EP0572529A1 - Aptamere specifique de biomolecules et procede de production - Google Patents

Aptamere specifique de biomolecules et procede de production

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Publication number
EP0572529A1
EP0572529A1 EP92907174A EP92907174A EP0572529A1 EP 0572529 A1 EP0572529 A1 EP 0572529A1 EP 92907174 A EP92907174 A EP 92907174A EP 92907174 A EP92907174 A EP 92907174A EP 0572529 A1 EP0572529 A1 EP 0572529A1
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EP
European Patent Office
Prior art keywords
aptamer
oligonucleotides
target
oligonucleotide
aptamers
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP92907174A
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German (de)
English (en)
Other versions
EP0572529A4 (fr
Inventor
John J. Toole
Linda C. Griffin
Louis C. Bock
John A. Latham
Daryl Dean Muenchau
Steven Krawczyk
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Gilead Sciences Inc
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Gilead Sciences Inc
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Publication date
Application filed by Gilead Sciences Inc filed Critical Gilead Sciences Inc
Publication of EP0572529A1 publication Critical patent/EP0572529A1/fr
Publication of EP0572529A4 publication Critical patent/EP0572529A4/fr
Withdrawn legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/115—Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/16—Aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/315—Phosphorothioates
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/318—Chemical structure of the backbone where the PO2 is completely replaced, e.g. MMI or formacetal
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/33—Chemical structure of the base
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/33—Chemical structure of the base
    • C12N2310/332—Abasic residue
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/33—Chemical structure of the base
    • C12N2310/335—Modified T or U
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/914—Hydrolases (3)
    • G01N2333/948—Hydrolases (3) acting on peptide bonds (3.4)
    • G01N2333/974—Thrombin

Definitions

  • the present invention is directed to a method for identifying oligonucleotide sequences which
  • biomolecules including peptides, hydrophobic molecules, and target features on cell surfaces, in particular extracellular proteins, and the use of these sequences to detect and/or isolate the target molecules and the resulting compositions.
  • the instant invention is exemplified by obtaining
  • compositions through the use of disclosed methods, that comprise oligonucleotide sequences which bind to Factor X, thrombin, kinins, eicosanoids and extracellular proteins.
  • the invention is also directed to improvements in methods to identify specific binding sequences for target substances and methods of use of such specific binding sequences. More specifically, it concerns: (1) the use of oligonucleotides containing modified monomer residues to expand the repertoire of candidate oligomer sequences; (2) the use of identifying and amplifying oligonucleotides without attached flanking regions or structural constraints, but which nevertheless are capable of specific binding to desired targets; and (3) the design and use of conjugates designed to bind specific target cells and induce an immune response to the target cells.
  • Binding Oligonucleotides Conventional methods of therapeutic treatment based on binding and inhibition of therapeutic target molecules as well as detection and isolation of proteins and other molecules have employed small molecules, antibodies and the like which specifically bind such substances.
  • oligonucleotides for non-oligonucleotide targets. See, e.g., Blackwell et al., Science (1990) 250: 1104-1110; Blackwell et al., Science (1990) 250:1149-1151: Tuerk, C., and Gold, L., Science (1990) 249:505-510; Ellington et al., Nature (1990) 346:818- 822.
  • aptamers Such oligonucleotides have been termed "aptamers" herein.
  • the Tuerk reference describes the use of an in vitro selection and enrichment procedure to obtain RNA molecules that bind to an RNA binding protein. In this method, a pool of RNAs that are completely randomized at specific positions is subjected to selection for binding to a desired protein. The selected RNAs are then
  • amplified as double-stranded DNA that is competent for subsequent in vitro transcription.
  • the newly transcribed RNA is then enriched for better binding sequences and recycled through this procedure.
  • the amplified selected sequences are subjected to sequence determination using dideoxy sequencing. Tuerk and Gold applied this
  • RNA molecules which are bound by T4 DNA polymerase utilizes the polymerase chain reaction (PCR) technique, as described by Saiki, R.K., et al., Science (1988) 239:487-491, to amplify the selected RNAs.
  • PCR polymerase chain reaction
  • DNA yielding approximately 10 15 individual sequences was amplified by PCR and transcribed into RNA. It was thought that the complexity of the pool was reduced in the amplification/transcription steps to approximately 10 13 different sequences.
  • the pool was then applied to an affinity column containing the dye and the bound sequences subsequently eluted, treated with reverse transcriptase and amplified by PCR. The results showed that about one in 10 random sequence RNA molecules folds in such a way as to bind specifically to the ligand.
  • TDA target detection assay
  • molecules such as serum proteins, kinins, hydrophobic molecules such as eicosanoids, or extracellular proteins.
  • oligonucleotide or aptamer (iv) target molecule binding mediated by single-stranded DNA and (v) target-specific binding of short oligonucleotides or oligonucleotide analogs that are derived from a larger full-length parent oligonucleotide (aptamer) molecule.
  • kinins are peptides which are formed in biological fluids by the activation of kininogens.
  • Kinins have been shown to exert numerous physiological and pathological actions such as exhibiting hypotensive effects, causing pain, mediating reactive hyperaemia in exocrine glands, playing a role in vascular and cellular events that accompany the inflammatory processes,
  • inflammatory diseases such as rheumatoid arthritis and other forms of arthritis, vascular changes occurring in migraine, myocardial infarction, cardiovascular failure, carcinoid and postgastrectomy dumping syndromes,
  • Eicosanoids are a family of fatty acid derivatives which include the various prostaglandins, thromboxanes, leukotrienes and prostacyclin. Eicosanoids are widespread and produce a remarkably broad spectrum of effects embracing nearly every biological function. For example, eicosanoids have been shown to affect the cardiovascular system, blood, smooth muscle, kidney and urine formation, the central nervous system, inflammatory and immune responses, afferent nerves and pain, as well as several metabolic functions. For a general review of eicosanoids and their biological significance, see
  • Particular cells can be characterized by the presence of certain proteins on their surface. These proteins can serve a variety of functions including providing binding cites for other biomolecules and/or virus receptors. It is also known that it is possible to differentiate normal cells of a given type from abnormal cells by the type and/or amount of characteristic protein on the cells' surface. Since it is known that it is possible to differentiate different types of cells by the characteristic proteins present on their surface,
  • oligonucleotides could be used to bind to characteristic proteins at the cell surface. Although such binding does occur, it is not highly specific, i.e., a given
  • oligonucleotide may bind to cellular proteins on two very different types of cell lines. Further, even if a
  • oligonucleotide is found to be specific to a particular characteristic protein, it is difficult to isolate the desired oligonucleotide and produce it in sufficient amounts so as to allow it to be useful as a probe to identify particular cell lines having particular characteristic proteins thereon.
  • the invention herein provides an approach and utilizes a binding selection method combined with PCR or other amplification methods to develop aptamers that bind peptide molecules such as factor X, kinins, hydrophobic molecules such as eicosanoids, and extracellular
  • aptamers that specifically bind to these targets are obtained starting from a pool of randomized
  • PCR has made possible the isolation and analysis of specific nucleic acid fragments from a wide variety of sources
  • application of PCR to isolate and analyze a particular nucleic acid region heretofore has required knowledge of the nucleic acid sequences either flanking or within the region of
  • Flanking primer sequences impose limits on aptamer structural diversity: either the ability to bind is affected by the primers, thereby eliminating from consideration a class of binding agents, or occasionally, the primers actually participate in or facilitate binding by conferring structure. Flanking sequence thus may impose constraints which make aptamers so identified suboptimal for drug development.
  • RNA generally is converted to DNA prior to amplification using reverse transcriptase, a process that is not equally efficient with all sequences, resulting in loss of some aptamers from a selected pool.
  • Modified Bases in Polymerization Reactions A large number of modifications which behave in a known manner in polymerase reactions is known. Otvos, L., et al., Nucleic Acids Res (1987) 1763-1777, report the enzyme catalyzed incorporation of 5-(1-alkenyl)-2'-deoxyuridines into DNA.
  • nucleotide triphosphates utilizing the modified base are also known in the foregoing publications.
  • Immune Recognition Mechanisms This invention is also related to the use of specific binding oligomers in immune recognition mechanisms.
  • Various immune features are also related to the use of specific binding oligomers in immune recognition mechanisms.
  • tumors are associated with a decreased level of the histocompatibility antigens that may play a role in eliciting a CTL response.
  • Viruses have also been able to mask viral antigens at the cell surface. In the case of HIV, heavy glycosylation of the envelope protein
  • Attenuated virus vaccines are used in some cases in order to expose the immune system to antigens that present
  • CTL responses appear to be based upon specific contacts between a plurality of surface antigens serving as signals for both self and non-self cells.
  • aptamers that are stable, versatile, and highly specific for their intended targets.
