below the sequence.
  • Colonies were transferred from plates to 200 ml 2xTY/Zn/Tet (2xTY containing 50 ⁇ M Zn(CH3.C00) 2 and 15 ⁇ g/ml tetracycline) and grown overnight. Phage were purified from the culture supernatant by two rounds of precipitation using 0.2 volumes of 20% PEG/2.5M NaCl containing 50, ⁇ M Zn(CH3.C00) 2 , and resuspended in zinc finger phage buffer (20 mM HEPES pH7.5, 50 mM NaCl, 1 mM MgCl 2 and 50 ⁇ M Zn(CH3.C00) 2 ).
  • Streptavidin-coated paramagnetic beads (Dynal) were washed in zinc finger phage buffer and blocked for 1 hour at room temperature with the same buffer made up to 6% in fat-free dried milk (Marvel). Selection of phage was over three rounds: in the first round, beads (1 mg) were saturated with biotinylated oligonucleotide ( ⁇ 80 nM) and then washed prior to phage binding, but in the second and third rounds 1.7 nM oligonucleotide and 5 ⁇ g poly dGC (Sigma) were added to the beads with the phage. Binding reactions (1.5 ml) for 1 hour at 15° C.
  • the phage selection procedure based on affinity purification, is illustrated schematically in FIG. 1 : zinc fingers (A) are expressed on the surface of fd phage(B) as fusions to the the minor coat protein (C). The third finger is mainly obscured by the DNA helix. Zinc finger phage are bound to 5′-biotinylated DNA oligonucleotide [D ] attached to streptavidin-coated paramagnetic beads [E ], and captured using a magnet [F ]. ( Figure adapted from Dynal AS and also Marks et al. (1992 J. Biol. Chem. 267, 16007-16105).
  • FIG. 3 shows sequences (Seq ID No.s 3-8) of DNA oligonucleotides used to purify (i) phage displaying the first three fingers of TFIIIA, (ii) phage displaying the three fingers of Zif268, and (iii) zinc finger phage from the phage display library.
  • the Zif268 consensus operator sequence used in the X-ray crystal structure (Pavletich & Pabo 1991 Science 252, 809-817) is highlighted in (ii), and in (iii) where “X” denotes a base change from the ideal operator in oligonucleotides used to purify phage with new specificities. Biotinylation of one strand is shown by a circled “B”.
  • Phage display of 3-finger DNA-Binding Domains from TFIIIA or Zif268 Prior to the construction of a phage display library, the inventors demonstrated that peptides containing three fully functional zinc fingers could be displayed on the surface of viable fd phage when cloned in the vector Fd-Tet-SN. In preliminary experiments, the inventors cloned as fusions to pill firstly the three N-terminal fingers from TFIIIA (Ginsberg et al., 1984 Cell 39, 479-489), and secondly the three fingers from Zif268 (Christy et al., 1988), for both of which the DNA binding sites are known.
  • Peptide fused to the minor coat protein was detected in Western blots using an anti-plll antibody (Stengele et al., 1990 J. Mol. Biol. 212, 143-149). Approximately 10-20% of total P-III in phage preparations was present as fusion protein.
  • Phage displaying either set of fingers were capable of binding to specific DNA oligonucleotides, indicating that zinc fingers were expressed and correctly folded in both instances.
  • Paramagnetic beads coated with specific oligonucleotide were used as a medium on which to capture DNA-binding phage, and were consistently able to return between 100 and 500-fold more such phage, compared to free beads or beads coated with non-specific DNA.
  • phage displaying the three fingers of Zif268 were diluted 1:1.7 ⁇ 10 3 with Fd-Tet-SN phage not bearing zinc fingers, and the mixture incubated with beads coated with Zif268 operator DNA, one in three of the total phage eluted and transfected into E.
  • coli were shown by colony hybridisation to carry the Zif268 gene, indicating an enrichment factor of over 500 for the zinc finger phage.
  • zinc fingers displayed on fd phage are capable of preferential binding to DNA sequences with which they can form specific complexes, making possible the enrichment of wanted phage by factors of up to 500 in a single affinity purification step. Therefore, over multiple rounds of selection and amplification, very rare clones capable of sequence-specific DNA binding can be selected-from a large library.
  • a phage display library of zinc fingers from Zif268 The inventors have made a phage display library of the three fingers of Zif268 in which selected residues in the middle finger are randomised ( FIG. 2 ), and have isolated phage bearing zinc fingers with desired specificity using a modified Zif268 operator sequence (Christy & Nathan 1989 Proc. Natl. Acad. Sci. USA 86, 8737-8741) in which the middle DNA triplet is altered to the sequence of interest ( FIG. 3 ).
  • a modified Zif268 operator sequence Greek & Nathan 1989 Proc. Natl. Acad. Sci. USA 86, 8737-8741
  • FIG. 3 In order to be able to study both the primary and secondary putative base recognition positions which are suggested by database analysis (Jacobs 1992 EMBO J.
