Cloning and Expression of Pur Protein

1. Introduction

2. Background Of The Invention

3. Summary Of The Invention

4. Description Of The Drawings

5. Detailed Description

5.1. The Pur Element

5.2. The Pur Protein

5.2.1. Isolation And Cloning Of PUR DNA

5.2.2. Construction Of Expression Vectors Containing The PUR Coding Sequence

5.2.3. Identification Of Transfectants Or Transformants Expressing The PUR Gene Product

5.2.4. The PUR Protein

5.3. Inhibitors Of PUR Protein

5.3.1. PUR Antibodies

5.3.2. Anti-Sense RNA And Ribozymes

5.3.3. Triplex DNA Formation

5.3.4. PUR-Related Derivatives, Analogues, And Peptides

5.4. Uses Of PUR Protein And Its Inhibitors

6. Example: Identification And Characterization Of The PUR Protein And Its Sequence Element

6.1. Materials And Methods

6.1.1. Plasmids And Oligonucleotides Used

6.1.2. Gel Shift Assays

6.1.3. Determination Of The Molecular Weight Of The DNA-Binding Protein

6.1.4. Methylation Interference Analysis

6.1.5. DNA Synthesis Assays

6.2. Results

6.2.1. A Region Of Stably Bent DNA 1.65 kb Upstream Of The c-myc P1 Promoter

6.2.2. Protein Specifically Bound To A Purine-Rich Sequence Element Adjacent To The DNA Bend

6.2.3. UV Irradiation Cross-Links A Polypeptide With The Single-Stranded 24-mer Containing The PUR Element

6.2.4. Methylation Interference Analysis Of Contact Points For Protein Binding To The PUR Element

6.2.5. A Pattern Of Guanosine Bases Is Required For Single-Strand Binding Specificity

6.2.6. PUR Factor Preferentially Binds A Single-Stranded Versus Double-Stranded PUR Element

6.2.7. A Consensus PUR Element Conserved In Eukaryotes

6.2.8. PUR Element Oligonucleotides Delay The Onset Of DNA Replication In Serum Stimulated Human Fibroblast

7. Example: Cloning And Sequencing PUR Gene Product

7.1. Materials And Methods

7.1.1. Oligonucleotides Used

7.1.2. Screening Of Expression Libraries For Proteins With Affinity For The Labeled, Single-Stranded PUR Element

7.1.3. Determination And Analysis Of The Nucleotide Sequence Of PUR.alpha.

7.1.4. DNA Binding Studies Of The PUR-lacZ Fusion Protein

7.1.5. Tissue Culture, Poly(A).sup.+ RNA Preparation, And Hybridization Analysis

7.1.6. 5' And 3' Extension Of PUR.alpha. mRNA 54

7.1.7. Screening Libraries By DNA - DNA Hybridization

7.1.8. PUR-GST Fusion Proteins

7.1.9. Retinoblastoma Protein Binding Assays

7.2. Results

7.2.1. Isolation Of PUR Clones From A .lambda.gt11 Expression Library Based On Affinity For The PUR Element

7.2.2. Specificity Of Single-Stranded DNA Binding By PUR.alpha.

7.2.3. Screen Of HeLa Cell Library Reveals At Least One Additional Protein With A PUR Repeat Module

7.2.4. Retinoblastoma Gene Product Binds to PUR-GST Fusion Protein

The present invention relates to the PUR protein, to nucleotide sequences and expression vectors encoding PUR, and to methods for inhibiting PUR activity.

The PUR protein binds specifically to single stranded DNA in regions that coincide with eukaryotic origins of DNA replication and the 5' flanking regions of a number of cellular oncogenes that are frequently found amplified in cancer cells. Inhibitors of PUR activity may be useful for treatment of hyperproliferative diseases such as cancers that result from amplification and/or over expression of cellular oncogenes.

Cell division is a carefully regulated process that involves two events, the duplication of genomic DNA and the physical division of the two daughter cells. Before each new cell division cycle, a decision must be made by the cell of whether to proceed through a new round of DNA replication or withdraw from the cell cycle into a quiescent non-proliferating state. When regulation of this process breaks down the result is uncontrolled cell proliferation which may lead to diseases such as cancer.

Investigators of eukaryotic DNA replication have been faced with the challenge of identifying and characterizing both the specific chromosomal origins of replication and the regulatory proteins that control initiation of replication. Elucidation of the molecular mechanisms regulating DNA replication should lead to the development of therapeutic applications directed at inhibiting DNA replication and cell division.

Studies of DNA replication in mammalian cells has been difficult, due in part to the lack of suitable methods for mapping origins in large and complex genomes. In less complex organisms, such as prokaryotes, yeast and DNA tumor viruses, recent developments have lead to the identification of both cis-acting elements and polypeptides that bind specifically to these elements.

Several proteins from prokaryotes have been characterized which play a role in DNA replication and which bind to single-stranded DNA. The amino acids involved in DNA binding by certain of these proteins have been identified (Gutierrez et al., 1991 J. Biol. Chem. 266, 2104-2111). However, none of these single-stranded DNA binding proteins is known to have any sequence specificity.

In yeast, Saccharomyces cerevisae, cis-acting replication origins, referred to as ARS elements (autonomous replicating sequences), have been identified by their ability to allow extrachromosomal maintenance of plasmids. In general, yeast ARS sequences have a significantly higher A+T content than average chromosomal DNA. Recently a 67 kD protein, referred to as ACBP (ARS-consensus binding protein) has been purified from yeast cell extracts and shown to bind preferentially to the T-rich single stranded DNA sequences found at the 3' end of the yeast ARS element (Hofmann and Gasser, 1991 Cell 64:951-960).

In a number of DNA tumor viruses, the sequences required for autonomous replication have also been mapped. Perhaps, the best studied of these viruses is Simian Virus 40 (SV40) and a single-stranded DNA-binding protein referred to as RP-Ab is required for replication initiated at the SV40 origin in vitro (Wobbe et al., 1987 Proc. Natl. Acad. Sci. 84:1834-1838; Erdile et al., 1991 J. Biol. Chem. 266:12090-12098). No sequence specificity has been reported for DNA binding by RP-A.

These results raise the possibility that sequence-specific, single-stranded-DNA binding proteins may serve an important function in the initiation of DNA replication. At this time, however, no amino acid sequence has been reported for any mammalian protein known to bind specifically to a single-stranded DNA element. Included in the invention are reagents that interfere with the specific protein/protein interaction observed between the PUR protein and the Retinoblastoma protein (RB).

The present invention relates to the PUR gene and the biologically active polypeptide coded for by the PUR DNA sequence. The present invention also relates to inhibitors of PUR activity which may include neutralizing anti-PUR antibodies, anti-sense RNA and ribozyme molecules that are specifically targeted to prevent translation of PUR mRNA and to derivatives, analogues and PUR related polypeptides that inhibit PUR activity. Also included in the invention are reagents that interfere with the specific DNA/protein interaction between the PUR protein and PUR element, such as oligonucleotides that bind and form triplex helical structures at the PUR element.

The invention is based, in part, on the discovery and characterization of the PUR element consensus DNA sequence. The location of PUR elements is found to coincide with regions of DNA that are believed to represent origins of replication. The PUR element is also found 5' to a number of cellular genes including the frequently amplified c-myc, int-2 and lck oncogenes suggesting that PUR elements may also function to regulate gene expression.

The invention is also based on the isolation and characterization of a cDNA clone coding for a cellular factor, referred to as the PUR protein, which binds in a sequence specific manner to single-stranded PUR element DNA sequence. In addition, the invention is based on the discovery that the PUR protein binds specifically to the retinoblastoma protein, herein referred to as RB protein. The retinoblastoma gene is perhaps the most extensively studied of the tumor suppressor genes. Current interest in RB is based on observations that inactivation of RB frees cells from the normal growth constraints imposed by a functional RB. Inactivation of RB results in uncontrolled cell proliferation and tumor cell growth. The invention also relates to methods for controlling the cell cycle by manipulating the interaction of PUR and/or RB so that their activity is regulated. Inhibition of PUR protein activity may be of therapeutic value in the treatment of hyper-proliferative diseases such as cancers which result from amplification or overexpression of cellular oncogenes.

FIG. 1. Structural features in a region of DNA bending upstream of the human c-myc gene. Positions of DNase 1-hypersensitive sites and CTF/NF-1 consensus binding sites are indicated by solid arrows at the top (Siebenlist et al., 1984, Cell 37:381-391). The open arrow (RIC) denotes the center of a zone of initiation of DNA replication (Vassilev, L., and E. M. Johnson, 1990, Mol. Cell. Biol. 10:4899-4904). The position of the 467-bp insert of plasmid pMYC47 is indicated and expanded below, showing the bend center as identified in FIG. 2. pMYC47 contains a tandem duplicate of this fragment. Restriction endonuclease cleavage sites are abbreviated as follows: HIII, HindIII; P, PstI; Spl, Spel; HI, HpaI; X, XhoI; S, Sau3AI; H, HaeIII; D, DdeI; R, Rsal; A12, AvaII; A1, AvaI.

FIGS. 2A and 2B. Location of an intrinsically bent DNA segment upstream of the c-myc gene. A tandemly duplicated 467-bp Sau3A1 fragment mapped as in FIG. 1 (-1970 to -1504 from the P1 transcription start site), was cloned in plasmid pMYC47 and excised for bending analysis. It yields a 973-bp fragment including polylinker sequences. The tandem repeat was treated with single-site restriction enzymes to yield circular permutations of the 467-bp fragment. Enzymes are abbreviated as in FIG. 1. Lane M1 contains markers from the Bethesda Research Laboratories 1-kb ladder; lane M2 contains the 481-bp Bgl1-Xmn1 fragment of pUC19. Asterisks indicate two marker bands which are themselves more than 10% retarded due to bending (Stellwagen, N.C., 1983, Biochemistry 22:6186-6193). (A) Polyacrylamide gel electrophoresis showing anomalous migration of 467-bp fragments at 4.degree. C. (I, bracket at left). (The top band in lane S is a partial digestion product.) In lane D (Ddel digest), two fragments of 252 and 254 bp, are also produced from the original 973-bp plus polylinker sequences. One of these is retarded relative to the other at 4.degree. C. (II, arrows at left). (B) Elimination of bending at 60.degree. C. No anomalous migration of the 467-bp fragments is seen (I), and the 252- and 254-bp fragments now migrate together (II).

FIG. 3. Specificity of protein binding to the purine-rich strand of an element near the center of DNA bending. The probe is end-labeled single-stranded 24-mer MF0677, (SEQ ID. NO: 3) described in Section 6.1.1, corresponding to the purine-rich strand of nucleotides -1648 to -1625 upstream of the human c-myc P1 transcription start site. The left lane is the standard gel band shift binding reaction, described in Section 6.1.3, with no added competitor; the right lane is the reaction with an added HeLa nuclear extract. Unlabeled competitors are at 100X excess. Self, 24-mer MF0677; (SEQ ID. NO: 3) GGG>AAA, MM0677, (SEQ ID. NO: 12) the 24-mer mutated as indicated; dhfr G-A, DR3529 (SEQ ID NO: 8) (purine-rich 24-mer from the hamster dhfr replication initiation locus); dhfr C-T, DF3506, (SEQ ID. NO: 13) (pyrimidine-rich complement to DR3529); NSmycl and NSmyc2, MF0562 (SEQ ID. NO: 14)and MR0740, (SEQ ID. NO: 16) respectively (irrelevant control oligonucleotides from the c-myc locus).