  • the aptamers of the invention may be determined as well as synthesized using modified nucleotides and internucleotide linkages.
  • these aptamers may be obtained from mixtures of candidate oligomers with completely unpredetermined sequences, without the necessity for inclusion of PCR primer sequences in the candidate pool. The efficiency of the method to determine suitable aptamers is further enhanced by separation of the complex containing
  • the aptamers of the present invention find a variety of utilities including therapeutic and diagnostic utilities as well as functioning as laboratory and industrial reagents.
  • the aptamers of the invention can be coupled to various auxiliary substances such as label or solid support.
  • the invention is directed to an aptamer containing at least one binding region capable of binding specifically to a target molecule wherein the aptamer is a single-stranded DNA.
  • a single-stranded DNA aptamers can be constructed to bind specifically to a wide variety of target substances including proteins, peptides, glycoproteins, lipids, glycolipids, carbohydrates, and various small molecules.
  • Such single-stranded DNA aptamers are advantageously stable as compared to RNA counterparts. It has been heretofore thought that the three-dimensional structure of double-stranded DNA limited the structural diversity of the molecule. The inventors herein are unaware of any prior demonstration of structural diversity for single-or double-stranded DNA sufficient to provide the range of conformations necessary to provide aptamers to
  • RNA structures such as pseudoknots
  • the invention is directed to aptamers that have relatively short specific binding regions of less than 15 nucleotide residues and which may, themselves, be relatively small molecules containing less than 16 nucleotide residues. The limited length of these aptamers is advantageous in facilitating
  • the invention is directed to aptamers with very low dissociation constants with respect to their target molecules (that do not normally bind oligonucleotides) of less than 20 ⁇ 10 -9 ; and with high specificity for their targets of at least 5-fold differential in binding affinity as compared to competing substances.
  • the invention is directed to aptamers that bind to a wide variety of target molecules, especially those selected from the group consisting of bradykinin, PGF2 ⁇ , CD4, HER2, IL-1 receptor, Factor X, and thrombin.
  • target molecules especially those selected from the group consisting of bradykinin, PGF2 ⁇ , CD4, HER2, IL-1 receptor, Factor X, and thrombin.
  • the invention is directed to complexes of the target molecules and the aptamers of the invention and to methods to obtain and to use the
  • modified oligonucleotides in the candidate pool and to include modified nucleotides in the amplifying step of the method; to enhance the efficiency of the method by isolating the complex between the successful members of the candidate pool and the target molecule; and to obtain aptamers that bind cell surface factors using a
  • aptamers may be used as specific binding agents in conjugates designed to modulate the immune system.
  • Figure 1 is a chart depicting thrombin aptamer consensus-related sequences.
  • Figure 2 is a plot of in vivo thrombin inhibition obtained from primates using a 15-mer aptamer.
  • the invention is directed to a method which permits the recovery and deduction of aptamers which bind specifically to desired targets including those
  • bradykinin as well as other small peptide hormones such as the vasoconstrictor endothelin (a 21-mer peptide), small hydrophobic molecules such as
  • eicosanoids including PGF2 ⁇
  • extracellular proteins such as thrombin
  • molecules that are contained at the cell surface such as IL-1 receptor and CD4.
  • these aptamers can be used as a separation tool for retrieving the targets to which they specifically bind.
  • the target substances can be recovered in useful quantities.
  • these oligonucleotides can be used in diagnosis by employing them in specific binding assays for the target
  • the specifically binding oligonucleotides can also be used for in vivo imaging or histological analysis.
  • the aptamers of the invention may be coupled to auxiliary substances that enhance or complement the function of the aptamer.
  • auxiliary substances include, for example, labels such as radioisotopes, fluorescent labels, enzyme labels and the like; specific binding reagents such as antibodies, additional aptamer sequence, cell surface receptor ligands, receptors per se and the like; toxins such as diphtheria toxin, tetanus toxin or ricin; drugs such as antiinflammatory, antibiotic, or metabolic
  • Suitable techniques for coupling of aptamers to desired auxiliary substances are generally known for a variety of such auxiliary substances, and the specific nature of the coupling procedure will depend on the nature of the auxiliary substance chosen.
  • Coupling may be direct covalent coupling or may involve the use of synthetic linkers such as those marketed by Pierce
  • the aptamers of the invention may be used alone in therapeutic applications or may be used as targeting agents to deliver pharmaceuticals or toxins to desired targets.
  • the aptamers may be used in diagnostic procedures and advantageously in this application include label. They may be used as reagents to separate target molecules from contaminants in samples containing the target molecules in which application they are
  • a particularly advantageous application of the aptamers of the invention includes their use in an immune recruitment procedure as targeting agents for the immunomodulating substance used in this procedure, as further described below.
  • a "target” or “target molecule” refers to a biomolecule that could be the focus of a therapeutic drug strategy or diagnostic assay, including, without limitation, proteins or portions thereof,
  • carbohydrates glycoproteins, lipids, phospholipids, nucleic acids, and generally, any biomolecule capable of turning a biochemical pathway on or off or modulating it, or which is involved in a predictable biological
  • Targets may be free in solution, like
  • thrombin or associated with cells or viruses, as in receptors or envelope proteins.
  • excluded from target molecules are substances to which DNA sequences normally bind such as nucleases, substrates wherein binding is effected by Watson-Crick base pairing modes of binding to nucleic acids, specific triple helix binding to nucleic acid sequences, and the like.
  • excluded from target molecules are those substances which natively bind the specific form of aptamer at issue.
  • nucleases that attack single-stranded DNA restriction endonucleases that attack double-stranded DNA with respect to single-stranded DNA and double-stranded DNA, respectively.
  • cell surface receptors specific for DNA or RNA are also excluded from cell surface receptors specific for DNA or RNA.
  • a wide variety of materials can serve as targets. These materials include intracellular,
  • glycosaminoglycans examples include glycolipids, including glycolipids and certain oligonucleotides.
  • a representative list of targets for which the aptamers of the invention may be prepared is set forth herein in Table 1 which follows the examples in the herein specification.
  • Some of the useful targets are peptides such as kinins and small low molecular weight carbohydrates such as prostaglandins. These targets have particular
  • kinin any of the peptide components enzymatically released by the activation of the various kininogens (hormogens).
  • kinin includes the mammalian kinins such as, but not limited to, bradykinin (BK), Lys-BK, Met-Lys-BK,
  • leukokinins leukokinins, colostrokinin, neurokinin; the various nonmammalian kinins; and metabolites of the above.
  • Kinins are small peptides having, on the average, 9-11 amino acids. As described above, there are several inherent problems associated with the use of conventional immunotechniques for working with kinins. Thus, the present invention provides an efficient method for the detection and isolation of these important substances. For a review of kinins and their significance, see
  • hydrophobic is meant a compound having non-polar groups such that the compound as a whole has a relatively low affinity for water and other polar solvents.
  • the hydrophobic molecules of the instant invention lack large numbers of groups that may participate in establishing noncovalent binding
  • interactions with aptamers include base stacking via aromatic rings in the target, polar and ionic interactions, and hydrogen bonding.
  • eicosanoid any of the several members of the family of
  • Such substances encompass the various prostaglandins, including but not limited to PGA, PGB, PGC, PGD, PGE, PGE1, PGE2, PGE2 ⁇ , PGF, PGF1G ⁇ , PGF2 ⁇ , PGG, PGG2, PGH, PGH2; the
  • thromboxanes such as but not limited to TXA2 and TXB2; prostacyclin (PGI2) and 6-keto-PGF1 ⁇ ; leukotrienes and precursors thereof such as LTB4 (a 5, 12 -dihydroxy
  • LTA4 a 5, 6-epoxide
  • LTD4 thesized by the removal of glutamic acid from LTC4
  • LTE4 resulting from the subsequent cleavage of glycine
  • LTF4 an ⁇ -glutamyl, cysteinyl derivative
  • SRS-A a mixture of LTC4 and LTD4 known as the "slow-reacting substance of anaphylaxis"
  • HPETE a mixture of LTC4 and LTD4 known as the "slow-reacting substance of anaphylaxis"
  • Eicosanoids are also intended to include synthetic eicosanoid analogs such as 16-methoxy-16-methyl-PGF20C and 15-methyl-PGF2 ⁇ (Guzzi, et al., J. Med. Chem. (1986) 29:1826-1832; Cheng, et al., Acta Acad. Med. Shanghai (1990) 17:378-381) or in vivo generated eicosanoid metabolites (Morrow, et al., Proc Natl. Acad. Sci (USA) (1990) 87:9383-9387).