  • the inventors have designed the library of the middle finger so that, relative to the first residue in the ⁇ -helix (position +1), positions ⁇ 1 to +8, but excluding the conserved Leu and His, can be any amino acid except Phe, Tyr, Trp and Cys which occur only rarely at those positions (Jacobs 1993 Ph.D. thesis, University of Cambridge).
  • position +9 which might make an inter-finger contact with Ser at position ⁇ 2 (Pavletich & Pabo 1991)
  • Arg or Lys the two most frequently occurring residues at that position.
  • the size of the phage display library required, assuming full degeneracy of the 8 variable positions, is (16 7 ⁇ 2 1 ) 5.4 ⁇ 10 8 , but because of practical limitations in the efficiency of transformation with Fd-Tet-SN, the inventors were able to clone only 2.6 ⁇ 10 6 of these.
  • the library used is therefore some two hundred times smaller than the theoretical size necessary to cover all the possible variations of the ⁇ -helix. Despite this shortfall, it has been possible to isolate phage which bind with high affinity and specificity to given DNA sequences, demonstrating the remarkable versatility of the zinc finger motif.
  • guanine has a particularly important role in zinc finger-DNA interactions.
  • G selects fingers with Arg at position +6 or ⁇ 1 of the ⁇ -helix respectively.
  • G is present in the middle position of a triplet (e.g. Table 1b), the preferred amino acid at position +3 is His.
  • G at the 5′ end of a triplet selects Ser or Thr at +6 (e.g. Table 1p).
  • Adenine is also an important determinant of sequence specificity, recognised almost exclusively by Asn or Gln which again are able to make bidentate contacts (Seeman et al., 1976).
  • Gln is often selected at position ⁇ 1 of the ⁇ -helix, accompanied by small aliphatic residues at +2 (e.g. Table 1b).
  • Adenine in the middle of the triplet strongly selects Asn at +3 (e.g. Table 1c-e), except in the triplet CAG (Table 1a) which selected only two types of finger, both with His at +3 (one being the wild-type Zif268 which contaminated the library during this experiment).
  • cytosine and thymine cannot reliably be discriminated by a hydrogen bonding amino acid side chain in the major groove (Seeman et al., 1976). Nevertheless, C in the 3′ position of a triplet shows a marked preference for Asp or Glu at position ⁇ 1, together with Arg at +1 (e.g. Table 1e.g.). Asp is also sometimes selected at +3 and +6 when C is in the middle (e.g. Table 1o) and 5′ (e-g. Table 1a) position respectively.
  • Asp can accept a hydrogen bond from the amino group of C, one should note that the positive molecular charge of C in the major groove (Hunter 1993 J. Mol. Biol. 230, 1025-1054) will favour an interaction with Asp regardless of hydrogen bonding contacts.
  • C in the middle position most frequently selects Thr (e.g. Table 1i), Val or Leu (e.g. Table 1o) at +3.
  • T in the middle position most often selects Ser (e.g. Table 1i), Ala or Val (e.g. Table 1p) at +3.
  • the aliphatic amino acids are unable to make hydrogen bonds but Ala probably has a hydrophobic interaction with the methyl group of T, whereas a longer side chain such as Leu can exclude T and pack against the ring of C.
  • Ser and Thr are selected at +6 (as is occasionally the case for G at the 5′ end).
  • Thymine at the 3′ end of a triplet selects a variety of polar amino acids at ⁇ 1 (e.g. Table 1d), and occasionally returns fingers with Ser at +2 (e.g. Table 1a) which could make a contact as seen in the tramtrack crystal structure (Fairall et al., 1993).
  • affinity selection can favour those clones whose representation in the library is greatest even though their true affinity for DNA is less than that of other clones less abundant in the library. Phage display selection by affinity is therefore of limited value in distinguishing between permissive and specific interactions beyond those base contacts necessary to stabilise the complex. Thus in the absence of competition from fingers which are able to bind specifically to a given DNA, the tightest non-specific complexes will be selected from the phage library. Consequently, results obtained by phage display selection from a library must be confirmed by specificity assays, particularly when that library is of limited size.
  • amino acid sequence biases observed within a family of functionally equivalent zinc fingers indicate that, of the ⁇ -helical positions randomised in this study, only three primary ( ⁇ 1, +3 and +6) and one auxiliary (+2) positions are involved in recognition of DNA. Moreover, a limited set of amino acids are to be found at those positions, and it is presumed that these make contacts to bases. The indications therefore are that a code can be derived to describe zinc finger-DNA interactions.
  • sequence homologies are strongly suggestive of amino acid preferences for particular base-pairs, one cannot confidently deduce such rules until the specificity of individual fingers for DNA triplets is confirmed. The inventors therefore defer making a summary table of these preferences until the following example, in which is described how randomised DNA binding sites can be used to this end.
  • the original position or context of the randomised finger in the phage display library might bear on the efficacy of selected fingers when incorporated into a new DNA-binding domain.