FIGS. 4A and 4B. Specific UV cross-linking of a polypeptide with the PUR element. In each experiment, end-labeled 24-mer oligonucleotide MF0677, (SEQ ID. NO: 3) corresponding to the G-A strand of the c-myc PUR element, was either subjected or not subjected to UV cross-linking in the presence or absence of a HeLa nuclear extract as described in Section 6.2.3. The mixture was then subjected to SDS polyacrylamide gel electrophoresis in a 10% gel and autoradiographed. (A) Time course of UV cross-linking. Lanes were reacted without and with HeLa nuclear extract, as indicated. Cross-linking was performed for the times indicated. B, bound label; U, unbound label. Positions of protein molecular weight markers are shown at the right. (B) Specificity of protein-DNA cross-linking. The lane at left represents the reaction with no protein. Reactions were performed in the presence of either 25 or 75 .mu.g of unlabeled poly(dI-dC), a carrier to reduce potential nonspecific binding, per ml. 0, no added unlabeled competitor oligonucleotide. All competitors were added at 300-fold molar excess over the labeled probe. S, excess of the specific unlabeled 24-mer MF0677; (SEQ ID. NO: 3) NS, excess of nonspecific oligonucleotide MF0562, (SEQ ID. NO: 14) dhfr, excess of 24-mer DR3529 (SEQ ID. NO: 8) representing the hamster dhfr version of the PUR element [reacted in 25 .mu.g of poly(dI-dC) per ml]. The position of the PUR-binding protein is indicated by an arrow.

FIGS. 5A and 5B. Methylation interference analysis of purine contact points by protein specifically binding the purine-rich strand of the PUR element. After derivatization of .sup.32 P-end-labeled 24-mer oligonucleotide MF0677, (SEQ ID. NO: 3) containing the PUR element, with dimethyl sulfate, the single-stranded probe was allowed to react with protein in HeLa nuclear extract. (A) Gel band shift following derivatization with two levels of dimethyl sulfate as described in Section 6.2.4. Lanes -, reaction with 53 mM dimethyl sulfate, calculated to derivatize approximately one purine base per oligonucleotide molecule; +, reaction with fivefold-higher dimethyl sulfate; T, reaction without added protein. Each half of the gel represents a single methylation reaction from which bands were purified for further sequence analysis as in panel B. (B) DNA was purified from B (bound), U (unbound), and T (total) bands from the reaction shown in lanes--of panel A, cleaved at methylated purine residues by reaction with piperidine, and subjected to electrophoresis and autoradiography as described in Section 6.1.5. Starred bases indicate those preferentially represented in U versus B lanes.

FIG. 6. Mutation analysis of nucleotides essential for specific binding to the PUR element. Gel retardation of single-stranded probes by protein from HeLa nuclear extract was performed as described in 6.1.4. The four oligonucleotides listed at the top were used as probes. Pur G-A is the oligonucleotide MF0677, (SEQ ID. NO: 3) and Mut. I, II, and III are mutated oligonucleotides MM0677 (SEQ ID. NO: 12) (GGG>AAA in FIG. 3), MA0677, (SEQ ID. NO: 1) and MB0677, (SEQ ID. NO: 18) respectively. Sequences are listed in 6.1.1. Lanes: a, standard binding reaction with no added competitor; b to e, reactions with added 30-fold excess of unlabeled competitor oligonucleotides PUR G-A, MM0677, (SEQ ID. NO: 12) MA0677, and MB0677, (SEQ ID. NO: 18) respectively.

FIG. 7. Affinity of the Pur factor for single-stranded versus double-stranded PUR element. Single-strand PUR oligonucleotide MF0677 (SEQ ID. NO: 3) was used as a probe in the standard gel band shift assay described in Section 6.1.3. Unlabeled single- or double-stranded oligonucleotides were added as competitors. Lane 1 has no added protein; lane 2 is the standard reaction with no added competitor. Excesses (3-, 30-, and 300-fold) of the following oligonucleotides were added: SS, single-stranded MF0677, (SEQ ID. NO: 3) DS, double-stranded version of the 24-mer containing the PUR element made by annealing MF0677 (SEQ ID. NO: 3) and MR0700; (SEQ ID. NO: 15) NS-SS, nonspecific single-stranded oligonucleotide MR0740 (SEQ ID. NO: 16).

FIG. 8. Sequence of the PUR element region upstream of the human c-myc gene (SEQ ID. NO: 24). Numbering at the left is relative to the HindIII cleavage site 2,325 bp upstream of the P1 transcription start site. Numbering at the right is relative to the P1 start site. Indicated are two repeats of the yeast ARS consensus element each with 10-of-11-bp homology (solid arrows), two repeats of the PUR consensus element of Table 1, the first with 100% homology and the second with 14 of-16-bp homology (dotted area), and the sequence of oligonucleotide MF0677 (SEQ ID. NO: 3), used in binding studies (open box). Additional repeated elements within this region (GAGGGA and ATTATAT) are also indicated.

FIG. 9 Specific oligonucleotide binding by .lambda.abs. .lambda.AB2 phage were plated, induced and transferred to nitrocellulose membranes. Each membrane was then cut in half, and the halves incubated separately in the presence of MF0677 (SEQ ID. NO: 3) oligonucleotide, .sup.32 P-end-labeled as described in Section 7.1.2. The left half was incubated in the presence of an excess of unlabeled non-specific competitor MF0562,(SEQ ID. NO: 14) while the right half was incubated in the presence of excess unlabeled specific competitor (MF0677) (SEQ ID. NO: 3).

FIGS. 10A and 10B. Nucleotide sequence of Pur.alpha.(SEQ ID. NO: 1). The nucleotide sequence shown is derived from phage clones .lambda.AB6 and .lambda.HE1. The amino acid sequence of the open reading frame is indicated beneath the nucleotide sequence. Numbering begins with the first methionine. The line beneath the sequence at base -9 indicates the first base of the .lambda.AB6 clone. Singly-underlined amino acid residues in bold type indicate class I repeats. Doubly-underlined amino acid residues in bold type indicate class II repeats.

FIG. 11. Two repeat motifs in Pur.alpha. and Pur.beta.. The class I repeat motifs (three from Pur.alpha. and one from Pur.beta.) are aligned at top, and the class II repeat motifs (two from Pur.alpha.) are aligned at bottom. Solid boxes indicate identical amino acid residues, dotted boxes indicate conservative changes.

FIGS. 12A and 12B. Arrangement of amino sequence domains in Pur.alpha.. A) Domain structure of Pur.alpha.. The glycine-rich and glutamine, glutamate-rich domains both contain 50% or more of those respective amino acids. The class I repeats and the Class II repeats are described in FIG. 11. The amphipathic helix is described in FIG. 12B B) Axial view of the predicted amphipathic helix of Pur.alpha.. Basic and aromatic faces are indicated. Numbers indicate the position of each amino acid residue in Pur.alpha.. Bracketed residues indicate the amino acids occupying the equivalent positions in the homologous region of Pur.beta..

FIG. 13 Gel Shift assay of protein extracts from .lambda.AB clones. Gel shift assays using labeled MF0677 probe were performed as described in Section 6.1.3.

Left: Assay of protein extracts prepared from lysates of .lambda.AB4. Lane 1 displays probe in the absence of protein. Lane 2 displays probe in the presence of a control protein extract prepared from Y1090 cells infected with .lambda.ovalb, a chicken ovalbumin gene clone in .lambda.gt11 (Clontech). Lane 3 displays probe in the presence of protein extract from Y1090 cells infected with .lambda.AB4. Lane 4 displays signal with 5-fold dilution .lambda.AB4 extract. Lanes 5 through 8 represent reactions similar to that of lane 3, but with cold competitor added; lane 5, 5-fold excess of MF0677:(SEQ ID. NO: 3) lane 6, 5-fold excess of polyA: lane 7, 20-fold excess of MF0677:(SEQ ID. NO: 3) lane 8, 20-fold excess of polyA. Filled arrows indicate bands specific to the clone, open arrows indicate bands present normally in E. coli. Right: Assay of lysogens derived from .lambda.AB6. Lanes 1 and 2 display signal from IPTG induced lysogen either in the presence (lane 1) or the absence (lane 2) of a 5-fold excess of MF0677 (SEQ ID. NO: 3). Lane 3 displays signal from uninduced lysogen. Lane 4 displays signal from IPTG-induced Y1090. Lane 5 indicates signal from uninduced Y1090.

FIG. 14 Blot hybridization of human mRNAs with Pur.alpha. probe. Poly A.sup.+ RNA prepared from tissue or culture cells was subjected to electrophoresis and blotted as described in Section 7.1.5. Membranes were probed with labeled-Pur.alpha. cDNA. Lanes are: pPUR6xBamHI-pPUR6 DNA digested with BamHI; NCI-H82--lung tumor cell line mRNA; HepG2--liver hepatoma mRNA. The lower box displays the results of hybridization of the same membrane to a glyceraldehyde phosphate dehydrogenase probe as a loading control.

FIG. 15 5' and 3' RACE extension of Pur.alpha. cDNA. Products of the RACE reactions outlined in Section 7.1.6 were subjected to electrophoresis in alkaline denaturating agarose gels, Southern blotted to Gene-Screen Plus membranes and hybridized to a Pur.alpha. probe. In each case numbers on right indicate molecular weight markers in kb. Lane 1 in each case indicates the reaction containing both primers. Lane 2 in each case represents a control reaction in which one primer was omitted. Primer PDT-01 (SEQ ID. NO: 21) (TATCTGCAGTTTTTTTTTTTTTTTTT) was used to anneal to the poly-A tail generated for both 5' and 3' RACE. Left: 5' RACE. Pur-specific primers used were EX-270 (SEQ ID. NO: 22) (CTCGGCGATCTTCAGGAA), corresponding to nucleotides 270 to 253, for the first amplification reaction, and EX-174 (SEQ ID. NO: 23) (TTCTAAGCTTCGTCTCGTGCTGCAGCCC), corresponding to nucleotides 174 to 157 plus a HindIII linker, for the second amplification reaction. Right: 3' RACE. Pur-specific primers used were EX-695 (SEQ ID. NO: 19) (TCTTCGATGTGGGCTCCAAC), corresponding to nucleotides 695 to 714, for the first amplification reaction, and EX-990 (SEQ ID. NO: 20) (ACACACACACACATGCATAC), corresponding to nucleotides 990 to 1009, for the second amplification reaction.

FIG. 16. Delay in the onset of DNA synthesis in serum-stimulated human fibroblasts, by PUR element oligonucleotides.

FIG. 17. Regions of homologies between PUR protein and SV40 Large T-antigen.