  • Eicosanoids are relatively low molecular weight compounds which are generally hydrophobic in nature. These substances normally have molecular weights under 400, but some naturally occurring variants are conjugated to one or several amino acids and these will have higher molecular weights. These variants are also encompassed by the subject invention. As described above, several synthetic eicosanoid analogs such as 16-methoxy-16-methyl-PGF
  • eicosanoids have not heretofore been easily detectable or isolatable using standard immunotechniques due to their ubiquitous nature.
  • the present invention provides an efficient method for the detection and isolation of these important substances.
  • Moncada S., et al., in The Pharmacological Basis of Therapeutics, Gilman, A.G., et al., eds. (MacMillan Publishing Company, New York), 7th Edition, pages 660-671, incorporated herein by reference in its entirety.
  • oligonucleotides potential target molecules for aptamer selection as oligonucleotides are very hydrophilic and highly
  • oligonucleotides that bind to targets utilized protein targets that normally bind to nucleic acids, or in the work described by Ellington, et al., Nature (1990) 346:818-822, target molecules with many possible
  • nucleic acid binding proteins binding to nucleic acid oligonucleotides is aided by the inherent binding
  • eicosanoid, PGF2 ⁇ has only 3 hydroxyl groups, two double bonds between adjacent methylene groups, a carboxylic acid group (which, as used herein, is present as an amide linkage for covalent attachment to a solid support) and a cyclopentyl ring.
  • the eicosanoids are extremely deficient in groups that may participate in noncovalent binding interactions.
  • oligonucleotides As used herein, “specifically binding oligonucleotides” or “aptamers” refers to
  • oligonucleotides having specific binding regions which are capable of forming complexes with an intended target molecule in an environment wherein other substances in the same environment are not complexed to the
  • oligonucleotide The specificity of the binding is defined in terms of the comparative dissociation
  • Kd constants of the aptamer for target as compared to the dissociation constant with respect to the aptamer and other materials in the environment or unrelated molecules in general.
  • the Kd for the aptamer with respect to the target will be 2-fold, preferably 5-fold, more preferably 10-fold less than Kd with respect to target and the unrelated material or accompanying
  • the Kd will be 50-fold less, more preferably 100-fold less, and more preferably 200-fold less.
  • the binding affinity of the aptamers herein with respect to targets and other molecules is defined in terms of Kd.
  • the value of this dissociation constant can be determined directly by well-known methods, and can be computed even for complex mixtures by methods such as those, for example, set forth in Caceci, M., et al., Byte (1984) 9:340-362. It has been observed, however, that for some small oligonucleotides, direct determination of Kd is difficult, and can lead to misleadingly high results. Under these circumstances, a competitive binding assay for the target molecule or other candidate substance may be conducted with respect to substances known to bind the target or candidate.
  • the value of the concentration at which 50% inhibition occurs (Ki) is, under ideal conditions, equivalent to Kd. However, in no event can Ki be less than Kd. Thus, determination of Ki, in the alternative, sets a maximal value for the value of Kd. Under those circumstances where technical
  • immunologically crossreactive is meant that antibodies raised with respect to the target crossreact under standard assay conditions with the candidate material.
  • the binding affinities of the antibodies for crossreactive materials as compared to targets should be in the range of 5-fold to 100-fold, generally about 10- fold.
  • aptamers which contain specific binding regions are specific with respect to unrelated materials and with respect to materials which do not normally bind such oligonucleotides such as nucleases and restriction enzymes.
  • the only apparent limitations on the binding specificity of the target/oligonucleotide couples of the invention concern sufficient sequence to be distinctive in the binding oligonucleotide and sufficient binding capacity of the target substance to obtain the necessary
  • binding regions containing sequences shorter than 10, e.g., 6-mers, are feasible if the appropriate interaction can be obtained in the context of the environment in which the target is placed. Thus, if there are few interferences by other materials, less specificity and less strength of binding may be required.
  • aptamer refers in general to either an oligonucleotide of a single defined sequence or a mixture of said oligonucleotides, wherein the mixture retains the properties of binding specifically to the target molecule.
  • aptamer denotes both singular and plural sequences of oligonucleotides, as defined hereinabove.
  • the aptamers of the invention are specifically binding oligonucleotides, wherein
  • oligonucleotide is as defined herein. As set forth herein, oligonucleotides include not only those with conventional bases, sugar residues and internucleotide linkages, but also those which contain modifications of any or all of these three moieties.
  • Single-stranded oligonucleotides refers to those oligonucleotides which contain a single covalently linked series of nucleotide residues.
  • Oligonucleotides include RNA or DNA sequences of more than one nucleotide in either single chain or duplex form and specifically includes short sequences such as dimers and trimers, in either single chain or duplex form, which may be intermediates in the production of the specifically binding
  • Oligomer is generic to polydeoxyribonucleotides (containing 2'-deoxy-D-ribose or modified forms thereof), i.e., DNA, to polyribonucleotides (containing D-ribose or modified forms thereof), i.e., RNA, and to any other type of polynucleotide which is an N-glycoside or C-glycoside of a purine or
  • pyrimidine base or modified purine or pyrimidine base or abasic nucleotides.
  • the oligomers of the invention may be formed using conventional phosphodiester-linked nucleotides and synthesized using standard solid phase (or solution phase) oligonucleotide synthesis techniques, which are now commercially available.
  • the oligomers of the invention may also contain one or more "substitute” linkages as is generally understood in the art. Some of these substitute linkages are non-polar and contribute to the desired ability of the oligomer to diffuse across membranes.
  • substitute linkages are defined herein as conventional alternative linkages such as phosphorothioate or phosphoramidate, are synthesized as described in the generally available literature.
  • linking groups include, but are not limited to embodiments wherein a moiety of the formula P(0)S, ("thioate”), P(S)S ("dithioate”), P(O)NR' 2 , P(O)R',
  • P(O)OR 6 CO, or CONR' 2 , wherein R' is H (or a salt) or alkyl (1-12C) and R 6 is alkyl (1-9C) is joined to
  • Dithioate linkages are disclosed and claimed in commonly owned U.S. application no. 248,517.
  • Substitute linkages that may be used in the oligomers disclosed herein also include nonphosphorous-based internucleotide linkages such as the 3'-thioformacetal (-S-CH 2 -O-), formacetal (-O-CH 2 -O-) and 3'-amine (-NH-CH 2 -CH 2 -) internucleotide linkages
  • One or more substitute linkages may be utilized in the oligomers in order to further facilitate binding with complementary target nucleic acid sequences or to increase the stability of the oligomers toward nucleases, as well as to confer permeation ability.
  • nucleoside or “nucleotide” is similarly generic to ribonucleosides or ribonucleotides, deoxyribonucleosides or deoxyribonucleotides, or to any other nucleoside which is an N-glycoside or C-glycoside of a purine or pyrimidine base, or modified purine or pyrimidine base.
  • the stereochemistry of the sugar carbons may be other than that of D-ribose in one or more residues.
  • analogs where the ribose or deoxyribose moiety is replaced by an alternate structure such as the 6-membered morpholino ring described in U.S. patent number 5,034,506 or where an acyclic structure serves as a scaffold that positions the base analogs described herein in a manner that permits efficient binding to target nucleic acid sequences or other
  • ⁇ anomer binds to targets in a manner similar to that for the ß anomers, one or more
  • nucleotides may contain this linkage or a domain thereof.
  • Modifications in the sugar moiety for example, wherein one or more of the hydroxyl groups are replaced with halogen, aliphatic groups, or
  • Nucleoside and nucleotide include those moieties which contain not only the natively found purine and pyrimidine bases A, T, C, G and U, but also modified or analogous forms thereof. Modifications include
  • alkylated purines or pyrimidines alkylated purines or pyrimidines, acylated purines or pyrimidines, or other heterocycles.
  • Such “analogous purines” and “analogous pyrimidines” are those generally known in the art, many of which are used as
  • chemotherapeutic agents An exemplary but not exhaustive list includes pseudoisocytosme, N 4 ,N 4 -ethanocytosme, 8- hydroxy-N 6 -methyladenme, 4-acetylcytosine, *5- (carboxyhydroxylmethyl) uracil, 5-fluorouracil,
  • 1-methylpseudouracil 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N 6 -methyladenine, 7-methylguanine, 5-methylaminomethyl uracil, 5-methoxy aminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'-methoxycarbonylmethyluracil, 5-methoxyuracil, 2-methylthio-N 6 -isopentenyladenine, uracil-5-oxyacetic acid methyl ester, pseudouracil, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,
  • N-uracil-5-oxyacetic acid methylester uracil-5-oxyacetic acid, queosine, 2-thiocytosine, 5-propyluracil,
  • nucleotide residues which are devoid of a purine or a pyrimidine base may also be included in the aptamers of the invention and in the methods for their obtention.
  • sugar residues in the oligonucleotides of the invention may also be other than conventional ribose and deoxyribose residues.