  • Selections from a library of the outer fingers of a three finger peptide are capable of producing fingers which bind DNA in various different modes, while selections from a library of the middle finger should produce motifs which are more constrained. Accordingly, Rebar and Pabo do not assume that the first finger of Zif268 will always bind a triplet, and screened with a tetranucleotide binding site to allow for different binding modes.
  • motifs selected from libraries of the outer fingers might prove less amenable to the assembly of multifinger proteins, since binding of these fingers could be perturbed on constraining them to a particular binding mode, as would be the case for fingers which had to occupy the middle position of an assembled three-finger protein.
  • motifs selected from libraries of the middle finger, having been originally constrained will presumably be able to preserve their mode of binding even when placed in the outer positions of an assembled DNA-binding domain.
  • FIGS. 10A-10C shows different strategies for the design of tailored zinc finger proteins.
  • a three-finger DNA-binding motif is selected en bloc from a library of three randomised fingers.
  • B A three-finger DNA-binding motif is assembled out of independently selected fingers from a library of one randomised finger (e.g. the middle finger of Zif268).
  • C A three-finger DNA-binding motif is assembled out of independently selected fingers from three positionally specified libraries of randomised zinc fingers.
  • FIG. 11 illustrates the strategy of combinatorial assembly followed by en bloc selection.
  • Groups of triplet-specific zinc fingers (A) isolated by phage display selection are assembled in random combinations and re-displayed on phage (B).
  • a full-length target site (C) is used to select en bloc the most favourable combination of fingers (D).
  • This example describes a new technique to deal efficiently with the selection of a DNA binding site for a given zinc finger (essentially the converse of example 1). This is desirable as a safeguard against spurious selections based on the screening of display libraries. This may be done by screening against libraries of DNA triplet binding sites randomised in two positions but having one base fixed in the third position. The technique is applied here to determine the specificity of fingers previously selected by phage display. The inventors found that some of these fingers are able to specify a unique base in each position of the cognate triplet. This is further illustrated by examples of fingers which can discriminate between closely related triplets as measured by their respective equilibrium dissociation constants. Comparing the amino acid sequences of fingers which specify a particular base in a triplet, we infer that in most instances, sequence specific binding of zinc fingers to DNA can be achieved using a small set of amino acid-base contacts amenable to a code.
  • This example presents a convenient and rapid new method which can reveal the optimal binding site(s) of a DNA binding protein by single step selection from small libraries and use this to check the binding site preferences of those zinc fingers selected previously by phage display.
  • the inventors have used 12 different mini-libraries of the Zif268 binding site, each one with the central triplet having one position defined with a particular base pair and the other two positions randomised.
  • Each library therefore comprises 16 oligonucleotides and offers a number of potential binding sites to the middle finger, provided that the latter can tolerate the defined base pair.
  • Each zinc finger phage is screened against all 12 libraries individually immobilised in wells of a microtitre plate, and binding is detected by an enzyme immunoassay.
  • a pattern of acceptable bases at each position is disclosed, which the inventors term a “binding site signature”.
  • the information contained in a binding site signature encompasses the repertoire of binding sites recognised by a zinc finger.
  • the binding site signatures allow progress towards a specificity code for the interactions of zinc fingers with DNA.
  • FIG. 4 gives the binding site signatures of individual zinc finger phage.
  • the figure represents binding of zinc finger phage to randomised DNA immobilised in the wells of microtitre plates.
  • DNA libraries are applied to columns of wells (down the plate), while rows of wells (across the plate) contain equal volumes of a solution of a zinc finger phage.
  • the identity of each library is given as the middle triplet of the “bound” strand of Zif268 operator, where N represents a mixture of all 4 nucleotides.
  • the zinc finger phage is specified by the sequence of the variable region of the middle finger, numbered relative to the first helical residue (position 1), and the three primary recognition positions are highlighted. Bound phage are detected by an enzyme immunoassay. The approximate strength of binding is indicated by a grey scale proportional to the enzyme activity. From the pattern of binding to DNA libraries, called the “signature” of each clone, one or a small number of binding sites can be read off and these are written on the right of the figure.
  • Bound phage were detected using HRP-conjugated anti-M13 IgG (Pharmacia) and developed as described (Griffiths et al., 1994). Optical densities were quantitated using software package SOFTMAX 2.32 (Molecular Devices Corp).
  • FIGS. 5A-5F is a series of graphs of fractional saturation against concentration of DNA (nM).
  • the two outer fingers carry the native sequence, as do the the two cognate outer DNA triplets.
  • the sequence of amino acids occupying helical positions ⁇ 1 to +9 of the varied finger are shown in each case.
  • the graphs show that the middle finger can discriminate closely related triplets, usually by a factor of ten.
  • the graphs allowed the determination of apparent equilibrium dissociation constants, as below.