FIG. 18. Expression of GST-PUR protein in E. coli. SDS polyacrylamide gel of various GST-fusion proteins eluded from a glutathione-linked agarose column. The last two lanes represent PUR-GST fusion protein prepared form two different strains of E. coli, DH5 and BL21-LYS.

FIG. 19. PUR binds the RB protein in WR2E3 cell extracts as determined by passage of extracts over PUR-GST columns. Column bound proteins were subjected to SDS-polyacyralmide gel electrophoresis and blotted onto nitrocellulose membrane. The RB protein was detected using anti-RB antibodies. PUR preferentially binds the unphosphorylated form of RB. Lane 1 is Retinoblastoma protein; Lane 2 is GST alone; Lane 3 is GST-T antigen fusion protein; Lane 4 is GST-ARP fusion protein which is another protein that interacts with the retinoblastoma protein and Lane 5 is GST-PUR fusion protein.

A purine rich 24 nucleotide DNA sequence referred to as the PUR element that is believed to play a role in initiation of DNA replication and perhaps regulation of gene expression is described. The PUR element occurs at a major site of DNA bending located 1.6 kB upstream of the transcription start site of the human c-myc gene, near the center of a reported zone of initiation of DNA replication.

The PUR protein, a 27 kD HeLa cell nuclear factor, was initially identified by its ability to bind in a sequence specific manner to single-stranded PUR element nucleotide sequences indicating a role for PUR protein in DNA replication and/or regulation of gene expression. A cDNA clone encoding a polypeptide with PUR element binding activity has been isolated and sequenced and that clone is described herein. The invention relates to the cloning, expression and production of the PUR protein, as well as to inhibitors of PUR protein which may have therapeutic value in the treatment of hyperproliferative diseases such as cancer.

Bending of DNA is a structural feature conserved at origins of replication in both eukaryotic and prokaryotic organisms. A major site of DNA bending is located 1.6 kB upstream of the transcription start site of the human c-myc gene. Gel-band shift assays and DNA methylation interference assays have more precisely defined the nucleotide sequences in this region of DNA that are important for DNA/protein interactions. This region of DNA is referred to as the PUR element and has the following nucleotide sequence (SEQ ID. NO: 3) GGAGGTGGTGGAGGGAGAGAAAAG.

A search of the GenBank nucleotide sequence data base for homologies to the 24 nucleotide c-myc PUR element reveals matches within previously identified zones of DNA replication, such as those found flanking the human and mouse c-myc gene, the hamster dhfr gene and stylonychia tubulin genes. In addition, matches were found in regions displayign ARS (autonomous replicating sequences) activity such as the direct repeat sequences of Entamoeba adn the yeast C2G1 ARS region. In addition, there are matches within the 5' regions of a number of cellular genes such as the hyman histone H4 and Beta-globin genes, and including the frequently amplified oncogenes c-myc, int-2, and lck suggesting that the PUR element may not only function during initiation of DNA replication but also in regulation of gene expression.

A role for the PUR element in initiation of DNA replication is supported by the examples detailed infra (Section 6.1.5 and 6.2.8.) in which the onset of cellular DNA replication is delayed in the presence of degenerate S-oligonucleotides designed to mimick the PUR element. Growth arrested human fibroblast, stimulated to proliferate by addition of fresh serum, were exposed to either PUR specific oligonucleotides or non-specific oligonucleotides. The incorporation of .sup.3 H-thymidine into newly synthesized DNA was measured and results indicate a delay in the onset of DNA replication in those cells exposed to PUR specific oligonucleotides (FIG. 16).

The PUR protein was initially identified as a 27 kD HeLa cell nuclear factor that bound in a sequence specific manner to single-stranded PUR element nucleotide sequences. A function for PUR protein in DNA replication and/or gene expression is indicated by the binding of PUR protein to specific regions of DNA involved in initiation of DNA replication and/or regulation of gene expression. A cDNA clone encoding a polypeptide with PUR binding activity has been isolated and sequenced.

The nucleotide coding sequence (SEQ. ID NO: 1) and deduced amino acid sequence of the human PUR protein is depicted in FIG. 10. In accordance with the invention, the nucleotide coding sequence for human PUR protein or its functional equivalent can be used to generate recombinant molecules which direct the expression of the PUR protein. The coding sequence of PUR may be obtained by cDNA cloning of RNA isolated and purified from cell sources that express PUR protein or by genomic cloning. cDNA libraries of clones may be prepared from DNA fragments generated using techniques known in the art, including but not limited to use of restriction enzymes.

The clones that contain the gene for PUR may be identified in a number of ways know in the art. For example, a portion of the PUR amino acid sequence can be used to deduce nucleotide sequence. The DNA sequence may then be chemically synthesized, radioactively end-labeled and used as a hybridization probe. Other methods which can be used include but are not limited to chemically synthesizing the gene sequence from derived amino acid sequence of PUR. Alternatively, in-vitro translation of selected mRNA followed by a functional or immunological assay of translation products can be used. For a review of cloning strategies which may be used, see, e.g., Maniatis, 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y.

In a specific embodiment described herein, the PUR gene was cloned by constructing a cDNA library into the bacteriophage expression system .lambda. gt11. The library was screened with radioactively labeled oligonucleotide MFO677 (SEQ OD NO:3) representing sequences found in the core of the PUR element. A PUR cDNA clone, designated PUR.alpha., was isolated and used to characterize PUR RNA and the PUR gene.

In accordance with the invention, nucleotide PUR sequences which encode PUR, peptide fragments of PUR, PUR fusion proteins or functional equivalents thereof may be used to generate recombinant DNA molecules that direct the expression of the PUR protein or a functionally active peptide, fusion protein or functional equivalent thereof, in appropriate host cells.

Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence, e.g., shown in FIG. 10A and 10B, may be used in the practice of the invention for the cloning and expression of the PUR protein. Such DNA sequences include those which are capable of hybridizing to the PUR sequence under stringent conditions, or those which would be capable of hybridizing under stringent conditions but for the degeneracy of the genetic code. The stringency conditions may be adjusted in a number of ways. For example, when performing polymerase chain reactions (PCR), the temperature at which annealing of primers to template takes place or the concentration of MgCl.sub.2 in the reaction buffer may be adjusted. When using radioactively labeled DNA fragments or oligonucleotides in hybridization reactions, the stringency may be adjusted by changes in the ionic strength of the wash solutions or by careful control of the temperature at which the washes are carried out.

Altered nucleotide sequences which may be used in accordance with the invention include deletions, additions or substitutions of different nucleotides resulting in a sequence that encodes the same or a functionally equivalent gene product. The gene product may contain deletions, additions or substitutions of amino acid residues within the sequence which result in silent changes thus producing a bioactive product. Such amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues involved. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; amino acids with uncharged polar head groups or nonpolar head groups having similar hydrophilicity values include the following: leucine, isoleucine, valine; glycine, alanine; asparagine, glutamine; serine, threonine; phenylalanine, tyrosine. As used herein, a functionally equivalent PUR protein refers to a peptide, polypeptide, protein or fusion protein that binds to the PUR element, but not necessarily with the same binding affinity of its counterpart native PUR protein. The design and engineering of constructs encoding PUR fusion proteins is described infra (Section 5.2.2.)

In an alternate embodiment of the invention, the coding sequence of the PUR protein could be synthesized, in whole or in part, using chemical methods well known in the art. See, for example, Caruthers, et al., 1980, Nuc. Acids. Res. Symp. Ser. 7: 215-233; Crea & Itrin, 1980, Nuc. Acids. Res. 9(10): 2331; Matteucci & Caruthers, 1980, Tetrahedron Letters 21: 719; and Chow & Kempe, 1981, Nuc. Acids. Res. 9(12): 2807-2817. Alternatively, the protein itself could be produced using chemical methods to synthesize the PUR protein amino acid sequence in whole or in part. For example, peptides can be synthesized by solid phase techniques, cleaved from the resin and purified by preparative high performance liquid chromatography. (E.g., see Creighton, 1983, Proteins, Structures And Molecular Principles, W. H. Freeman & Co., N.Y., pp. 50-60). The composition of the synthetic peptides may be confirmed by amino acid analysis or sequencing (e.g., the Edman degradation procedure; see Creighton, 1983, Proteins, Structures And Molecular Principles, W. H. Freeman & Co., N.Y., pp. 34-49).

The PURe cDNA can be used as a probe to detect the expression of PUR RNA. Northern blot analysis using mRNA prepared from human fetal liver tissue, HeLa cells, NCI-H82 cells and HepG2 cells reveal a similar pattern of multiple transcripts. Two major transcripts of 5.5 kB and 2.1 kB, and two minor transcripts of 3.3 kB and 2.8 kB were detected suggesting alternative splicing of a single PUR gene or the existence of a number of related genes.

The PUR.alpha. cDNA sequence may be used to isolate PUR.alpha. related genes. In a specific embodiment, a HeLa cell cDNA library was screened with a radioactively end-labeled fragment of the PUR cDNA clone. A number of clones were isolated, and one in particular was chosen for further sequence analysis. The clone, designated PUR-.beta., was found to be similar but not identical to the initially purified PUR cDNA clone demonstrating the existence of a family of related PUR proteins (FIGS. 11 and 12).

5.2.2. CONSTRUCTION OF EXPRESSION VECTORS CONTAINING THE PUR CODING SEQUENCE

In order to express a biologically active PUR protein, the nucleotide sequence coding for the PUR protein, or a functional equivalent including PUR fusion proteins, as described in Section 5.2.1, Supra, is inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequences. Methods which are well known to those skilled in the art can be used to construct expression vectors containing the PUR protein coding sequence operatively associated with appropriate transcriptional/translational control signals. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo recombination/genetic recombination. See, for example, the techniques described in Maniatis, et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory, N.Y. and Ausubel et al., 1989, Current Protocolsin Molecular Biology, Greene Publishing Associates & Wiley Interscience, N.Y.

A variety of host expression vector systems (i.e.-vectors which contain the necessary elements for directing the replication, transcription, and translation of PUR coding sequence) may be utilized equally well by those skilled in the art, to express PUR coding sequences. These include but are not limited to microorganisms such as bacteria transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing the PUR coding sequence; yeast transformed with recombinant yeast expression vectors containing the PUR coding sequence; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the PUR coding sequence; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing the PUR coding sequence; or animal cell systems infected with recombinant virus expression vectors (e.g., adenovirus, vaccinia virus) including cell lines engineered to contain multiple copies of the PUR DNA either stably amplified (e.g., CHO/dhfr) or unstably amplified in double-minute chromosomes (e.g., murine cell lines).

The expression elements of these vectors vary in their strength and specificities. Depending on the host/vector system utilized, any one of a number of suitable transcription and translation elements may be used. For instance, when cloning in mammalian cell systems, promoters isolated from the genome of mammalian cells, (e.g., mouse metallothionine promoter) or from viruses that grow in these cells, (e.g., vaccinia virus 7.5K promoter or Moloney murine sarcoma virus long terminal repeat) may be used. Promoters produced by recombinant DNA or synthetic techniques may also be used to provide for transcription of the inserted sequences.