  • substitution at the 2'-position of the furanose residue is particularly important.
  • Aptamer oligonucleotides may contain analogous forms of ribose or deoxyribose sugars that are generally known in the art.
  • An exemplary, but not exhaustive list includes 2' substituted sugars such as 2'-O-methyl-, 2'-O-alkyl, 2'-O-allyl, 2'-S-alkyl, 2'-S-allyl, 2'-fluoro-, 2'-halo, or 2'-azido-ribose, carbocyclic sugar analogs, ⁇ -anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs and abasic nucleoside analogs such as methyl riboside, ethyl riboside or propyl riboside.
  • pyrimidines can be advantageous in designing the final product. Additional techniques, such as methods of synthesis of 2'-modified sugars or carbocyclic sugar analogs, are described in Sproat, B.S. et al., Nucl Acid Res (1991) 19: 733 -738; Cotten, M. et al., Nuc Acid Res (1991) 19:2629-2635; Hobbs, J. et al., Biochemistry
  • primer refers to a sequence which is capable of serving as an initiator molecule for a DNA polymerase when bound to complementary DNA which is usually between 3-25 nucleotides in length.
  • a "type II restriction enzyme site” refers to a site possessed by the class of
  • restriction enzymes which cleaves one or both DNA strands at internucleotide linkages that are located outside of those associated with bases in the recognition sequence. This term is also meant herein to refer to a restriction enzyme such as Bcg I (New England Biolabs, catalog no. 545L) that makes two double stranded DNA cuts outside of its recognition sequence.
  • One of the objects of the invention is to identify aptamers useful as drugs per se or useful in drug development. Toward this end, selection criteria for targets and aptamers include:
  • the aptamer should selectively bind to the desired target, thereby inhibiting a biochemical pathway or generating a specific response (e.g., modulating an immune response or disrupting binding interactions between a receptor and its ligand);
  • the aptamer selected for use in diagnostic applications should have specificity for analyte (ligand) binding in those cases where the aptamer will be
  • the biochemical pathway that is inhibited or the biological response generated should be related to a pathological disease state in such a way that
  • the aptamer is specific so that it does not appreciably inhibit other pathways or
  • Preferred aptamers have or are capable of being adapted to have the pharmacokinetic characteristics of a practical drug (i.e., they must be absorbed, must penetrate to the site of action and must have a
  • the aptamer has an acceptable toxicological profile in animals and the results of human clinical trials must demonstrate an appropriate
  • the method for preparing the aptamers of the invention involves incubating a desired target molecule with a mixture of oligonucleotides under conditions wherein some but not all of the members of the oligonucleotide mixture form complexes with the target molecules.
  • the resulting complexes are then separated from the uncomplexed members of the oligonucleotide mixture and the complexed members which constitute an aptamer (at this stage the aptamer generally being a population of a multiplicity of oligonucleotide
  • the aptamer is recovered from the complex and amplified.
  • the resulting aptamer (mixture) may then be substituted for the starting mixture in repeated iterations of this series of steps.
  • the aptamer may be used as a obtained or may be sequenced and synthetic forms of the aptamer prepared. In this most generalized form of the method, the
  • oligonucleotides used as members of the starting mixture may be single-stranded or double-stranded DNA or RNA, or modified forms thereof. However, single-stranded DNA is preferred. The use of DNA eliminates the need for conversion of RNA aptamers to DNA by reverse
  • DNA is less susceptible to nuclease degradation than RNA.
  • the oligonucleotides that bind to the target are separated from the rest of the mixture and recovered and amplified. Amplification may be conducted before or after separation from the target molecule.
  • oligonucleotides are conveniently amplified by PCR to give a pool of DNA sequences.
  • the PCR method is well known in the art and described in, e.g., U.S. Patent Nos. 4,683,195 and 4,683,202 and Saiki, R.K., et al.,
  • RNA is initially used, the amplified DNA sequences are transcribed into RNA.
  • the recovered DNA or RNA in the original single-stranded or duplex form, is then used in another round of selection and amplification. After three to six rounds of selection/amplification, oligomers that bind with an affinity in the mM to ⁇ M range can be obtained for most targets and affinities below the ⁇ M range are possible for some targets.
  • PCR may also be performed in the presence of target.
  • amplification may be employed including standard cloning, ligase chain reaction, etc. (See e.g., Chu, et al., U.S. Patent No. 4,957,858).
  • linkers may be attached to each side to facilitate cloning into standard vectors. Aptamers, either in single or double stranded form, may be cloned and recovered thereby providing an alternative amplification method.
  • Amplified sequences can be applied to sequencing gels after any round to determine the nature of the aptamers being selected by target molecules. The entire process then may be repeated using the recovered and amplified duplex if sufficient resolution is not obtained.
  • Amplified sequences can be cloned and individual oligonucleotides then sequenced. The entire process can then be repeated using the recovered and amplified oligomers as needed. Once an aptamer that binds specifically to a target has been selected, it may be recovered as DNA or RNA in single-stranded or duplex form using conventional techniques.
  • a selected aptamer may be sequenced and resynthesized using one or more modified bases, sugars and linkages using conventional techniques.
  • the specifically binding oligonucleotides need to contain the sequence-conferring specificity, but may be extended with flanking regions and otherwise derivatized.
  • the starting mixture of oligonucleotide may be of undetermined sequence or may preferably contain a randomized portion, generally including from about 3 to about 400 nucleotides, more preferably 10 to 100
  • the randomization may be complete, or there may be a preponderance of certain sequences in the mixture, or a preponderance of certain residues at particular positions.
  • the randomized sequence is preferably flanked by primer sequences which permit the application of the polymerase chain reaction directly to the recovered oligonucleotide from the complex.
  • the flanking sequences may also contain other convenient features, such as restriction sites which permit the cloning of the amplified sequence.
  • hybridization regions generally contain 10 to 30, more preferably 15 to 25, and most preferably 18 to 20, bases of known sequence.
  • the oligonucleotides of the starting mixture may be conventional oligonucleotides, most preferably single-stranded DNA, or may be modified forms of these conventional oligomers as described hereinabove.
  • oligonucleotides containing conventional phosphodiester linkages or closely related forms thereof standard oligonucleotide synthesis techniques may be employed.
  • Oligonucleotides may also be synthesized using solution phase methods such as triester synthesis, known in the art. The nature of the mixture is determined by the manner of the conduct of synthesis. Randomization can be achieved, if desired, by supplying mixtures of nucleotides for the positions at which randomization is desired. Any proportion of nucleotides and any desired number of such nucleotides can be supplied at any
  • any degree of randomization may be employed. Some positions may be randomized by mixtures of only two or three bases rather than the conventional four. Randomized positions may alternate with those which have been specified. It may be helpful if some portions of the candidate randomized sequence are in fact known.
  • the starting mixture of oligonucleotides subjected to the invention method will have a binding affinity for the target characterized by a Kd of 1 ⁇ M or greater. Binding affinities of the original mixture for target may range from about 100 ⁇ M to 10 ⁇ M to 1 ⁇ M, but, of course, the smaller the value of the dissociation constant, the more initial affinity there is in the starting material for the target. This may or may not be advantageous as specificity may be sacrificed by starting the procedure with materials with high binding affinity.
  • a ratio of binding affinity reflects the ratio of Kds of the comparative complexes. Even more preferred in the conduct of the method of the invention is the achievement of an enhancement of an affinity of a factor of 500 or more.
  • the method of the invention can be conducted to obtain the invention aptamers wherein the aptamers are characterized by consisting of single-stranded DNA, or by having a binding affinity to a target that does not normally bind oligonucleotides represented by a Kd of 20 ⁇ 10 -9 or less, or by having a specificity representing by a factor of at least 2, preferably 5, and more preferably 10 with respect to unrelated molecules, or by having a binding region of less than 15 nucleotide residues or a total size of less than 16 nucleotide residues, or by binding to particular target molecules.
  • the invention processes are also characterized by accommodating starting mixtures of oligonucleotides having a binding affinity for target characterized by a Kd of 1 ⁇ M or more by an enhancement of binding affinity of 50 or more, and by being conducted under physiological conditions.
  • physiological conditions means the salt concentration and ionic strength in an aqueous solution which characterize fluids found in human
  • physiological buffer or physiological saline. In general, these are
  • the concentration of various ions, in particular, the ionic strength, and the pH value impact on the value of the dissociation constant of the target/aptamer complex.
  • the initial mixture of candidate oligonucleotides will be referred to as the initial mixture of candidate oligonucleotides.
  • oligomers which contain at least one modified nucleotide residue or linking group.