  • K d [DNA ].[P ]/[DNA.P], using the software package KALEIDAGRAPHTM Version 2.0 programme (Abelbeck Software). Owing to the sensitivity of the ELISA used to detect protein-DNA complex, the inventors were able to use zinc finger phage concentrations far below those of the DNA, as is required for accurate calculations of the K d .
  • the technique used here has the advantage that while the concentration of DNA (variable) must be known accurately, that of the zinc fingers (constant) need not be known (Choo & Klug 1993 Nucleic Acids Res. 21, 3341-3346).
  • the top row of FIG. 4 shows the signature of the second finger of wild type Zif268. From the pattern of strong signals indicating binding to oligonucleotide libraries having GNN, TNN, NGN and NNG as the middle triplet, it emerges that the optimal binding site for this finger is T/G,G,G, in accord with the published consensus sequence (Christy & Nathans 1989 Proc. Natl. Acad. Sci. USA 86, 8737-8741). This has implications for the interpretation of the X-ray crystal structure of Zif268 solved in complex with consensus operator having, TGG as the middle triplet (Pavletich & Pabo 1991).
  • binding site signatures can give insight into the details of zinc finger-DNA interactions.
  • the binding site signatures of other zinc fingers reveal that the phage selections performed in example 1 yielded highly sequence-specific DNA binding proteins. Some of these are able to specify a unique sequence for the middle triplet of a variant Zif268 binding site, and are therefore more specific than is Zif268 itself for its consensus site. Moreover, one can identify the fingers which recognise a particular oligonucleotide library, that is to say a specific base at a defined position, by looking down the columns of FIG. 4 . By comparing the amino acid sequences of these fingers one can identify any residues which have genuine preferences for particular bases on bound DNA. With a few exceptions, these are as previously predicted on the basis of phage display, and are summarised in Table 2.
  • Table 2 summarises frequently observed amino acid-base contacts in interactions of selected zinc fingers with DNA.
  • the given contacts comprise a “syllabic” recognition code for appropriate triplets.
  • Cognate amino acids and their positions in the ⁇ -helix are entered in a matrix relating each base to each position of a triplet.
  • Auxiliary amino acids from position +2 can enhance or modulate specificity of amino acids at position ⁇ 1 and these are listed as pairs.
  • Ser or Thr at position +6 permit Asp +2 of the following finger (denoted Asp ++2) to specify both G and T indirectly, and the pairs are listed.
  • the specificity of Ser +3 for T and Thr +3 for C may be interchangeable in rare instances while Val +3 appears to be consistently ambiguous.
  • the binding site signatures also reveal an important feature of the phage display library which is important to the interpretation of the selection results.
  • All the fingers in our panel, regardless of the amino acid present at position +6, are able to recognise G or both G and T at the 5′ end of a triplet.
  • the probable explanation for this is that the 5′ position of the middle triplet is fixed as either G or T by a contact from the invariant Asp at position +2 of finger 3 to the partner of either base on the complementary strand, analogous to those seen in the Zif268 (Pavletich & Pabo 1991 Science 252, 809-817) and tramtrack (Fairall et al., 1993) crystal structures (a contact to NH 2 of C or A respectively in the major groove).
  • position +2 is able to specify the base directly 3′ of the ‘cognate triplet’, and can thus work in conjunction with position +6 of the preceding finger.
  • the binding site signatures whilst pointing to amino acid-base contacts from the three primary positions, indicate that auxiliary positions can play other parts in base recognition.
  • a clear case in point is Gln at position ⁇ 1, which is specific for A at the 3′ end of a triplet when position +2 is a small non-polar amino acid such as Ala, though specific for T when polar residues such as Ser are at position +2.
  • the strong correlation between Arg at position ⁇ 1 and Asp at position +2, the basis of which is understood from the X-ray crystal structures of zinc fingers, is another instance of interplay between these two positions.
  • the amino acid at position +2 is able to modulate or enhance the specificity of the amino acid at other positions.
  • binding site signature of a zinc finger reveals its differential base preferences at a given concentration of DNA. As the concentration of DNA is altered, one can expect the binding site signature of any clone to change, being more distinctive at low [DNA], and becoming less so at higher [DNA] 0 as the K d of less favourable sites is approached and further bases become acceptable at each position of the triplet. Furthermore, because two base positions are randomly occupied in any one library of oligonucleotides, binding site signatures are not formally able to exclude the possibility of context dependence for some interactions. Therefore to supplement binding site signatures, which are essentially comparative, quantitative determinations of the equilibrium dissociation constant of each phage for different DNA binding sites are required. After phage display selection and binding site signatures, these are the third and definitive stage in assessing the specificity of zinc fingers.
  • FIGS. 5A-5F Examples of such studies presented in FIGS. 5A-5F show reveal that zinc finger phages bind the operators indicated in their binding site signatures with K d s in the range of 10 ⁇ 8 -10 ⁇ 9 M, and can discriminate against closely related binding sites by factors greater than an order of magnitude. Indeed FIGS. 5A-5F shows such differences in affinity for binding sites which differ in only one out of nine base pairs. Since the zinc fingers in our panel were selected from a library by non-competitive affinity purification, there is the possibility that fingers which are even more discriminatory can be isolated using a competitive selection process.