Specific initiation signals are also required for sufficient translation of inserted protein coding sequences. These signals include the ATG initiation codon and adjacent sequences. In cases where the entire PUR gene including its own initiation codon and adjacent sequences are inserted into the appropriate expression vectors, no additional translational control signals may be needed. However, in cases where only a portion of the coding sequence is inserted, exogenous translational control signals, including the ATG initiation codon must be provided. Furthermore, the initiation codon must be in phase with the reading frame of the PUR coding sequences to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of transcription attenuation sequences, enhancer elements, etc.

For example, in cases where an adenovirus is used as an expression vector, the PUR coding sequence may be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite ladder sequence. This chimeric gene may then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region E3 or E4) will result in a recombinant virus that is viable and capable of expressing PUR in infected hosts. Similarly, the vaccinia 7.5K promoter may be used.

An alternative expression system which could be used to express PUR is an insect system. In one such system, Autographa californica nuclear polyhidrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The PUR coding sequence may be cloned into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter). Successful insertion of the PUR coding sequence will result in inactivation of the polyhedrin gene and production of non-occluded recombinant virus (i.e., virus lacking the proteinaceous coat coded for by the polyhedrin gene). These recombinant viruses are then used to infect Spodoptera frugiperda cells in which the inserted gene is expressed.

Retroviral vectors prepared in amphotropic packaging cell lines permit high efficiency expression in numerous cells types. This method allows one to assess cell-type specific processing, regulation or function of the inserted protein coding sequence.

In addition, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Expression from certain promotes can be elevated in the presence of certain inducers. (e.g., zinc and cadmium ions for metallothionein promoters). Therefore, expression of the genetically engineered PUR may be controlled. This is important if the protein product of the cloned foreign gene is lethal to host cells. Furthermore, modifications (e.g., phosphorylation) and processing (e.g., cleavage) of protein products are important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of protein. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed.

Fusion protein vectors may be used to express PUR fusion protein. The purified PUR fusion protein may be used to raise antisera against the PUR protein to study the biochemical properties of the PUR protein and/or to engineer PUR fusion proteins with different binding affinities for the PUR element, and/or for the RB protein. Possible expression vectors include but are not limited to, vectors that express .beta.-galactosidase and trpE fusions, maltose-binding protein fusions and glutathione-S-transferase fusions (carrier regions). Methods which are well known to those skilled in the art can be used to construct expression vectors containing PUR protein coding sequences. See, e.g., Maniatis, 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y.

The carrier region of the fusion protein may be used for purification of the PUR fusion protein. For example, antibodies against the carrier protein may be used in affinity chromatography for purification of the fusion protein. Alternatively, amylose resin may be used for purification of maltose binding protein fusions or glutathione-agarose beads may be used for purification of glutathione-S-transferase fusion proteins. The expression vectors may also contain polylinker sequences that encode specific protease cleavage sites so that any cloned protein may be released from its carrier protein by treatment with a specific protease. For example, DNA sequences encoding the thrombin or factor Xa cleavage sites may be included in the fusion protein vectors.

In a specific embodiment described herein, the PUR coding sequence was inserted into the pGEX-1.lambda.T expression vector containing the tac IPTG inducible promoter region and the coding region for the amino terminus of glutathione-S-transferase. After induction with IPTG, the GST-PUR fusion protein was purified from lysed cells using glutathione-linked agarose beads.

The host cells which contain the recombinant PUR coding sequence and which express the biologically active, mature product may be identified by at least four general approaches: (a) DNA-DNA, DNA-RNA or RNA-antisense RNA hybridization; (b) the presence or absence of "marker" gene functions; (c) assessing the level of transcription as measured by the expression of PUR mRNA transcripts in the host cell; and (d) detection of the mature gene product as measured by immunoassay and, ultimately, by its biological activity.

In the first approach, the presence of the human PUR coding sequence inserted in the expression vector can be detected by DNA-DNA hybridization using probes comprising nucleotide sequences that are homologous to the human PUR coding sequence.

In the second approach, the recombinant expression vector/host system can be identified and selected based upon the presence or absence of certain "marker" gene functions (e.g., thymidine kinase activity, resistance to antibiotics, resistance to methotrexate, transformation phenotype, occlusion body formation in baculovirus, etc.). For example, if the PUR coding sequence is inserted within a market gene sequence of the vector, recombinants containing the PUR coding sequence can be identified by the absence of the marker gene function. Alternatively, a marker gene can be place in tandem with the PUR sequence under the control of the same or different promoter used to control the expression of the PUR coding sequence. Expression of the marker in response to induction or selection indicates expression of the PUR coding sequence.

In the third approach, transcriptional activity of the PUR coding region can be assessed by hybridization assays. For example, polyadenylated RNA can be isolated and analyzed by Northern blot using a probe homologous to the PUR coding sequence or particular portions thereof. Alternatively, total nucleic acids of the host cell may be extracted and assayed for hybridization in such probes.

In the fourth approach, the expression of the mature protein product can be assessed immunologically, for example by Western blots, immunoassays such as radioimmuno-precipitation, enzyme-linked immunoassays and the like. The ultimate test of the success of the expression system, however, involves the detection of the biologically active PUR gene product. One of the properties associated with PUR protein is its sequence specific affinity for the PUR element. A possible method for detection of PUR protein activity might involve the use of gel-band shift assays.

The PUR protein was initially characterized as a factor present in HeLa cell nuclear extracts, that bound in a sequence specific manner to single-stranded PUR element sequence. Screening of a .lambda.gt11 expression library, with radioactively end-labeled PUR element sequences, represented by the oligonucleotide MF0677, resulted in the isolation of a cDNA clone encoding a protein with single-stranded binding activity matching that of the PUR factor.

The deduced amino acid sequence of PUR.alpha. reveals a modular repeat structure unique among known DNA-binding proteins. There are three repeats of a 23 amino-acid motif (class I repeats) interspersed with two repeats of a 26 amino-acid motif (class II repeats). The class I repeats are shown by single underlining in the sequence of FIG. 10A and 10B, and the class II repeats are shown by double underlining. While the sequence between these repeats is not conserved, the distance between the class I repeats is highly regular. The repeats themselves are not identical but preserve a number of strictly conserved amino acids of fixed distances along the repeats, indicated by solid boxing in FIG. 11, and a high percentage of conservatively-substituted amino acids, indicated by dotted-line boxing in FIG. 11.

In addition to repeat modules, PUR.alpha. contains several notable structural features denoted in FIG. 12A. Near the amino-terminal end of PUR.alpha. there is a prominent sequence of 28 glycine residues broken only by a single serine residue. Similar glycine stretches are present in proteins serving a wide variety of functions, including helix-destabilizing proteins (Haynes et al., 1987 Proc. Natl. Acad. Sci. US 79:4083-4087). Carboxyl terminal to all of the repeat modules there is a region (residues 261 through 274) of alpha helix (Chou and Fasman, 1974 Biochemistry 13:222-245; Levin et al., 1986 FEBS Lett. 205:303-308) upon which the amino acid side chains confer a strongly amphipathic character. The amphipathic helix is ordered with opposing basic and aromatic side chains, as presented in the helical wheel of FIG. 12B. Similar amphipathic helices are present in several DNA-binding proteins thought to play a role in transcriptional activation (Ptashne, 1988, Nature 335:683-689). The carboxyl terminus of the PUR.alpha. molecule consists of glutamine-glutamate-rich domain. The entire sequence from residue 276 through 321 is 50% glutamine and glutamate residues. There is one sequence of 7 consecutive glutamine residues, and near the carboxyl terminus there is a sequence of 5 glutamate residues broken by a single glycine. Glutamine-rich domains have been implicated as transcriptional activation regions in several DNA-binding proteins (Courey et al., 1989, Cell 59:827-836). At the border between the amphipathic helix and the glutamine-glutamate-rich domain there is the motif Ser-Glu-Glu-Met (residues 275 through 278). The serine in this motif is a potential phosphorylation site for casein kinase II (Kennelly and Krebs, 1991, J. Biol. chem. 266:15555-15558), although it is not known whether the motif serves this function in Pur.alpha..

In addition, the PUR.alpha. molecule shares a region of protein homology with the DNA tumor virus protein SV40 large T-antigen (FIG. 17). The region of SV40 T-antigen, sharing homology with PUR.alpha., is of particular interest as it is the region of T-antigen involved in the protein/protein interaction between SV40 large T-antigen and the retinoblastoma (RB) gene product.

Experiments were done to examine whether PUR.alpha. could function as SV40 large T-antigen and bind to RB protein. A PUR-GST protein was expressed in E. coli followed by immobilization of the fusion protein on a glutathione-linked agarose column. WR2E3 cell extracts were passed over the PUR-GST column and bound proteins were eluted with excess glutathione. The eluted proteins were subjected to SDS polyacrylamide gel electrophoresis and blotted onto nitrocellulose membrane. The presence of RB protein was detected using anti-Rb antibodies. As illustrated in FIG. 17, the PUR-GST fusion protein is able to bind cellular RB with the same affinity as SV40 large T-antigen. In addition, the PUR-GST fusion protein seems to preferentially bind the unphosphorylated form of RB.

The specific affinity of PUR protein for DNA sequences located at origins of replication suggest that PUR protein may play a role in regulation of cell proliferation. The observed protein/protein interaction between the PUR protein and the RB protein further supports the view that the PUR protein is involved in regulation of cell proliferation. The PUR protein also binds 5' to a number of cellular oncogenes that include c-myc, int-2 and lck, indicating that PUR may also regulate gene expression. Inhibitors of PUR protein may function to selectively inhibit the replication and/or gene expression of specific genetic loci associated with PUR elements.

Within the scope of the invention is the production of polyclonal and monoclonal antibodies that bind PUR or PUR related proteins. Antibodies to PUR may be useful as diagnostic and therapeutic agents. More specifically, antibodies that bind PUR protein and which neutralize PUR activity may be of particular therapeutic value. For example, antibodies that bind PUR protein and in doing so, prevent PUR binding to RB or to PUR element DNA sequences may be useful in therapies designed to inhibit cell proliferation.

For the production of antibodies, various host animals may be immunized by injection with the PUR protein including but not limited to rabbits, mice, rats, etc. Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and corynebacterium parvum.

Monoclonal antibodies to the PUR protein may be prepared by using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include but are not limited to the hybridoma technique originally described by Kohler and Milstein, (Nature, 1975, 256:495-497), the human B-cell hybridoma technique (Kosbor et al., 1983, Immunology Today, 4:72; Cote et al., 1983, Proc. Natl. Acad. Sci., 80:2026-2030) and the EBV-hybridoma technique (Cole et al., 1985, Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). In addition, techniques developed for the production of "chimeric antibodies" (Morrison et al., 1984, Proc. Natl. Acad. Sci., 81:6851-6855; Neuberger et al., 1984, Nature, 312:604-608; Takeda et al., 1985, Nature, 314:452-454) by splicing the genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce PUR-specific single chain antibodies.