  • the modification In order for the modified oligomer to yield useful results, the modification must result in a residue which is "read" in a known way by the polymerizing enzyme used in the amplification procedure. It is not necessary that the modified residue be incorporated into the oligomers in the amplification process, as long it is possible to discern from the nucleotide incorporated at the corresponding position the nature of the modification contained in the candidate, and provided only one round of complexation/amplification is needed. However, many of the modified residues of the invention are also susceptible to enzymatic incorporation into
  • the amplified sequence must include the modified residue, unless the entire pool is sequenced and resynthesized to include the modified residue.
  • the modified base may be included in the oligomeric mixtures useful in the method of the invention.
  • the nature of the sugar moiety may also be modified without affecting the capacity of the sequence to be usable as a specific template in the synthesis of new DNA or RNA.
  • the efficacy of the process of selection and amplification depends on the ability of the PCR reaction faithfully to reproduce the sequence actually complexed to the target substance.
  • the target substance contains modified forms of cytosine (C*)
  • the PCR reaction must recognize this as a modified cytosine and yield an oligomer in the cloned and sequenced product which reflect this characterization.
  • the modified form of cytosine (C*) is included in the PCR reaction as dC*TP, the resulting mixture will contain C* at positions represented by this residue in the original member of the candidate mixture.
  • amplified mixture is used in a second round, this new mixture must contain the modification.
  • modified oligonucleotides and linking groups may arbitrarily by used in the synthesized form of the aptamer.
  • modified oligonucleotides in the methods and aptamers of the invention provides a tool for expansion of the repertoire of candidates to include large numbers of additional oligonucleotide sequences.
  • expansion of the candidate pool may be especially important as the demonstration of binding to proteins, for example, in the prior art is limited to those
  • Modifications of the oligonucleotide may be necessary to include all desired substances among those targets for which specific binding can be achieved.
  • one preferred method comprises incubating the target with a mixture of oligonucleotides, wherein these oligonucleotides contain at least one modified nucleotide residue or linkage, under conditions wherein complexation occurs with some but not all members of the mixture; separating the complexed from uncomplexed oligonucleotides, recovering and amplifying the complexed oligonucleotides and optionally determining the sequence of the recovered nucleotides.
  • amplification is also conducted in the presence of modified nucleotides.
  • a method for making aptamers is provided, based on the discovery that the presence of flanking sequences (usually primer binding sequences) on the oligonucleotides of the candidate mixture may limit aptamer structural diversity and/or inhibit binding, thereby resulting in less than the full range of structural variation that is possible in a given pool of aptamers.
  • This embodiment may use mixtures of unbiased oligonucleotide pools, and provides the ability to then engineer appropriate means for amplifying the desired oligonucleotides (putative aptamers).
  • linkers may be added to both ends as described herein (much in the same manner as a sticky end ligation).
  • the linkers are partially double stranded and have some overhang to and at both ends to facilitate cloning into a standard cloning vector.
  • One of the overhangs should be a random sequence to provide complementarity to permit binding to the aptamer.
  • the other overhang may provide necessary bases for sticky end ligation.
  • the mixture may be of completely unknown sequence.
  • the oligonucleotides comprising the pool also may be of partially known sequence, but without flanking primer regions.
  • the invention is not limited to first generation aptamers, but may be practiced to identify second and third generation aptamers as well.
  • Oligonucleotides comprising the pool from which second and third generation aptamers may be identified, may have, for example, 40%-70% of their sequences known or predetermined.
  • oligonucleotide pool from which aptamers are identified may be reduced, either by using known sequences, or through the processes of retention and selection by which these aptamers are made. As pool size and pool diversity is reduced, more aptamers capable of more specific binding are recovered. Stated in another way, the quantity of oligonucleotides in the pool and the diversity and/or complexity of the pool are inversely related.
  • step (g) repeating steps a-f using said first aptamers of step (f), or a portion thereof, to comprise a second pool of oligonucleotides for use in step (a), thereby generating a second aptamer population which may be used to repeat steps (a) - (f), and optionally
  • step (h) repeating steps (a) - (f) using said second aptamers of step (g), or a portion thereof, a sufficient number of times so as to identify an optimal aptamer population from which at least one consensus region may identified in at least two of the aptamers from said optimal aptamer population, the presence of which may be correlated with aptamer to target binding or to aptamer structure.
  • This method includes methods for selectively attaching and removing flanking regions to aptamers, thereby permitting aptamer recovery in high yield.
  • One such method comprises,
  • oligonucleotides having a second type II restriction enzyme recognition site different from the site at the 5' end;
  • a duplex comprising a first (upper) strand, having a 5' linker complement portion, an oligonucleotide complement portion and a 3' linker complement portion, and a second (lower) strand, comprising a 5' linker portion, an oligonucleotide portion and a 3' linker portion;
  • Another method of effecting amplification comprises,
  • a double stranded DNA linker of known sequence having at least 2-4 bases of random sequence present as a 3' overhang, said 2-4 bases capable of hybridizing to the 3' end of said oligonucleotides, the linker having a first type II restriction enzyme
  • oligonucleotides amplifying said oligonucleotides, thereby generating duplexes comprising a first (upper) strand, having a 5' linker complement portion, an oligonucleotide complement portion and a 3' linker complement portion, and a second (lower) strand, comprising a 5' linker portion, an oligonucleotide portion and a 3' linker portion;
  • oligonucleotide by attaching the product of step 4 above to a solid support, removing the 3' linker by digesting with a type II restriction enzyme capable of recognizing said first type II restriction enzyme binding site, removing the 5' linker complement and the oligonucleotide complement by heat denaturation, annealing a 5' linker complement to the upper strand, and removing the 5' linker portion by digesting with a type II restriction enzyme capable of recognizing the second type II
  • the method includes attaching a single RNA residue to the 5' linker portion and removing it after amplification by cleaving the RNA linkage.
  • the complexed oligonucleotides which are now an aptamer, are recovered and amplified from the complex.
  • the recovered aptamer is then mixed with the second, undesired, substance from which the target is to be distinguished under conditions wherein members of the aptamer population which bind to said second substance can be complexed.
  • This complex is then separated from the remaining oligonucleotides of the aptamer.
  • the resulting unbound second aptamer population is then recovered and amplified.
  • the second aptamer population is highly specific for the target as compared to the second substance.
  • the negative selection step may be conducted first, thus mixing the original oligonucleotide mixture with the undesired substance to complex away the members of the
  • the uncomplexed oligonucleotides are then recovered and amplified and incubated with the target under conditions wherein those members of the
  • oligonucleotide mixture which bind targets are complexed.
  • the resulting complexes then removed from the uncomplexed oligonucleotides and the bound aptamer population is recovered and amplified as usual.
  • the positive round is conducted preferably with the target expressed at the surface of a cell, said expression typically occurring through recombinant
  • the negative round of selection is conducted with similar cells which have similar surface materials associated with them, but which do not express the desired target.
  • the methods and aptamers of the present invention can also be directed to cell surface proteins.
  • a pool of oligonucleotides is brought into contact with a first known cell line which is known to express a particular cell surface protein which is uniquely identified with that cell line and sufficient time is allowed for the oligonucleotides to bind to the protein on the cell surfaces.
  • the cells are isolated with oligonucleotides bound thereto and the oligonucleotides are removed. This procedure is referred to herein as "positive screening".
  • the removed oligonucleotides are brought into contact with a second cell line which is identical to the first cell line, except that the second cell line does not express the particular identifying cell surface protein; binding is allowed to occur and any oligonucleotides which bind to the second cell line are isolated and discarded.
  • This procedure is referred to as "negative screening”.
  • the "positive” and “negative” screening steps can be repeated a multiplicity of times in order to obtain
  • oligonucleotides which are highly specific for the cell surface proteins being expressed on the first cell line.
  • the highly specific oligonucleotides may then be
  • a preferred variation for selection of aptamers that bind to surface antigens involves a procedure wherein negative selection is first carried out followed by a positive selection.
  • a pool of random oligonucleotides is combined with a tissue culture medium.
  • the oligonucleotides are allowed to remain in contact with the cell cultures for a sufficient period of time to allow binding between oligonucleotides and cell surfaces which lack the target molecule.
  • a negative selection process has been carried out, i.e., oligonucleotides which are not the desired aptamers can be eliminated by their binding to nontarget surfaces.
  • a positive selection step is carried out. This is done by combining the oligonucleotides which did not bind to the surfaces lacking target
  • aptamers oligonucleotides
  • the oligonucleotide mixture is brought into contact with a first known cell line which is known to express a particular cell surface protein which is uniquely identified with that cell line. After allowing sufficient time for the oligonucleotides to bind to the protein on the cell surfaces, procedures are carried out to isolate the cells with oligonucleotides bound thereto and the oligonucleotides are removed. This procedure is referred to herein as "positive screening".