  • Measurements of dissociation constants allow different triplets to be ranked in order of preference according to the strength of binding.
  • the examples here indicate that the contacts from either position ⁇ 1 or +3 can contribute to discrimination.
  • the ambiguity in certain binding site signatures referred to above can be shown to have a basis in the equal affinity of certain figures fingers for closely related triplets. This is demonstrated by the K d s of the finger containing the amino acid sequence RGDALTSHER (Seq ID No. 100) for the triple triplets TTG and GTG.
  • a code for zinc ringer-DNA recognition One would expect that the versatility of the zinc finger motif will have allowed evolution to develop various modes or binding to DNA (and even to RNA), which will be too diverse to fall under the scope of a single code. However, although a code may not apply to all zinc finger-DNA interactions, there is now convincing evidence that a code applies to a substantial subset. This code will fall short of being able to predict unfailingly the DNA binding site preference of any given zinc finger from its amino acid sequence, but may yet be sufficiently comprehensive to allow the design of zinc fingers with specificity for a given DNA sequence.
  • DNA recognition involves four fixed principal (three primary and one auxiliary) positions on the ⁇ -helix, from where a limited and specific set of amino acid-base contacts result in recognition of a variety of DNA triplets.
  • a code can describe the interactions of zinc fingers with DNA. Towards this code, one can propose amino acid-base contacts for almost all the entries in a matrix relating each base to each position of a triplet (Table 2).
  • Arg in order that Ala may pick out T in the triplet GTG, Arg must not be used to recognise G from position +6, since this would distance the former too far from the DNA (see for example the finger containing the amino acid sequence RGDALTSHER) (Seq ID No. 100).
  • the pitch of the ⁇ -helix is 3.6 amino acids per turn, positions ⁇ 1, +3 and +6 are not an integral number of turns apart, so that position +3 is nearer to the DNA than are ⁇ 1 or +6.
  • short amino acids such as His and Asn, rather than the longer Arg and Gln, are used for the recognition of purines in the middle position of a triplet.
  • the versatility of the finger motif will likely allow other modes of binding to DNA.
  • one must take into account the malleability of nucleic acids such as is observed in Fairall et al., where a deformation of the double helix at a flexible base step allows a direct contact from Ser at position +2 of finger 1 to a T at the 3′ position of the cognate triplet.
  • water may be seen to play an important role, for example where short side chains such as Asp, Asn or Ser interact with bases from position ⁇ 1 (Qian et al., 1993 J. Am. Chem. Soc. 115, 1189-1190; Shakked et al., 1994 Nature (London) 368, 469-478).
  • the coded interactions of zinc fingers with DNA can be used to model the specificity of individual zinc fingers de novo, or more likely in conjunction with phage display selection of suitable candidates.
  • the additive effect of multiply repeated domains offers the opportunity to bind specifically and tightly to extended, and hence very rare, genomic loci.
  • zinc finger proteins might well be a good alternative to the use of antisense nucleic acids in suppressing or modifying the action of a given gene, whether normal or mutant.
  • extra functions could be introduced to these DNA binding domains by appending suitable natural or synthetic effectors.
  • murine cells made growth factor-independent by the action of the oncogene (Daley et al., 1988 Proc. Natl. Acad. Sci. U.S.A. 85, 9312-9316) are found to revert to factor dependence on transient transfection with a vector expressing the designed zinc finger polypeptide.
  • DNA-binding proteins designed to recognise specific DNA sequences could be incorporated in chimeric transcription factors, recombinases, nucleases etc. for a wide range of applications.
  • the inventors have shown that zinc finger mini-domains can discriminate between closely related DNA triplets, and have proposed that they can be linked together to form domains for the specific recognition of longer DNA sequences.
  • One interesting possibility for the use of such protein domains is to target selectively genetic differences in pathogens or transformed cells. Here one such application is described.
  • CML chronic myelogenous leukaemia
  • the breakpoints usually occur in the first intron of the c-ABL gene and in the breakpoint cluster region of the BCR gene (Shtivelman et al., 1985 Nature 315, 550-554), and give rise to a p210 BCR-ABL gene product (Konopka et al., 1984 Cell 37, 1035-1042).
  • ALL acute lymphoblastic leukaemia
  • the breakpoints usually occur in the first introns of both BCR and c-ABL (Hermans er al., 1987 Cell 51, 33-40), and result in a p190 BCR-ABL gene product ( FIG. 6 ) (Kurzrock et al., 1987 Nature 325, 631-635).
  • FIG. 6 shows the nucleotide sequences (Seq ID No.s 9-11) of the fusion point between BCR and ABL sequences in p190 cDNA, and of the corresponding exon boundaries in the BCR and c-ABL genes. Exon sequences are written in capital letters while introns are given in lowercase.