Antibody fragments which contain specific binding sites for the PUR protein may be generated by known techniques. For example, such fragments include but are not limited to: the F(ab').sub.2 fragments which can be produced by pepsin digestion of the antibody molecule and the Fab fragments which can be generated by reducing the disulfide bridges of the F(ab').sub.2 fragments. Alternatively, Fab expression libraries may be constructed (Huse et al., 1989, Science, 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity to PUR protein.

Also within the scope of the invention are oligoribonucleotide sequences, that include anti-sense RNA molecules and ribozymes that function to inhibit the translation of PUR mRNA. Anti-sense RNA molecules act to directly block the translation of mRNA by binding to targeted mRNA and preventing protein translation.

Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. The mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by a endonucleolytic cleavage. Within the scope of the invention are engineered hammerhead motif ribozyme molecules that specifically and efficiently catalyze endonucleolytic cleavage of PUR RNA sequences.

Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the target molecule for ribozyme cleavage sites which include the following sequences, GUA, GUU and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target gene containing the cleavage site may be evaluated for predicted structural features such as secondary structure that may render the oligonucleotide sequence unsuitable. The suitability of candidate targets may also be evaluated by testing their accessibility to hybridization with complementary oligonucleotides, using ribonuclease protection assays.

Both anti-sense RNA molecules and ribozymes of the invention may be prepared by any method known in the art for the synthesis of RNA molecules. These include techniques for chemically synthesizing oligoribonucleotides well known in the art such as for example solid phase phosphoamite chemical synthesis. Alternatively, RNA molecules may be generated by invitro and in-vivo transcription of DNA sequences encoding the RNA molecule. Such DNA sequences may be incorporated into a wide variety of vectors which incorporate suitable RNA polymerase promoters such as the T7 or SP6 polymerase promoters.

Various modifications to the RNA molecules may be introduced as a means of increasing intracellular stability and half-life. Possible modifications include but are not limited to the addition of flanking sequences of ribo- or deoxy- nucleotides to the 5' and/or 3' ends of the molecule or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the oligoribonucleotide backbone.

Oligodeoxyribonucleotides can form sequence-specific triple helices by hydrogen bonding to specific complementary sequences in duplexed DNA. Interest in triple helices has focused on the potential biological and therapeutic applications of these structures. Formation of specific triple helices may selectively inhibit the replication and/or gene expression of targeted genes by prohibiting the specific binding of functional trans-acting factors.

Included in the scope of the invention are specific deoxyribonucleotide sequences, synthesized in a DNA synthesizer, that form triple helices with the PUR consensus element, which corresponds to nucleotides 7-22 of the MFO677 oligonucleotide (SEQ. ID NO.: 3), but wherein nucleotide 9 and/or 10 of SEQ. ID NO.: 3 can be substituted with any nucleotide and nucleotides 19-22 of SEQ. ID NO.: 3 can be substituted with either adenine or guanine. The PUR element is comprised predominantly of long repeats of G/A nucleotide sequences which are characteristic of target sequences favoring DNA triplex formation. Triple helix formation, at the site of PUR elements, may function to inhibit DNA replication and/or transcription of DNA sequences found adjacent to the element by preventing the binding of trans-acting factors such as PUR protein. Support for this is provided by experimental data demonstrating a delay in onset of DNA replication in cells exposed to PUR element oligonucleotides (FIG. 16).

The production and use of derivatives, analogues and peptides related to PUR are also envisioned and are within the scope of the invention. Such derivatives, analogues and peptides may be used to compete with full length wild-type PUR protein for binding to the PUR consensus element and in doing so inhibit PUR protein activity. The inhibition of PUR protein function may be utilized in several applications, including but not limited to, the treatment of hyperproliferative diseases such as cancer.

In a specific embodiment, a series of deletion mutants in the PUR coding region may be constructed and analyzed to determine the minimum amino acid sequence requirements for binding to the PUR consensus element. Deletion mutants of the PUR coding sequence may be constructed using methods known in the art which include but are not limited to use of nucleases and/or restriction enzymes; site-directed mutagenesis techniques, PCR, etc. The mutated polypeptides expressed may be assayed for their ability to bind to the PUR element by gel-band shift assays.

The DNA sequence encoding the desired mutated PUR polypeptide may then be cloned into an appropriate expression vector for overexpression in either bacteria or eukaryotic cells. Peptides may be purified from cell extracts in a number of ways including but not limited to ion-exchange chromatography or affinity chromatography using PUR element DNA sequences bound beads. Alternatively, polypeptides may be synthesized by solid phase techniques followed by cleavage from resin and purification by high performance liquid chromatography.

A search of the Genebank nucleotide sequence data base for homologies to the 24 nucleotide PUR element reveals a number of matches. Among the matches identified were those mapping to regions of the genome previously reported to be zones for initiation of DNA replication suggesting a role for PUR in initiation of DNA replication. Homologies were also observed in the 5' region of a number of cellular oncogenes including c-myc, int-2, and lck suggesting a potential role for PUR in regulation of gene expression. In fact, the structure of PUR protein shares a number of features in common with transactivating domains of many transcription factors and the region of PUR binding 5' to the myc gene, is a region previously reported to contain positively-acting transcriptional control elements (Hay et al. 1985, Genes Dev. 1:659-671). A number of factors are involved in both replication and transcription in prokaryotic, lower eukaryotic and viral systems.

Inhibitors of PUR activity may be useful for inhibiting cellular DNA replication and proliferation of specifically targeted cells. The therapeutic value of anti-PUR reagents for treatment of hyperproliferative diseases resulting from gene amplification is supported by the association of PUR elements with regions 5' to a number of oncogenes frequently found amplified in tissue derived from tumors. For example, using Southern and/or slot blot techniques, it has been shown that int-2 is amplified in cases of T-lymphoblastic leukemias (Tycko et al., J. Exp. Med. 174:867-73). In breast cancer specimens, c-myc, int-2 and lck, have also been shown to be amplified and in one particular study in which 49 cases of breast cell carcinomas were studied a correlation between tumor progression (i.e. metastatic vs. non-metastatic) and the level of c-myc and int-2 amplification was observed (Donovan-Peluso et al., 1991, Am. J. Pathol. 138:835-45). Studies have also detected overexpression of c-myc and int-2 in tumors of the bladder, esophagus and kidney (Tsutsumi et al. 1988, Jpn J. Cancer Res, 79:428-32).

In an embodiment of the invention anti-PUR antibodies capable of neutralizing the activity of PUR protein may be used to inhibit PUR activity. Small peptide fragments representative of regions of the PUR protein that competitively bind to the PUR element or the RB protein, and in doing so block the wild type protein from binding and carrying out its function may also be used to inhibit PUR activity. In yet another embodiment antisense or ribozyme molecules, designed on the basis of PUR DNA sequence, may be utilized to block translation and expression of PUR gene product. Finally, oligonucleotides complementary to the PUR element may be designed to form a triplex helical structure at the PUR element thereby preventing the binding of PUR protein.

The subsection below describes the characterization of a sequence element, referred to as the PUR element, found 1.6 Kb upstream of the cellular c-myc gene. The PUR element is located in a region of DNA bending activity which is a structural feature frequently associated with origins of DNA replication. Also described below is the identification of a polypeptide, having a molecular weight of approximately 37,000 and referred to as the PUR protein, that binds specifically to single-stranded DNA containing the PUR element sequence.

Plasmid pMYC47 (FIG. 1) was constructed by cloning the 467-bp Sau3A1 fragment of the c-myc upstream region into the BamHI site of pUC19 and screening for clones containing two copies of the fragment in the same orientation. The sequences of oligonucleotides used are as follows:

Circular permutation experiments were performed as described by Wu and Crothers (1984, Nature 308:509-513). The 973-bp EcoRI-PstI fragment of pMYC47, containing a tandem dimer of the 467-bp Sau3AI fragment shown in FIG. 1, was purified from low-melting-point agarose gels by melting at 65.degree. C. for 10 min followed by phenol extraction and ethanol precipitation. Restriction fragments generated by digestion of the 973-bp fragment were subjected to electrophoresis in 12.5% polyacrylamide gels, using Tris-borate-EDTA (TBE) buffer at 4.degree. C., stained with ethidium bromide, and visualized by UV irradiation.

Nuclear extracts were prepared from HeLa cells according to the procedure of Dignam et al. (1983, Nucleic Acids Res. 11:1475-1489). Gel shift assays were performed as described by Ausubel et al. (1989, Current Protocols in Molecular Biology 2:12.2.1-12.2.10). Binding reaction mixtures contained 0.5 .mu.g of poly(dI-dC), 4.5 .mu.g of bovine serum albumin, 1 to 3 .mu.g of nuclear extract protein, and 0.5 ng of oligonucleotide probe (end-labeled with T4 polynucleotide kinase and [.gamma.-.sup.32 P]ATP to approximately 60 Ci/mmol) in a total of 20 .mu.l of binding buffer (9 mM N-2-hydroxethylpiperazine-N'-2-ethanesulfonic acid [HEPES, pH 7.9], 9% glycerol, 45 mM KCl, 0.25 mM dithiothreitol, 0.25 mM phenylmethysulfonyl fluoride) unless specified otherwise. Binding was carried out for 15 min at 30.degree. C. Electrophoresis was conducted in TBE buffer at 150 V for 2 h at 4.degree. C. Gels were dried onto Schleicher & Schuell GB002 paper and autoradiographed on Kodak XAR5 film.

The molecular weight of the PUR DNA-binding factor was determined by using a UV cross-linking technique (Chodosh et al., 1986, Mol. Cell. Biol. 6:4723-4733). Aliquots of a standard binding reaction mixture, using as a probe end-labeled single-stranded oligonucleotide MF0677 (SEQ. ID NO: 3) as outlined for the gel shift assay, were spotted onto plastic wrap covering a UV transilluminator filter (Fotodyne model 3-4500) and exposed to two 15-W, 252-nm UV lamps for various lengths of time. The aliquots were then mixed with an equal volume of 2x sample buffer (4% sodium dodecyl sulfate [SDS], 20% glycerol, 0.001% bromophenol blue, 0.28M 2-mercaptoethanol, 125 mM Tris-HCl[pH 6.6] and subjected to electrophoresis in a discontinuous 12% polyacrylamide gel containing SDS. After electrophoresis, the gel was dried and autoradiographed as described above.

Methylation interference analysis was conducted as described previously (Postel et al., 1989, Mol. Cell. Biol. 9:5123-5133). MF0677 (SEQ. ID NO: 3) was end labeled with polynucleotide kinase and [.gamma.-.sup.32 P]ATP and partially methylated with dimethyl sulfate as described by Maxam and Gilbert (1980, Methods Enzymol. 65:499-560). Methylated probe was precipitated twice, suspended in Tris-EDTA, and used in standard gel shift assays. After autoradiography, bands for free and bound probe were excised, case in 1% agarose gels, and transferred by electrophoresis to NA-45 paper (Schleicher & Schuell). DNA fragments were recovered from the paper pieces by incubation at 68.degree. C. for 30 min in 200 .mu.l of elution buffer (10 mM Tris-Cl [pH 8.0], 1 mM EDTA, 1M NaCl) and ethanol precipitated. The dried pellet was suspended in 100 .mu.l of 1M piperidine and incubated at 95.degree. C. for 30 min. After lyophilization, the pellets were suspended in formamide stop buffer (USB Scientific), and aliquots containing equal counts per minute (as measured by Cerenkov counting) were analyzed by electrophoresis on a 20% sequencing gel, dried, and autoradiographed as described above.