  • targeted surface protein may be extensively washed in buffered saline or in tissue culture medium to remove low affinity aptamers and uncomplexed oligonucleotides.
  • the cells are treated with one or more of a number of agents that permit recovery of bound aptamers.
  • the cells may be treated enzymatically with trypsin or other proteases to cleave the targets at the cell surface, thus releasing the bound aptamers.
  • the cells containing bound aptamers may be washed in a detergent or high ionic strength solution in order to disrupt binding between the cells and aptamers.
  • the aptamers recovered at this point consist of a pool of different sequences that bind to different cell surface targets, including the target of interest.
  • Aptamers from the first tissue culture cells may be recovered from solution by precipitation or may be used directly if reagents used to remove aptamers do not significantly affect cells in the second tissue culture.
  • the aptamer mixture is then incubated with the second (null) cell culture under similar conditions.
  • the mixture brought into contact with a second cell line which is identical to the first cell line, except that the second cell line does not express the particular identifying cell surface protein. Binding is allowed to occur and any oligonucleotides which bind to the second cell line are isolated and discarded.
  • This procedure is referred to as "negative screening”.
  • the "positive” and “negative” screening steps can be repeated a multiplicity of times in order to obtain oligonucleotides which are highly specific for the cell surface proteins being expressed on the first cell line.
  • the highly specific oligonucleotides have been determined and isolated, they are subjected to PCR technology for amplification as above.
  • the resulting "aptamers" can be labeled and thereafter effectively used to identify the presence of the first cell line expressing the particular cell surface protein.
  • This method identifies target features on cell surfaces such as proteins, especially hetero- or
  • a preferred variation of this method involves a procedure wherein negative selection is first carried out followed by a positive selection.
  • a pool of random oligonucleotides is combined with a tissue culture medium.
  • oligonucleotides are allowed to remain in contact with the cell cultures for a sufficient period of time to allow binding between oligonucleotides and cell surfaces which lack the target molecule.
  • a negative selection process has been carried out, i.e., oligonucleotides which are not the desired aptamers can be eliminated by their binding to nontarget surfaces.
  • a positive selection step is carried out. This is done by combining the oligonucleotides which did not bind to the surfaces with no target molecules thereon with a cell culture containing the target molecule on their surface.
  • Such a negative-positive selection protocol can be carried out in a medium containing human or bovine serum in order to select aptamers under simulated physiological conditions.
  • Aptamers which are selected in the presence of serum may be rendered nuclease-stable by the use of PCR primers with modified internucleotide linkages that are nuclease-stable as described in commonly assigned copending Application Publication No. WO90/15065
  • candidate aptamers are added to a tissue culture medium lacking serum.
  • the serum-free medium is incubated with cells which lack the target molecules on their surfaces.
  • a cell culture which contains the target molecules on their surfaces is combined with any
  • oligonucleotides which are tightly bound to the target molecules on the cells are nuclease resistant as they are inaccessible to the nucleases due to their physical association with the target molecules.
  • the medium i.e., the serum containing the nucleases
  • the cells are washed and caused to release the oligonucleotides or aptamers bound thereto by treatment of the cells with proteases and/or detergents. Any oligomers which are substantially degraded by the nucleases will not be amplified during amplification processing.
  • the present inventors have found that the nuclease activity present within the serum is primarily a 3' exonuclease activity.
  • the presence of 3' exonuclease activity during target binding may be used with a candidate aptamer pool that has a short primer at the 3' end as a nuclease target. Accordingly, if the 3' end, which includes the primer, is degraded by the nuclease, the oligonucleotides attached to the degraded primers will not be amplified during amplification processing and will thereby be eliminated.
  • a similar short primer sequence (6-10 bases) at the 5' end could also be utilized in the same manner if 5' exonucleases are added to the medium during the selection protocol.
  • Kd dissociation constant
  • transfectant cells the first tissue culture cells
  • parental cells the second tissue culture cells
  • multiple rounds of selection and aptamer amplification will be necessary in order to provide multiple opportunities to enrich for aptamers that specifically bind to the target structure.
  • competitive binding analyses can be performed using the selected oligonucleotide species and radiolabeled substance.
  • oligonucleotide species can inhibit the target protein in a functional assay.
  • oligonucleotides selected for binding to CD4 the human lymphocyte
  • transmembrane protein may be tested for their ability to inhibit HIV-1 infection of human lymphocytes in culture.
  • the original oligonucleotide mixture can be synthesized according to the desired contents of the mixture and can be separated by adding the oligonucleotide mixture to a column
  • Complexes between the aptamer and targeted agent are separated from uncomplexed aptamers using any suitable technique, depending on the method used for complexation. For example, if columns are used, nonbinding species are simply washed from the column using an appropriate buffer. Specifically bound material can then be eluted.
  • the complexes can be separated from the uncomplexed oligonucleotides using, for example, the mobility shift in electrophoresis technique (EMSA), described in Davis, R.L., et al., Cell (1990) 60 : 733 .
  • MSA mobility shift in electrophoresis technique
  • aptamer-target molecule complexes are run on a gel and aptamers removed from the region of the gel where the target molecule runs.
  • Unbound oligomers migrate outside these regions and are separated away. Finally, if complexes are formed on filters, unbound aptamers are eluted using standard techniques and the desired aptamer recovered from the filters.
  • separation of the complexes involves detachment of target-aptamer complexes from column matrices as follows.
  • covalently or noncovalently coupled target molecules is synthesized. Any standard coupling reagent or procedure may be utilized, depending on the nature of the support and the target molecule.
  • covalent binding may include the formation of disulfide, ether, ester or amide linkages.
  • the length of the linkers used may be varied by conventional means.
  • Noncovalent linkages include antibody-antigen interactions, protein-sugar interactions, as between, for example, a lectin column and a naturally-occurring oligosaccharide unit on a peptide.
  • Lectins are proteins or glycoproteins that can bind to complex carbohydrates or oligosaccharide units on glycoproteins, and are well-described in The Lectins
  • Lectins are isolated from a wide variety of natural sources, including peas, beans, lentils, pokeweed and snails.
  • Concanavalin A is a particularly useful lectin.
  • linking chemistries are also available.
  • disulfide-derivatized biotin may be linked to a target molecule by coupling through an amine or other functional group.
  • the resulting target-S-S- biotin complex could then be used in combination with avidin-derivatized support.
  • Oligonucleotide-target complexes could then be recovered by disulfide bond cleavage.
  • target may be coupled via a cis-diol linker, and oligonucleotide-target complexes may be recovered by mild oxidation of the vicinal diol bond using NaIO 4 or other appropriate reagents.
  • Linking chemistries will be selected on the basis of (i)
  • the oligomer mixture is added to and incubated with the support to permit oligonucleotide-target
  • oligonucleotides by removing unbound oligomers from the support environment. For example, if columns are used, nonbinding species are simply washed from the column using an appropriate buffer.
  • the target molecules are uncoupled from the support.
  • the uncoupling procedure depends on the nature of the
  • Targets bound through disulfide linkages may be removed by adding a sulfhydryl reagent such as dithiothreitol or ⁇ -mercaptoethanol.
  • Targets bound to lectin supports may be removed by adding a complementary monosaccharide (e.g., ⁇ -methyl-mannoside, N-acetylglucosamine, glucose, N-acetylgalactosamine, galactose or other saccharides for concanavalin A).
  • Oligonucleotides specifically bound to the target can then be recovered by standard denaturation techniques such as phenol extraction.
  • the method of elution of target-oligonucleotide complex from a support has superior unexpected properties when compared with standard oligonucleotide elution techniques. This invention is not dependent on the mechanism by which these superior properties occur.
  • oligonucleotide or target Removing oligonucleotide- target complexes enables the recovery of oligonucleotides specific to target only, while eliminating oligonucleotides binding to the support, or the support in conjunction with oligonucleotide or target. At each cycle of selection, this method may give up to 1,000- fold enrichment for specifically binding species.
  • Aptamers can also be selected in the above methods using a pool of oligonucleotides that vary in length as the starting material.
  • a pool of oligonucleotides that vary in length as the starting material.
  • several pools of oligonucleotides having random sequences are synthesized that vary in length from e . g. 50 to 60 bases for each pool and containing the same flanking primer-binding sequences.
  • Equal molar amounts of each pool are mixed and the variable-length pool is then used to select for aptamers that bind to the desired target substance, as described above.
  • This protocol selects for the optimal species for target binding from the starting pool and does not limit aptamers to those of a given length.
  • pools of mixed length aptamers can be used in parallel in separate selections and then combined and further selected to obtain the optimal binders from the size range initially used.
  • three pools, A, B and C can be used.