  • Line 1 shows p190 BCR-ABL cDNA; line 2 the BCR genomic sequence at junction of exon 1 and intron 1; and line 3 the ABL genomic sequence at junction of intron 1 and exon 2 (Hermans et al 1987).
  • the 9 bp sequence in the p190 BCR-ABL cDNA used as a target is underlined, as are the homologous sequences in genomic BCR and c-ABL.
  • Facsimiles of these rearranged genes act as dominant transforming oncogenes in cell culture (Daley et al., 1988) and transgenic mice (Heisterkamp et al., 1990 Nature 344, 251-253).
  • the cDNAs bear a unique nucleotide sequence at the fusion point of the BCR and c-ABL genes, which can be recognised at the DNA level by a site-specific DNA-binding protein.
  • the present inventors have designed such a protein to recognise the unique fusion site in the p190 BCR-ABL c-DNA. This fusion is obviously distinct from the breakpoints in the spontaneous genomic translocations, which are thought to be variable among patients.
  • the design of such peptides has implications for cancer research, the primary aim here is to prove the principle of protein design, and to assess the feasibility of in vivo binding to chromosomal DNA in available model systems.
  • a nine base-pair target sequence (GCA, GAA, GCC) for a three zinc finger peptide was chosen which spanned the fusion point of the p190 BCR-ABL cDNA (Hermans et al., 1987).
  • the three triplets forming this binding site were each used to screen a zinc finger phage library over three rounds as described above in example 1.
  • the selected fingers were then analysed by binding site signatures to reveal their preferred triplet, and mutations to improve specificity were made to the finger selected for binding to GCA.
  • a phage display mini-library of putative BCR-ABL-binding three-finger proteins was cloned in fd phage, comprising six possible combinations of the six selected or designed fingers (1A, 1B; 2A; 3A, 3B and 3C) linked in the appropriate order. These fingers are illustrated in FIG. 7 (Seq ID No.s 12-17). In FIG. 7 regions of secondary structure are underlined below the list, while residue positions are given above, relative to the first position of the ⁇ -helix (position 1). Zinc finger phages were selected from a library of 2.6 ⁇ 10 6 variants, using three DNA binding sites each containing one of the triplets GCC, GAA or GCA.
  • Binding site signatures indicate that fingers 1A and 1B specify the triplet GCC, finger 2A specifies GAA, while the fingers selected using the triplet GCA all prefer binding to GCT. Amongst the latter is finger 3A, the specificity of which we believed, on the basis of recognition rules, could be changed by a point mutation. Finger 3B, based on the selected finger 3A, but in which Gln at helical position +2 was altered to Ala should be specific for GCA. Finger 3C is an alternative version of finger 3A, in which the recognition of C is mediated by Asp +3 rather than by Thr +3.
  • the mini library was screened once with an oligonucleotide containing the 9 base-pair BCR-ABL target sequence to select for tight binding clones over weak binders and background vector phage. Because the library was small, the inventors did not include competitor DNA sequences for homologous regions of the genomic BCR and c-ABL genes but instead checked the selected clones for their ability to discriminate.
  • the peptide 1A-2A-3B henceforth referred to as the anti-BCR-ABL peptide, was used in further experiments.
  • the anti-BCR-ABL peptide has an apparent equilibrium dissociation constant (K d ) of 6.2 ⁇ 0.4 ⁇ 10 ⁇ 7 M for the p190 BCR-ABL cDNA sequence in vitro, and discriminates against the similar sequences found in genomic BCR and C-ABL DNA, by factors greater than an order of magnitude ( FIG. 8 ). Referring to FIG.
  • the graph shows binding (measured as an A 450-650 ) at various [DNA]. Binding reactions and complex detection by enzyme immunoassay were performed as described previously, and a full curve analysis was used in calculations of the K d (Choo & Klug 1993). The DNA used were oligonucleotides spanning 9 bp either side of the fusion point in the cDNA or the exon boundaries.
  • the measured dissociation constant is higher than that of three-finger peptides from naturally occurring proteins such as Spl (Kadonga et al., 1987 Cell 51, 1079-1090) or Zif268 (Christy et al., 1988), which have K d s in the range of 10 ⁇ 9 M, but rather is comparable to that of the two fingers from the tramtrack (ttk) protein (Fairall et al., 1992).
  • affinity of the anti-BCR-ABL peptide could be refined, if desired, by site-directed mutations or by “affinity maturation” of a phage display library (Hawkins et al., 1992 J. Mol. Biol. 226, 889-896).
  • the peptide was fused to the VP16 activation domain from herpes simplex virus (Fields 1993 Methods 5, 116-124) and used in transient transfection assays ( FIG. 9 ) to drive production of a CAT (chloramphenicol acetyl transferase) reporter gene from a binding site upstream of the TATA box (Gorman et al., Mol. Cell. Biol. 2, 1044-1051).