The human fibroblast cell line GM2522 was allowed to grow to confluence over a period of 7-8 days at 37.degree. C. After 7 days in culture, the confluent monolayers have depleted the medium of serum growth factors and the cells have growth arrested. The cells were then stimulated to progress synchronously through the cell cycle by removing the depleted medium and replacing it with fresh medium containing 15% FCS. Sixteen hours prior to serum stimulation the cells were exposed to 3 MM concentrations of S-oligonucleotides that were designed to mimick the pyrimidine-rich strand of the PUR element. The pools of degenerate 14-mer oligonucleotides were based on the following sequence: 5'-CCCTTCGCCGCCTC-3'. The controls for the experiment included plates containing non-specific oligonucleotides and plates in which no oligonucleotides had been added. The rate of DNA synthesis was determined by measuring the amount of .sup.3 H-thymidine incorporated into newly synthesized cellular DNA. Each time point represents the average of 3 plates.

To begin characterization of sequence elements within the potential c-myc replication initiation zone, we sought to map the site(s) of stable DNA bending in this region. Experiments of Kumar and Leffak (1989, Nucleic Acids Res. 17:2819-2833) had previously suggested at least one site in this region, but localization with regard to restriction cleavage sites by cyclic permutation had not been performed. Plasmid pMYC47 was created by introducing two copies of the 467-bp Sau3A fragment of the c-myc locus, spanning the region from bp -1970 to -1504 upstream of the c-myc P1 transcription start site, into the BamHI site of pUC19. This region includes much of the potential initiation zone as well as possible transcriptional control sequences (FIG. 1). The two insert copies are in the same orientation. Cyclic permutation experiments were performed by isolating the 973-bp PstI-EcoRI fragment (which contains both copies of the c-myc fragment) from agarose gels and then digesting aliquots with several different restriction endonucleases, each with a unique cleavage site in the 467-bp segment, prior to electrophoresis on polyacrylamide gels (FIG. 2). Each digest generates a 467-bp fragment plus two smaller end fragments. Reduced gel mobility is considered indicative of bending, greatest reduction in mobility occurring when the bend is near the center of a given fragment. It can be seen that RsaI generates a fragment with greatest reduction in mobility. Further evidence for the presence of a bend can be derived from the smaller fragments generated in these digestions. The two smaller fragments generated by DdeI digestion are 252 and 254 bp in length, respectively. Electrophoresis at 4.degree. C. readily resolves these two bands (FIG. 2A, lane D). However, the two bands cannot be resolved by electrophoresis at 60.degree. C. (FIG. 2B, lane D), a temperature at which the anomalous mobility of bent DNA fragments is abolished (Diekmann, S. 1987, Nucleic Acids Res. 15:247-265). In this case, the degree to which the bend retards migration of the slower fragment relative to the unbent fragment is approximately 15%. The mobility of the 341-bp fragment generated by HaeIII digestion is also reduced at 4.degree. C. relative to molecular weight standards. The degrees of retardation of the various fragments are consistent with a bend centered between bp -1667 and -1587 upstream of the P1 start site.

To determine whether a protein(s) can bind to the region of the DNA bend, we first used as a probe a PCR-derived segment comprising 179 bp centered on the bend, as depicted in FIG. 1. Gel band shift assays using this probe revealed a clear protein-induced shift, creating one apparent band. Several oligonucleotides spanning this segment were tested for ability to compete with the segment in the gel shift assay, and competition was observed with use of a 24 bp double-stranded oligonucleotide representing a sequence near the center of the segment. These data are not shown because subsequent experiments have demonstrated the single-strand preference of protein binding to this region. In all experiments using a given putative double-stranded oligonucleotide, it is an inevitable possibility that a single-stranded version of the oligonucleotide, conceivably generated by the reaction, is responsible for the binding or competition observed. Therefore, we present here only results demonstrating unequivocally the single-strand sequence specificity of binding to the original 24-mer. In gel shift assays, an oligonucleotide representing the purine-rich strand of the specifically competing sequence (MF0677) (SEQ. ID NO: 3) binds a factor occurring in nuclear extracts of HeLa cells (FIG. 3). The binding is sequence specific, since an excess of the unlabeled oligonucleotide effectively prevents formation of the complex in competition experiments, whereas excesses of oligonucleotides with unrelated sequences taken from the c-myc locus do not (FIG. 3). In additional experiments, we have determined that the unlabeled oligonucleotide similarly inhibits binding to the labeled one when an excess of single-stranded M13 DNA is substituted for poly(dI-dC). A nonspecific single-stranded oligonucleotide (MR0740) (SEQ. ID NO:16)does not inhibit binding to the labeled probe in the presence of M13 DNA (data not shown). An oligonucleotide in which the three consecutive guanosine residues in MF0677 (SEQ ID NO:3) have been substituted with adenosine residues (MM0677(SEQ. ID NO:12); GGG>AAA in FIG. 3) competes poorly for binding of the factor. However, an oligonucleotide with a sequence occurring within the origin of DNA replication near the CHO dhfr gene (DR3529(SEQ. ID NO:8); dhfr G-A in FIG. 3) is an effective competitor. The complement of DR3529 (SEQ. ID. NO: 13), DF3506 (SEQ. ID NO: 8) (dhfr C-T in FIG. 3), does not compete. In additional experiments (not shown), we have observed that the factor binds to the dhfr purine-rich oligonucleotide DR3529 (SEQ. ID NO: 3), used as a labeled probe, and that this binding is effectively competed for by a 20-fold excess of unlabeled c-myc oligonucleotide MF0677 (SEQ. ID NO:3). We term the purine-rich binding element the PUR element.

Results of gel band shift experiments have suggested thus far that only ohe protein or protein complex is involved in binding the c-myc bend region. We sought to identify any binding protein by UV-induced covalent linkage of the protein to the purine-rich 24-mer, MF0677 (SEQ. ID NO:3). UV cross-linking of the factor in HeLa nuclear extracts to .sup.34 P-end-labeled MF0677 (SEQ. ID NO:3) generates a labeled band representing bound complex on protein SDS-polyacrylamide gels. FIG. 4 shows that the amount of this protein bound increases with increased time of exposure to UV. At 2 min, the band detected is narrowly centered on approximately 28 kD. The oligonucleotide contributes relatively little to migration on protein SDS-gels (Chodosh et al., 1986, Mol. Cell. Biol. 6:4723-4733). Nonetheless, the molecular weight obtained by this technique must be considered approximate. Formation of the labeled complex is inhibited by a 100-fold excess of unlabeled MF0677 (SEQ. ID NO:8) (FIG. 4B, lane S) but not by a similar excess of nonspecific competitor (FIG. 4B, lane NS). A similar complex forms with the DR3529 (SEQ. ID NO:3) oligonucleotide, containing the PUR element sequence version from the dhfr origin region (FIG. 4B, lane dhfr). We term the 28-kDa polypeptide which binds the PUR element Pur.

Partial methylation was performed by using dimethyl sulfate with the aim of methylating approximately one purine residue per oligonucleotide molecule (FIG. 5, lanes -). Use of fivefold-greater dimethyl sulfate in the methylation reaction reduces subsequent binding of the factor to MF0677 by more than 80% (FIG. 5A, lanes +). Bands representing bound, unbound, and total DNA from the partial methylation experiment of FIG. 5A were excised and subjected to specific depurination using a piperidine reaction (Maxam, A. M. and W. Gilbert, 1980, Methods in Enzymol. 65:499-560). The vast majority of bound oligonucleotide is unmethylated (FIG. 5B, lane B) as uncleaved material remaining near the gel origin. The residual protein binding (FIG. 5A, lanes +) and cleavage bands (FIG. 5B, lane B) may reflect the greater flexibility of the sugar-phosphate backbone in single-stranded DNA molecules, presumably reducing the steric interference due to the methyl group. The vast majority of unbound probe (FIG. 5B, lane U) is methylated, and thus cleaved by the piperidine reaction, and migrates into the gel. Comparison of lanes B and U clearly shows a pattern of guanosine bases that are underrepresented in lane B and overrepresented in lane U. Methylation of these G residues interferes with protein binding. These G residues, highlighted by stars in the sequence in FIG. 5B, are implicated as contact points with Pur. One of these G residues is present in the G triplet motif. This is consistent with results of FIG. 3, showing that altering GGG to AAA reduces protein binding. No adenosine bases are implicated by this experiment as contact points. However, A is somewhat less susceptible than G to cleavage in this protocol. Thymidine bases are not methylated. Additional experiments will be required to document clearly any contact points with T in this single-stranded oligonucleotide.

Methylation interference results reveal guanosine-protein contact points within the PUR element. It is conceivable that Pur can bind a subcombination of G residues and that more than one such combination exists in the PUR element. For example, either GNGG or GGNGG could be a binding motif, and each is represented three times in the PUR 24-mer. We tested this possibility by using synthetic oligonucleotides with G bases selectively mutated in three combinations (FIG. 6). In each of the combinations, competition for binding to the PUR element is nearly abolished. All three mutations bind protein weakly (lanes a). It is important to note that the gel shown was run at 4.degree. C. When mutant-protein complexes are subjected to electrophoresis at room temperature, they decompose readily, whereas the PUR G-A-protein complex does not. Mut. I in FIG. 6 is the GGG>AAA mutation also shown in FIG. 3. Mut. III has three of the G contact points shown in FIG. 5 disrupted, and it is the least able to compete with added unlabeled DNA. Mut. II is nearly at the level of Mut. III in this regard, and it has only two contact points disrupted, but at the 5' end of the molecule. These data indicate that at least three of the contact points of FIG. 5 are important for initial binding and that disrupting one, two, or three of them seriously disrupts the protein-DNA complex. The data rule out either GNGG or GGNGG as a binding motif, since mutants which do not bind effectively still retain these motifs. The three mutants are equally purine rich. Therefore, the data show that any purine-rich segment is not in itself sufficient to bind Pur. Results are consistent with the notion that one Pur molecule can contact all the observed contact points in the PUR element. These data do not, however, rule out a cooperative mechanism in which binding of one Pur molecule to a G subcombination greatly increases binding of the next Pur molecule.

We used the double-stranded version of the PUR 24-mer, unlabeled, in competition for protein binding with the labeled single-stranded, purine-rich version. For this procedure, double-stranded oligonucleotides were gel purified from annealed single strands. The double-stranded oligonucleotide for PUR does inhibit binding to the single-stranded version (FIG. 7, lanes 3 to 5), but only at molar concentrations nearly 10-fold higher than does the single-stranded version. A nonspecific single-stranded oligonucleotide does not inhibit binding at any concentration tested (lanes 6 to 8). Similarly, nonspecific double-stranded oligonucleotides [poly(dI-dC)] do not inhibit binding, even at greater than 1,000-fold excess over the labeled probe (lane 12). These results indicate that Pur has an affinity for the double-stranded PUR element. The possibility cannot be excluded that some generation of single-stranded PUR element occurs in the binding reaction and that this is responsible for part of the inhibition. It is unlikely to be responsible for all of the inhibition, however, since that would involve unwinding nearly 10% of the added double-stranded oligonucleotide. In any case, it is clear that affinity for the double-stranded element is at least 10-fold lower than its affinity for the single-stranded, purine-rich PUR sequence.