  • Pool A can consist of oligonucleotides having random sequences that vary in length from e.g. 30 to 40 bases;
  • pool B can have sequences varying in length from e.g. 40 to 50 bases;
  • pool C can have sequences varying in length from 50 to 60 bases. It is to be understood that the lengths described above are for illustrative purposes only. After selection to obtain binders from A, B, and C, all aptamers are mixed together.
  • a number of rounds of selection are done as described above to obtain the best binders from the initial species selected in the 30-to 60-base range. Note that with this technique, not all possible species in some of the pools are used for selection. If the number of sites available for binding are increased, i.e., if a column is used and the size of the column increased, more species can be included for selection. Furthermore, this method allows for the selection of oligomers from the initial starting pool that are of optimal length for binding the targeted agent.
  • Aptamers containing the specific binding sequences discerned through the method of the invention can also be derivatized in various ways. For example, if the aptamer is to be used for separation of the target substance, conventionally the oligonucleotide will be derivatized to a solid support to permit chromatographic separation. If the oligonucleotide is to be used to label cellular components or otherwise for attaching a detectable moiety to target, the oligonucleotide will be derivatized to include a radionuclide, a fluorescent molecule, a chromophore or the like.
  • the oligonucleo tide is to be used in specific binding assays, coupling to solid support or detectable label, and the like are also desirable. If it is to be used in therapy, the oligonucleotide may be derivatized to include ligands which permit easier transit of cellular barriers, toxic moieties which aid in the therapeutic effect, or
  • the aptamer may also be included in a suitable expression system to provide for in situ
  • consensus sequence refers to a nucleotide sequence or region (which may or may not be made up of contiguous nucleotides), which is found in one or more regions of at least two aptamers, the presence of which may be
  • a consensus sequence may be as short as three nucleotides long. It also may be made up of one or more noncontiguous sequences with nucleotide sequences or polymers of hundreds of bases long interspersed between the consensus sequences. Consensus sequences may be identified by sequence comparisons between individual aptamer species, which comparisons may be aided by computer programs and other tools for modeling secondary and tertiary structure from sequence information.
  • the consensus sequence will contain at least about 3 to 20 nucleotides, more commonly from 6 to 10 nucleotides.
  • Consensus sequence means that certain positions, not necessarily contiguous, of an oligonucleotide are specified. By specified is meant that the composition of the position is other than completely random. Not all oligonucleotides in a mixture may have the same nucleotide at such position; for example, the consensus sequence may contain a known ratio of particular nucleotides.
  • a consensus sequence might consist of a series of four positions wherein the first position in all members of the mixture is A, the second position is 25% A, 35% T and 40% C, the third position is T in all oligonucleotides, and the fourth position is G in 50% of the oligonucleotides and C in 50% of the oligonucleotides.
  • oligonucleotides that contain that sequence may be made by conventional synthetic or recombinant means. These aptamers, termed “secondary aptamers,” may also function as target-specific aptamers of this invention.
  • secondary aptamer may conserve the entire nucleotide sequence of an isolated aptamer, or may contain one or more additions, deletions or substitutions in the
  • a mixture of secondary aptamers may also function as target-specific aptamers, wherein the mixture is a set of aptamers with a portion or portions of their nucleotide sequence being random or varying, and a conserved region which contains the consensus sequence. Additionally, secondary aptamers may be synthesized using one or more of the modified bases, sugars and linkages described herein using conventional techniques and those described herein. Immune Recruitment
  • the present invention also provides a method whereby immune response is elicited in a desired manner through the use of agents which are directed to specific targets on cells involved in a pathological condition of interest.
  • the aptamers prepared herein are useful as targeting agents in this method.
  • the known ability of various materials to elicit strong immune responses is exploited so as, in turn, to stimulate the immune response to target pathologic cells, which may themselves otherwise have the ability to reduce or escape effective CTL responses.
  • a targeting agent is identified that
  • a conjugate is formed with a moiety known to act itself as an immunogen, for example as an antigen for eliciting a strong CTL response in the organism.
  • a conjugate is formed with a moiety known to act itself as an immunogen, for example as an antigen for eliciting a strong CTL response in the organism.
  • the targeting agent is an oligonucleotide which binds to a specific target on a cell surface
  • the immunomodulatory component of the conjugate is a polypeptide which elicits a strong CTL response.
  • aptamers of the invention are useful in diagnostic, research and therapeutic contexts.
  • aptamers are particularly well suited for binding to biomolecules that are identical or similar between different species.
  • Classes of molecules such as kinins and eicosanoids generally do not serve as good antigens because they are not easily recognized as foreign by the immune systems of animals that can be used to generate antibodies.
  • Antibodies are generally used to bind analytes that are detected or quantitated in various diagnostic assays. Aptamers represent a class of
  • the aptamers of the invention are therefore particularly useful as diagnostic reagents to detect the presence or absence of the target substances to which they specifically bind.
  • diagnostic tests are conducted by contacting a sample with the specifically binding oligonucleotide to obtain a complex which is then detected by conventional means.
  • the specifically binding oligonucleotide to obtain a complex which is then detected by conventional means.
  • aptamers may be labeled using radioactive, fluorescent, or chromogenic labels and the presence of label bound to solid support to which the target substance has been bound through a specific or nonspecific binding means detected.
  • the specifically binding aptamers may be used to effect initial complexation to the support.
  • Means for conducting assays using such oligomers as specific binding partners are generally known to track those for standard specific binding partner based assays.
  • This invention also permits the recovery and deduction of oligomeric sequences which bind specifically to cell surface proteins and specific portions thereof. Therefore, these oligonucleotides can be used as a separation tool for retrieving the substances to which they specifically bind.
  • a separation tool for retrieving the substances to which they specifically bind.
  • these oligonucleotides can be used in diagnosis by employing them in specific binding assays for the target substances.
  • detectable moieties such as radioisotopes
  • the specifically binding oligonucleotides can also be used for in vivo imaging or histological analysis.
  • oligomers of the invention are characterized by their ability to target specific
  • the specifically binding oligonucleotides of the invention are especially helpful in effecting the isolation and purification of substances to which they bind.
  • the oligonucleotide containing the specific binding sequences is conjugated to a solid support and used as an affinity ligand in chromatographic separation of the target substance.
  • the affinity ligand can also be used to recover previously unknown substances from sources which do not contain the target substance by virtue of binding similarity between the intended target and the unknown substances.
  • the aptamers of the invention can be formulated for a variety of modes of administration, including systemic and topical or
  • injection is preferred, including intramuscular, intravenous,
  • the aptamers of the invention are formulated in liquid solutions, preferably in physiologically compatible buffers such as Hank's solution or Ringer's solution.
  • the aptamers may be formulated in solid form and redissolved or suspended immediately prior to use.
  • Lyophilized forms are also included.
  • Systemic administration can also be by transmucosal or transdermal means, or the oligomers can be administered orally.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration bile salts and fusidic acid derivatives.
  • detergents may be used to facilitate permeation.
  • Transmucosal administration may be through nasal sprays, for example, or using suppositories.
  • the oligomers are formulated into conventional oral formulation
  • administration forms such as capsules, tablets, and tonics.
  • the oligomers of the invention are formulated into ointments, salves, gels, or creams, as is generally known in the art.
  • oligonucleotides may also be employed in expression systems, which are administered according to techniques applicable, for instance, in applying gene therapy.
  • the present invention is also directed to a method whereby immune response is elicited in a desired manner through the use of agents which are directed to specific targets on cells involved in a pathological condition of interest.
  • any of a number of different materials which bind to cell surface antigens may be employed.
  • antibodies to target cell surface antigens will generally exhibit the
  • ligands for any receptors on the surface of the pathologic cells of interest may suitably be employed as targeting agent.
  • Yet another class of potentially valuable targeting agents is oligonucleotides of the requisite binding selectivity.
  • polyclonal anti-sera are prepared in conventional ways, for example by injecting a suitable mammal with antigen to which antibody is desired, assaying the antibody level in serum against the antigen, and preparing anti-sera when the titers are high.
  • preparations may also be prepared conventionally, such as by the method of Koehler and Milstein using, e.g., peripheral blood lymphocytes or spleen cells from
  • suitable immunoreactive fragments may also be employed, such as the Fab, Fab', or F(ab') 2 fragments.
  • Fab fragment antigen binding
  • Fab' fragment antigen binding domain
  • F(ab') 2 fragments fragment antigen binding fragments
  • Many antibodies suitable for use in forming the targeting mechanism are already available in the art.
  • the use of immunologically reactive fragments as substitutes for whole antibodies is described by Spiegelberg, H.L., in "Immunoassays in the Clinical Laboratory” (1978) 3:1-23.
  • One known surface antigen to which antibodies can be raised is the extracellular domain of the HER2/nu associated with breast tumors.