  • CAT chloramphenicol acetyl transferase
  • reporter plasmids pMCAT6BA, pMCAT6A, and pMCAT6B were constructed by inserting 6 copies of the p190 BCR-ABL target site (CGCAGAAGCC) (Seq ID No. 121), the c-ABL second exon-intron junction sequence (TCCAGAAGCC) (Seq ID No. 122), or the BCR first exon-intron junction sequence (CGCAGGTGAG) (Seq ID No. 123) respectively, into pMCAT3 (Luscher et al., 1989 Genes Dev. 1507-1517).
  • CGCAGAAGCC p190 BCR-ABL target site
  • TCCAGAAGCC c-ABL second exon-intron junction sequence
  • CGCAGGTGAG BCR first exon-intron junction sequence
  • the anti-BCR-ABL/VP16 expression vector was generated by inserting the in-frame fusion between the activation domain of herpes simplex virus VP16 (Fields 1993) and the Zn finger peptide in the pEF-BOS vector (Mizushima & Shigezaku 1990 Nucl. Acids Res. 18, 5322).
  • C3H10T1/2 cells were transiently co-transfected with 10 mg of reporter plasmid and 10 mg of expression vector.
  • RSVL de Wet et al., 1987 Mol. Cell Biol. 7, 725-737
  • Rous sarcoma virus long terminal repeat linked to luciferase was used as an internal control to normalise for differences in transfection efficiency.
  • Plasmid pGSEC which has five consensus 17-mer GAL4-binding sites upstream from the minimal promoter of the adenovirus Elb TATA box
  • pMlVP16 vector which encodes an in-frame fusion between the DNA-binding domain of GAL4 and the activation domain of herpes simplex virus VP16, were used as a positive control (Sadowski et al., 1992 Gene 118, 137-141).
  • C3H10T1/2 cells were transiently cotransfected with a CAT reporter plasmid and an anti-BCR-ABL/VP 16 expression vector (pZN1A).
  • This construct was used to transiently transfect the IL-3-dependent murine cell line Ba/F3 (Palacios & Steinmetz 1985 Cell 41, 727-734), or alternatively Ba/F3+p190 and Ba/F3+p210 cell lines previously made IL-3-independent by integrated plasmid constructs expressing either p190 BCR-ABL or p210 BCR-ABL , respectively. Staining of the cells with the 9E10 antibody followed by a secondary fluorescent conjugate showed efficient nuclear localisation in those cells transfected with the anti-BCR-ABL peptide.
  • the anti-BCR-ABL expression vector was generated in the pEF-BOS vector (Mizushima & Shigezaku 1990), including an 11 amino acid c-myc epitope tag (EQKLISEEDLN) SEQ ID NO: 124 at the carboxy-terminal end, recognizable by the 9E10 antibody (Evan et al., 1985) and the nuclear localization signal PKKKRKV SEQ ID NO: 125 of the large T antigen of SV40 virus (Kalderon et al., 1984) at the amino-terminal end.
  • EQKLISEEDLN 11 amino acid c-myc epitope tag
  • PKKKRKV nuclear localization signal
  • Three glycine residues were introduced downstream of the nuclear localization signal as a spacer, to ensure exposure of the nuclear leader from the folded molecule.
  • Ba/F3 cells were transfected with 25 mg of the anti-BCR-ABL expression construct tagged with the 9E10 c-myc epitope as described (Sanchez-Garcia & Rabbitts 1994 Proc. Natl. Acad. Sci. U.S.A. in press) and protein production analyzed 48 h later by immunofluorescence-labelling as follows.
  • Cells were fixed in 4% (w/v) paraformaldehyde for 15 min, washed in phosphate-buffered saline (PBS), and permeabilized in methanol for 2 min. After blocking in 10% fetal calf serum in PBS for 30 min, the mouse 9E10 antibody was added.
  • PBS phosphate-buffered saline
  • FITC fluorescein isothiocyanate
  • SIGMA conjugated goat anti-mouse IgG
  • the blots were performed as follows: 10 mg of total cytoplasmic RNA, from the cells indicated, was glyoxylated and fractionated in 1.4% agarose gels in 10 mM NaPO 4 buffer, pH 7.0. After electrophoresis the gel was blotted onto HYBOND-N (Amersham), UV-cross linked and hybridized to an 32 P-labelled c-ABL probe. Autoradiography was for 14 h at ⁇ 70° C. Loading was monitored by reprobing the filters with a mouse b-acting ⁇ -actin cDNA.
  • a DNA-binding protein designed to recognise a specific DNA sequence in vitro is active in vivo where, directed to the nucleus by an appended localisation signal, it can bind its target sequence in chromosomal DNA. This is found on otherwise actively transcribing DNA, so presumably binding of the peptide blocks the path of the polymerase, causing stalling or abortion.
  • the use of a specific polypeptide in this case to target intragenic sequences is reminiscent of antisense oligonucleotide- or ribozyme- based approaches to inhibiting the expression of selected genes (Stein & Cheng 1993 Science 261, 1004-1012).