We searched the GenBank nucleotide sequence data base for homologies by using the 24-nucleotide sequence comprising the c-myc PUR element region. Numerous matches were recorded from sequences throughout the eukaryotes, particularly from gene 5' flanking regions and replication origins. These primarily centered on a 16-bp core of strong homology, which is presented as a consensus sequence which correspnds to nucleotides 7-22 of the MFO677 oligonucleotide (SEQ. ID NO.: 3), but wherein nucleotide 9 and/or 10 of SEQ. ID NO.: 3 can be substituted with any nucleotide and nucleotides 19-22 can be substitited with either adenine or guanine. No homologies to the consensus sequence were found in prokaryotic, plasmid, or phage genomes. Most of these were in gene 5' flanking regions. Four of the best homologies were in regions previously identified as origins of DNA replication or as elements conferring ARS activity. Surprisingly, one of the best consensus matches was to a sequence repeated near the center of the hamster dhfr replication initiation zone. (This finding compelled us to repeat earlier experiments adding this sequence as shown in FIGS. 3 and 4). The dhfr PUR element is located approximately 17 kb 3' to the dhfr gene, a position not known to harbor any transcriptional regulatory sequences. The PUR element is also located 5' to the mouse c-myc gene and to both human and mouse N-myc genes. At least four of the best matches are near genes known to be selectively amplified in cells of their respective organisms.

A comparison of the PUR consensus sequence with FIG. 5 indicates that not all important guanosine contact points for the HeLa Pur protein, detected by methylation interference, are represented in the consensus sequence. Conversely, several purine residues at the 3' end of the PUR consensus sequence are not detected as contact points for the HeLa protein by methylation interference. One plausible explanation for this is that certain purine bases are important for recognition of double-stranded DNA although they are not actually contact points in the stable DNA-protein complex. For example, certain purine bases may be required to maintain double-stranded DNA in a bent configuration, important for recognition, although the single-stranded DNA-protein complex involves other base contact points.

Oligonucleotides designed to mimick the pyrimidine rich strand of the PUR element, delay the onset of DNA synthesis in serum-stimulated human fibroblast when compared to plates containing either no oligonucleotides or non-specific oligonucleotides (FIG. 16). These results provide further evidence that the PUR element and the PUR protein play a role in the regulation of cell proliferation and DNA replication.

The subsections below describe the cloning and sequencing of a complementary DNA representing the human PUR gene and the sequence specific single-stranded DNA binding properties of the encoded protein. The deduced amino acid sequence of PUR protein reveals several motifs shared in common between DNA-binding proteins and helix-destabilizing proteins. Northern blot analysis indicates that a family of PUR related genes may exist. Attempts to isolate cDNA clones representing PUR related genes has resulted in the isolation of a PUR related cDNA clone referred to as PUR.beta..

Oligonucleotide MF0677 (SEQ. ID NO:3) (GGAGGTGGTGGAGGGAGAGAAAAG) is a 24-mer representing the c-myc sequence element initially established as binding to Pur. The oligonucleotides used as competitors with MF0677 in binding experiments are listed in Table II.

Binding of various synthetic oligonucleotides to protein extract of .lambda.AB6 lysogen. Binding reactions were performed as gel-shift assays as described in Section 6.1.2. The labeled probe in each reaction was oligonucleotide MF0677 (SEQ. ID NO:3). Competing oligonucleotides were added in either 5-fold or 20-fold excess.

a. Single-stranded oligonucleotides used were the following: MF0677 (SEQ. ID NO:3), the 24-mer representing the PUR element site originally detected upstream of the human c-myc gene; MC0677 (SEQ. ID. NO:6), ME0677 (SEQ. ID NO:6), MG0677 (SEQ. ID. NO:4), MH0677 (SEQ ID NO:11) MI0677 (SEQ. ID NO;9), and MJ0677 (SEQ. ID NO:3), mutants of oligonucleotide MF0677 in which indicated residues have been replaced by T; DR3529 (SEQ. ID NO:8), a 24-mer representing the hamster dhfr version of the PUR element; POLYG(SEQ. ID NO:7) and POLYA, (SEQ. ID. NO:25) homopolymers representing the two most common bases in the PUR element.

b. Following autoradiography of the gel-shift assay results, bands were scanned with a densitometer. Values given represent the per cent of binding activity remaining.

The following two oligonucleotides were used as non-specific competitors in the screening of expression libraries:

Oligonucleotides used as primers in 3' and 5' RACE experiments are listed in the legend to FIG. 15.

A human fetal liver library (Clontech Cat. No. HL1005, prepared in vector .lambda.gt11) was screened for clones which bind the purine-rich sequence from upstream of the c-myc gene (oligonucleotide MF0677 (SEQ. ID NO:3), essentially as has been described previously for double-stranded oligonucleotides (Singh et al., 1988 Cell 52:415-423; Singh, 1989, In Current Protocols in Molecular Biology, Volume 2, Ausubel et al. (Greene Publishing Associates and Wiley Interscience) p. 12.7.1-12.7.10. The library was plated on E. coli strain Y1090 on a total of six 150 mm plates at a density of 5.times.10.sup.4 PFU per plate. Plates were incubated at 42.degree. C. for 3 hours. The plates were then overlayed with nitrocellulose filters which had previously been saturated with 10 mM IPTG and then dried. The plates were incubated for a further 6 hours at 37.degree. C. and then stored at 4.degree. C. while the filters were being screened. After lifting from plates, filters were immersed in binding buffer (50 mM KC1, 10 mM N-2-hydroxyethyl-piperazine-N'-2-ethanesulfonic acid [HEPES], pH7.8, 0.2 mM EDTA, and 0.5 mM DTT) containing 5% non fat milk powder (Carnation) and gently shaken at room temperature for 60 minutes. Filters were then washed for five minutes at room temperature three times in binding buffer. Filters were then shaken gently for 60 minutes at room temperature in 15 ml of binding buffer containing 10.sup.6 cpm of probe (MF0677 (SEQ. ID NO:3) labeled by polynucleotide kinase) and 5 .mu.g/ml of each of MF0562 (SEQ. ID NO:14) and MR0740 (SEQ. ID NO:16). Filters were washed four times in binding buffer (50 ml per filter) at room temperature for 7 minutes and then blotted dry before autoradiography. Potential positives were pooled and rescreened.

Inserts in .lambda.gt11 were cloned into M13 bacteriophage and sequenced by the dideoxy-termination technique (Sanger et al., 1977 Proc. Natl. Acad. Sci. USA 74:5463-5467). Sequence analysis was conducted using the IBI Pustell programs.

Y1090 clones lysogenized with .lambda.AB5 and .lambda.AB6 were isolated by infection at a multiplicity of infection of 10, followed by plating on agar containing Luria broth and incubating overnight at 32.degree. C. as has been previously described (Singh, 1989, In Current Protocols in Molecular Biology, V12 Ausubel et al. (Greene Publishing Associates and Wiley Interscience) p. 12.7.1-12.7.10). Lysogens were then identified by their sensitivity to growth at 42.degree. C. To prepare protein extracts, lysogens were grown at room temperature with shaking in Luria broth until they reached mid-log phase. IPTG was then added to 5 mM and the cultures were incubated at 37.degree. C. for 2 hours with shaking. Aliquots of 1.0 ml of each culture were pelleted at 13,000 x g for 2 minutes, and each pellet was resuspended in 50 .mu.l of extraction buffer (10 mM HEPES, pH 7.9, 1 mM EDTA, 1 mM DTT, 1 mM PMSF). Each sample was sonicated six times for 5 sec at an amplitude of 10 microns. To each such protein extract 40 .mu.l of 50% glycerol plus 10 .mu.l of 5M NaCl were added, and extracts were then incubated for 15 minutes at 4.degree. C. The extracts were cleared by 30 minute centrifugation at 13,000 x g at 4.degree. C. Protein extracts were prepared for phage lysates as follows. Phage were plated on 150 mm plates at a density of 10.sup.5 per plate and incubated at 37.degree. C. for 9 hours. The top agar was collected, mixed with 10 ml of extraction buffer and incubated at 4.degree. C. for 1 hour. The agar was then removed by centrifugation at 12000 xg for 10 minutes and the supernatant dialyzed against extraction buffer for 6 hours at 4.degree. C. Aliquots (2.mu.l ) of each protein extract were used in gel shift assays, as have previously been described for nuclear extracts (Bergemann and Johnson, 1992 Mol. Cell. Biol. 12: 1257-1265).

Cell lines used for the preparation of mRNA were grown in suspension in one litre Corning spinner flasks. HeLa cells were grown in Dulbecco's Modified Eagle Medium (GIBCO), human hepatoma cells (HepG2) were grown in Joklik Modified Eagle Medium (Sigma), and small cell lung carcinoma cells (NCI-NH2) were grown in RPMI 1640 medium (GIBCO). All media were supplemented with 10% fetal calf serum, 50 U/mL penicillin G and 50 .mu.g/mL streptomycin. Cells were pelleted at 1,600 x g for 5 minutes. Human fetal liver tissue, second trimester, was kindly supplied by Sunkara Rao, Renata Dische and Stave Kohtz. For preparation of RNA, tissue was frozen in liquid nitrogen and ground in a Biopulverizer. Total RNA was extracted from both tissues and harvested cells as previously outlined (Chirgwin et al., 1979, Biochemistry 18:5294-5299). RNA samples were passed twice through oligo dT-cellulose columns to purify poly(A).sup.+ RNA (Aviv and Leder, 1972 Proc. Natl. Acad. Sci. 69:1408-1412). The RNA concentration of each sample was determined by absorbance at 260 nm. Poly(A).sup.+ RNA (10 .mu.g per lane) was subjected to electrophoresis on 1.2% agarose gels containing 2.2% formaldehyde at 2.5 V/cm for 3.75 hours (Sambrook et al., 1989, In Molecular Cloning VI. 1, p. 7.43-7.45 Cold Spring Harbor Laboratory Press). RNA was transferred to Gene Screen Plus membranes (Du Pont), exposed to UV for 2 minutes and based at 80.degree. C. in a vacuum oven for 2 hours. Filters were prehybridized for 3 hours at 70.5.degree. C. in northern hybridization solution (50 mM N-tris(hydroxyl)methyl-2-aminoethanesulfonic acid [TES], pH 7.0, 25 mM Na.sub.2 HPO.sub.4, 25 mM NaH.sub.2 PO.sub.4, 0.3 M NaC1, 30 mM trisodium citrate, 1% SDS, 10% dextran sulphate, 100 .mu.g/mL sonicated salmon sperm DNA and 100 .mu.g/mL yeast RNA), and hybridization to the probe was performed in the same solution at 70.5.degree. C. for 17 hours. The probe used was the 777 bp PstI fragment of the Pur.alpha. cDNA (nucleotides 165 through 941), labeled with .sup.32 P-phosphate by a random priming procedure (Feinberg and Vogelstein, 1983, Anal. Biochem. 137:266-267). After hybridization, filters were washed twice for 5 minutes each in 2xSSC +SDS (SSC is 150 mM NaC1, 15 mM sodium citrate, pH 7.0) at 70.5C. and once for 30 minutes in 0.1xSSC+1% SDS at 70.5.degree. C. Filters were then rinsed in 2xSSC and autoradiographed on Kodak XAR film.

HepG2 cell poly(A).sup.+ RNA prepared as described was employed for rapid amplification of cDNA ends (RACE). Rapid amplification of the 3' cDNA end of Pur was carried out essentially as described previously (Frohman et al., 1988 Proc. Natl. Acad. Sci. USA 85:8998-9002). Positions of the primers used are detailed in the legend to FIG. 7. One microgram of HepG2 cell poly(A).sup.+ RNA in 13 .mu.l of distilled water was denatured at 70.degree. C. for 5 minutes and immediately chilled on ice. The first strand cDNA was synthesized with 20 .mu.M primer PDT-01 (SEQ. ID NO:21) and 200 U of reverse transcriptase from the SuperScript Preamplification System (BRL) according to. the manufacturer's instructions, except that 20 U of RNasin (Promega) was included in the reaction. One microliter of cDNA from the reverse transcription reaction mix was then PCR amplified in 100 .mu.l reaction volume with addition of 2.5 U of Taq polymerase using two primers (PDT-01 (SEQ. ID NO:21) and EX-695 (SEQ. ID NO:19), each 100.mu.M). The PCR profile was as follows: denaturation of 94.degree. C. for 1 minute, annealing reaction of 54.degree. C .for 2 minutes, and extension at 72.degree. C. for 5 minutes. One microliter of the first amplification reaction was used for the second amplification of 3' cDNA end of Pur. The primer EX-990 (SEQ. ID NO:20) (100.mu.M) was substituted for primer EX-695 (SEQ. ID NO:19). The PCR reaction was performed for 20 cycles in the same reaction buffer, performed as described at 65.degree. C. for 6 hours. The membranes were then washed twice in 2xSSC+1% SDS at 65.degree. C. each for 5 minutes, twice in 0.1xSSC+1% SDS at 65.degree. C. each for 30 minutes, once for 5 minutes in 0.1xSSC and autoradiographed as described above.

A .lambda.ZAP II library of HeLa cell cDNAs was kindly supplied by J. L. Manley. The library was screened for clones of Pur using previously described techniques (Benton and Davis, 1977 Science 196:180-182; Quertermous, 1989 In Current Protocols in Molecular Biology, Vol. 2 Ausubul et al. (Green Publishing Associates and Wiley Interscience); Strauss, 1989 In Current Protocols in Molecular Biology, Vol. 2 Ausubul et al. (Green Publishing Associates and Wiley Interscience). The 777 bp PstI fragment, outlined for use in Northern analysis, was labeled by priming of the Klenow polymerase reaction with random hexanucleotides (Feinberg and Vogelstein, 1983 Anal. Biochem 137:266-267), and hybridized to the filters in hybridization solution (20 mM Tris HC1, Ph 7.6, 10% dextran sulphate, 24 mM sodium phosphate buffer, pH 7.6, 0.1% SDS, 750 mM NaC1, 75 mM trisodium citrate) at 60.degree. C. in wash buffer (40 mM sodium phosphate buffer, pH 7.2, 1 mM EDTA, 5% SDS). Finally, the filters were rinsed twice in 2xSSC and dried prior to autoradiography.

An Eco R1 DNA fragment, containing the PUR coding region, was inserted into the Eco R1 site of the expression vector pGEX-1.lambda.T. The resulting recombinant expression vector contains the PUR coding region fused to the amino-terminal region of the glutathione-S-transferase protein.

Competent E. coli cells were transformed with recombinant DNA and transformants were selected for on LB/ampicillin plates. For preparation of GST-PUR fusion protein, transformed colonies were inoculated into LB/ampicillin media. The expression of the fusion protein was induced by addition of IPTG to 0.1 mM into the culture media.

Cells were lysed and the extracts were passed over a column containing glutathione-linked agarose beads. The column was washed and the bound protein was eluted by passing a solution containing excess glutathione over the column. The eluted proteins were separated on a SDS polyacrylamide gel and visualized by Coomassie Blue staining of gel.

A PUR-GST fusion protein was expressed in E. coli followed by immobilization of the fusion protein on a glutathione-linked agarose column. WR2E3 cell extracts were passed over the PUR-GST fusion protein column and the bound proteins were eluted with a buffer containing excess glutathione. The eluted proteins were subjected to SDS polyacrylamide gel electrophoresis and blotted onto nitrocellulose membrane. The presence of RB protein was detected using anti-RB antibodies.

There is one sequence of 7 consecutive glutamine residues, and near the carboxy terminus there is a sequence of 5 glutamate residues broken by a single glycine. Glutamine-rich domains have been implicated as transcriptional activation regions in several DNA-binding proteins (Courey et al., 1989 Cell 59:827-836). At the border between the amphipathic helix and the glutamine-glutamate-rich domain there is the motif Ser-Glu-Glu-Met (residues 275 through 278). The serine in this motif is a potential phosphorylation site for casin Kinase II (Kennelly and Krebs, 1991 J. Biol. Chem. 266:15555-15558), although it is not known whether the motif serves this function in Pur.alpha..

Protein extracts derived from either phage lysates or lysogens of .lambda.AB5 and .lambda.AB6 display the presence of three bands in gel shift assays, using labeled MF0677 (SEQ. ID NO:3) as probe, which are not present in controls (solid arrows in FIGS. 13, A and B). The controls employed are either uninfected Y1090 bacteria or lysogen uninduced by IPTG. The clone-specific bands only appear after induction by IPTG, indicating that they result from the fusion of the open reading frame indicated for .lambda.AB6 in FIG. 2 to the .beta.-galactosidase gene. The bands are clearly competed by a 20-fold excess of MF0677 (SEQ. ID NO:3), but not by a 20-fold excess of polyA oligonucleotide, indicating the sequence-specific nature of the DNA-binding by the fusion proteins. The band nearest the top of the gel is most likely the intact fusion protein since that molecule would be approximately 140 kD in size and would migrate slowly. The two more rapidly-migrating bands generated by each clone are most likely proteolytic products of this larger molecule. There are at least two lower bands in each gel lane that are contributed by E. coli (open arrows in FIGS. 13, A and B), and these proteins are not induced by IPTG (FIG. 13B, lanes 4 and 5). The E. coli proteins also possess some specific affinity for the Pur element.

The specificity of single-stranded DNA binding by Pur was examined in detail by constructing a series of mutated versions of the binding sequence, MF0677 (SEQ. ID NO:3), which was used in competition experiments with labeled MF0677 (SEQ. ID NO:3) (Table II). Reduction in level of competition by oligonucleotides in which successive guanosine residues are replaced by thymidine residues indicates that the sequence GGAGG is the minimal requirement for binding, although guanosine residues amino-terminal to this sequence are required for optimal binding. The adenosine residues at the 3' end of MF0677 (SEQ. ID NO:3) are not required for binding despite the fact that these residues are part of the consensus distribution PUR element. These results concur well with the binding site inferred from methylation interference studies of Pur activity in HeLa cell nuclear extracts (Bergmann and Johnson, 1992 Mol. Cell. Biol. 12:1257-1265). In those experiments protein contacts were observed with several guanosine residues in MF0677 (SEQ. ID NO:3), all of which are also important in the present mutational study. For example, the central G residue of a G triplet makes a prominent contact in methylation interference studies, and it is essential for binding by the cloned and expressed Pur protein (Table II, oligonucleotide MG0677 (SEQ. ID NO:4). These amplified 3'0 and 5' mRNA ends using PCR RACE techniques described in Section 7.1.6. Briefly, these employ one PCR primer specific for the Pur.alpha. sequence and another hybridizing to a poly dT tail formed at either the 3' or 5' end of a reverse transcript of the mRNA. The results of 3' RACE are shown in FIG. 14B. Three primary bands can be seen, indicating either that there are three transcripts hybridizing to the Pur.alpha. primer, that there are three major splicing products of a Pur.alpha. transcript, or that there are three major 3' termination sites for a Pur.alpha. transcript. Further studies of genomic Pur genes will distinguish between these possibilities. The results of 5' RACE are shown in FIG. 6C. Two primary bands can be seen at 200-300 nucleotides and a diffuse range of much less intense bands at 500-700 nucleotides. The smaller band represents artifactual stopping of either reverse transcriptase or Taq polymerase in the G-rich polyglycine sequence near the 5' end of the Pur.alpha. mRNA. The larger major band corresponds with the 5' end of the sequence shown in FIG. 2 and could represent the 5' end of the Pur.alpha. transcript. The diffuse smear at 500-700 nucleotides could conceivably represent longer Pur.alpha. transcripts. It is more likely, however, based on their low level of production, that they are derived from transcripts related to Pur.alpha. but with only partial homology to the Pur.alpha. primer. These 3' and 5' RACE results place the size of the Pur.alpha. mRNA in the range of 1.6 to 2.1 kb. Both the size of the major Pur.alpha. mRNA and the diversity of homologous species seen are consistent with results obtained by Northern hybridization.

Probing 2.times.10.sup.8 pfu of a HeLa cell cDNA library with radioactivity labeled 777 bp Pst I fragment (described in Section 7.1.7) of the Pur.alpha. cDNA resulted in the detection of several hybridizing clones. One of these yielded a new clone of Pur.alpha. which extends the sequence an additional 51 bp at the 5' end FIGS. 10A and 10B. Another of these hybridizing clones contains a cDNA, of similar, but not identical sequence to Pur.alpha.. This cDNA, designated Pur.beta. possesses a copy of the class I repeat module we have described in FIG. 11 followed by an amphipathic helix with considerable sequence similarity to that of Pur.alpha. (FIGS. 11 and 12). However, the 3' end of Pur.beta. lacks the glutamine-glutamate-rich domain present at that position in Pur.alpha..

A PUR-GST fusion protein was express in E. coli (FIG. 18). The fusion protein was bound to a glutathione-linked agarose column followed by passage of WR2E3 cell extracts over the PUR-GST column. The bound proteins were eluted and separated on an SDS polyacrylamide gel. The separated proteins were transferred to a nitrocellulose membrane and probed with anti-RB antibody. Results indicate that the PUR-GST fusion protein binds to the RB protein with the same affinity as SV40 Large T-antigen and that the PUR protein with the same affinity preferentially to the unphosphorylated form of the RB protein (FIG. 19).

The present invention is not to be limited in scope by the exemplified embodiments which are intended as illustrations of single aspects of the invention, and any clones, DNA or amino acid sequences which are functionally equivalent are within the scope of the invention. Indeed, various modifications of the invention in addition to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the appended claims.

It is also to be understood that all base pair sizes given for nucleotides are approximate and are used for purposes of description.