  • DNA-binding proteins can be tailored against genes altered by chromosomal translocations, or point mutations, as well as to regulatory sequences within genes. Also, like oligonucleotides which can be designed to repress transcription by triple helix formation in homopurine-homopyrimidine promoters (Cooney et al., 1988 Science 245, 725-730) DNA-binding proteins can bind to various unique regions outside genes, but in contrast they can direct gene expression by both up- or down-regulating, the initiation of transcription when fused to activation (Seipel er al., 1992 EMBO J.
  • phage display zinc finger library described in the preceding examples could be considered sub-optimal in a number of ways:
  • flanking fingers both recognised GCG triplets (in certain cases creating nearly symmetrical binding sites for the three zinc fingers, which enables the peptide to bind to the ‘bottom’ strand of DNA, thus evading the register of interactions we wished to set);
  • Asp++2 Asp+2 of finger three was dominant over the interactions of finger two (position+6) with the 5′ base of the middle triplet;
  • the middle finger is fully randomised in only four positions ( ⁇ 1, +2, +3 and +6) so that the library size is smaller and all codons are represented.
  • the library was cloned in the pCANTAB5E phagemid vector from Pharmacia, which allows higher transformation frequencies than the phage.
  • the first and third fingers recognise the triplets GAC and GCA, respectively, making for a highly asymmetric binding site.
  • Recognition of the 3′ A in the latter triplet by finger three is mediated by Gln-1/Ala+2, the significance of which is that the short Ala+2 should not make contacts to the DNA (in particular with the 5′ base of the middle triplet), thus alleviating the problem noted at (iii) above.
  • the human ras gene is susceptible to a number of different mutations, which can convert it into an oncogene.
  • a ras oncogene is found in a large number of human cancers.
  • One particular mutation is known as the G12V mutation (i.e. the polypeptide encoded by the mutant gene contains a substitution from glycine to valine). Because ras oncogenes are so common in human cancers, they are extremely significant targets for potential therapeutic methods.
  • a three finger protein has been designed which can recognise the G12V mutant of ras.
  • the protein was produced using rational design based on the known specificity rules.
  • a zinc finger framework (from one of the fingers selected to bind GCC) was modified by point mutations in position +3 to yield fingers recognising two additional different triplets.
  • the finger recognising GCC and the two derivatives were cloned in pCANTAB5E and expressed on the surface of phage.
  • the G12V-binding peptide “r-BP” was to be selected from a small library of related proteins. The reason a library was to be used is that while it was clear to us what 8/9 of the amino acid:base contacts should be, it was not clear whether the middle C of the GCC triplet should be recognised by +3 Asp, or Glu, or Ser, or Thr (see Table 2 above). Thus a three-finger peptide gene was assembled from 8 overlapping synthetic oligonucleotides which were annealed and ligated according to standard procedures and the ⁇ 300 bp product purified from a 2% agarose gel.
  • the gene for finger 1 contained a partial codon randomisation at position +3 which allowed for inclusion of each of the above amino acids (D, E, S & T) and also certain other residues which were in fact not predicted to be desirable (e.g. Asn).
  • the synthetic oligonucleotides were designed to have SfiI and NotI overhangs when annealed.
  • the ⁇ 300 bp fragment was ligated into SfiI/NotI -cut FdSN vector and the ligation mixture was electroporated into DH5 ⁇ cells. Phage were produced from these as previously described and a selection step carried out using the G12V sequence (also as described) to eliminate phage without insert and those phage of the library which bound poorly.
  • the amino acid sequence (Seq ID No. 18) of the fingers is shown in FIG. 12 .
  • the numbers refer to the ⁇ -helical amino acid residues.
  • the fingers (F1, F2 & F3) bind to the G12V mutant nucleotide sequence:
  • the bold A shows the single point mutation by which the G12V sequence differs from the wild type sequence.
  • Assay of the protein in eukaryotes requires the use of a weak promoter.
  • the anti-RAS (G12V) protein When expression of the anti-RAS (G12V) protein is strong, the peptide presumably binds to the wild-type ras allele (which is required) leading to cell death.
  • a regulatable promoter e.g. for tetracycline
  • the G12V mutation is a naturally occurring genomic mutation (not only a cDNA mutation as was the p190 bcr-abl) human cell lines and other animal models can be used in research.
  • the protein can be used to diagnose the precise point mutation present in the genomic DNA, or more likely in PCR amplified genomic DNA, without sequencing. It should therefore be possible, without further inventive activity, to design diagnostic kits for detecting (e.g. point) mutations on DNA. ELISA-based methods should prove particularly suitable.
  • the transferrin receptor is thought particularly useful but, in theory, any receptor molecule (preferably of high affinity) expressed on the surface of a human target cell could act as a suitable ligand, either for a specific immunoglobulin or fragment, or for the receptor's natural ligand fused or coupled with the zinc finger polypeptide.

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