  • Fendly B.M. et al. J Biol Resp Mod (1990)
  • alternate hosts since the antigen is not foreign to the host-bearing tumor
  • the antibody or fragment thereof would be coupled not to a toxin, but to an
  • targeting can be effected by utilizing receptor ligands which target receptors at the target cell surface, for example on the basis of complementarity of contours or charge patterns between the receptor and ligand.
  • receptor ligand refers to any substance, natural or synthetic, which binds specifically to a cell surface receptor, protein or glycoprotein found at the surface of the desired target cell population.
  • receptor ligands include lymphokine factors, for example, IL2 or viral or tumor antigens.
  • Oligonucleotides identified as binding to one or more surface antigen of the pathologic cells may also be used to form conjugates in a known manner, and are particularly preferred for use as targeting agents in accordance with the present invention.
  • an "immunological response" as discussed herein generally refers to the development in a mammal of either a cell- or antibody-mediated immune response to an agent of interest .
  • a response consists of the mammal producing antibodies and/or cytotoxic T-cells directed specifically to a particular agent.
  • an agent of interest e.g., an antibody to an agent of interest.
  • conjugate may constitute, e.g., the failure to produce antibodies or cytotoxic T-cells under circumstances (for example, in the presence of a particular antigen) which would normally result in the induction of a specific response.
  • moieties known to act as antigens for eliciting a strong CTL response include a wide range of biologically active materials. Particularly suitable for use in this regard are short peptide sequences, such as those which may correspond to the antigenic
  • sequences derived from viral or bacterial pathogens may be useful in stimulating a strong CTL response in the infected host organism.
  • immunomodulatory agents useful in the invention include fragments of the HLA Class I
  • glycoproteins or fragments thereof to stimulate a CTL response has been documented by Symington, F.W. et al., J Invest Dermatol (1990) 95:224-228.
  • Also known to elicit CTL responses are short regions of viral antigens such as those of the influenza virus nucleoprotein (Rothbard, J.B. et al., EMBO J (1989) 8:2321-2328) and sections of the murine minor histocompatibility antigens such as H- 25.3 cell surface antigen (Lai, P.K., Transplantation (1985) 39:638-643).
  • Other known agents which expand CTL as opposed to helper T-cells include interleukin-6 and cyclosporin A.
  • Coupling of the targeting agents with the immunomodulatory agents may be carried out using any of a variety of different techniques which are well known per se to those working in the field. The particular choice of coupling method depends on the chemical nature of the specific targeting and immunomodulatory agents.
  • the agents which constitute the conjugate is a polypeptide
  • well-known chemical methods for formation of chemical bonds with, e.g., functional groups on amino acid side-chains or preferably N-terminal amino or C-terminal carboxyl groups may be employed.
  • One common approach is the use of linkers which may be homobifunctional or
  • Suitable targets for binding a targeting agent include cell surface antigens which are specific to the pathologic cells which it is desired to treat. For example, most tumor antigens (such as the carcinoembryonic antigen associated with several types of cancer) do not generally elicit an effective CTL
  • the presence of the antigens on the surface of tumor cells enables the use of appropriately tailored targeting agents to deliver conjugate specifically to those cells.
  • the conjugates of the invention may be useful in preventing the progression or the cure of autoimmune disease.
  • autoimmune component such as diabetes or arthritis
  • conjugates of the invention to elicit an immune response against those immune cells which mediate the attack on self tissues, a positive effect on the course of the disease may be achieved.
  • a group of antigenically related immune cells that mediate the systemically inappropriate response could be targeted using a single conjugate specific for that antigen. Destruction of this marked population by the immune system should lead to an
  • the binding of appropriate conjugates to target antigens on cells could be employed as a means to mask recognition of those antigens or of the cell bearing the antigens. This could prevent the destruction of the cell carrying the antigens, and thus result in stasis of autoimmune disease progression.
  • an immune response stimulated by the immunomodulatory portion of the conjugate may result in other desirable immunologic responses in the organism.
  • a highly desirable response to other unmarked cells of the same type may result.
  • identifying a particular class of cells for recognition by various components of the immune system via the immunomodulatory portion of the conjugate it may be possible to induce a particular category of response (e.g., CTL-mediated destruction) to that category of cells as a whole, regardless of whether or not the cells are marked by conjugate.
  • Target molecules that are not conventionally considered to be biomolecules are also appropriate for the methods described herein.
  • Examples of “non- biomolecule” targets include intermediates or end- products generated by chemical synthesis of compounds used in therapeutic, manufacturing or cosmetic
  • oligonucleotides may be used to specifically bind to most organic compounds and are suitably used for isolation or detection of such compounds.
  • Bradykinin derivatized ToyopearlTM (Toso Haas, Inc.,
  • Bradykinin was coupled to the Toyopearl support through its amino termini according to the
  • Bradykinin (NH 2 -arg-pro-pro-gly-phe-ser-pro-phe-arg-COOH, acetate salt) was obtained from Bachem Feinchemikalien AG (Cat. No. H-1970). Toyopearl AF-carboxyl 650 M was converted to the NHS-ester by treatment with N-hydroxy succinimide (NHS) and diisopropyl carbodiimide in dioxane/DMF (1:1) for 24 hours. The support was washed with DMF, H 2 O, 200 mM NaHCO 3 and treated with a solution of bradykinin (20 mg of bradykinin/ml support) in 200 mM NaHCO 3 for 3 days.
  • the support was then washed and the coupling yield was determined by HCl digestion of the support (80°C for 8 hours) and a ninhydrin assay using free bradykinin as a standard. The yield was found to be 16 mg/ml support (16 ⁇ mole/ml support).
  • the coupled support was then capped by treatment with acetic acid (NHS-ester) in dioxane/200 mM NaHCO 3 buffer (1:1).
  • An underivatized capped support to be used as a control was made by treating Toyopearl AF-carboxyl 650M with acetic acid (NHS-ester) in dioxane/200 mM NaHCO 3 buffer (1:1), followed by washing.
  • NMS-ester acetic acid
  • DNA oligonucleotides containing a randomized sequence region were synthesized using standard solid phase techniques and phosphoramidite chemistry
  • DNA 18-mers with the following sequences were used as primers for PCR amplification of oligonucleotide
  • the 5' primer sequence was 5' HO-CGTACGGTCGACGCTAGC-OH 3' and the 3' primer sequence was 5' biotin-O- GGATCCGAGCTCCACGTG-OH 3'.
  • the biotin residue was linked to the 5' end of the 3' primer using commercially available biotin phosphoramidite (New England Nuclear, Cat. No. NEF-707).
  • the biotin phosphoramidite is incorporated into the strand during solid phase DNA synthesis using standard synthesis conditions.
  • bradykinin-derivatized Toyopearl support 400 ⁇ l bradykinin-derivatized Toyopearl support was loaded on a 1.5 ml column housing.
  • the column was washed with 3 ml of 20mM Tris-acetate buffer (pH 7.4) containing ImM MgCl 2 , 1 mM CaCl 2 , 5mM KCl and 140mM NaCl (the "selection buffer").
  • selection buffer the underivatized Toyopearl control support described in Example 1-A.
  • This amplified oligonucleotide pool (0.1 nmoles, about 6 copies of 1 ⁇ 10 13 unique sequences), doped with 5'- 32 P-labeled species, was used in the first selection round.
  • the pool was heated to 94°C for 3 minutes in selection buffer, allowed to cool to room temperature, applied to the control column in a volume of
  • elution buffer 500 mM Tris ⁇ HCl (pH 8.3), 20 mM EDTA
  • Aptamers were eluted in the first 2 or 3 fractions after the void volume. These fractions were combined and precipitated using ethanol and glycogen as the carrier.
  • the aptamer pellet was resuspended in 200 ⁇ l of ddH 2 O (deionized distilled water) and divided into two 0.5 ml siliconized Eppendorf tubes for PCR. All remaining counts on the column were removed by treatment with 0.1N NaOH (0.5 ml), although these species were not used in subsequent amplification and selections.
  • Two groups of selected aptamers were amplified by PCR using standard techniques and the following protocol.
  • a 200 ⁇ l PCR reaction consisted of the following: 100 ⁇ l template aptamer (approximately 2 pmoles); 20 ⁇ l buffer (100 mM Tris ⁇ Cl (pH 8.3), 500 mM KCl, 20 mM MgCl 2 ); 32 ⁇ l NTP's (5 mM conc total, 1.25 mM each ATP, CTP, GTP, and TTP); 20 ⁇ l primer 1
  • reaction lasted 1 minute. Primer annealing occurred at 60°C for 1 minute, and elongation of primed DNA strands using the Taq polymerase ran at 72°C for 2 minutes. The final elongation reaction to completely fill in all strands ran for 10 minutes at 72°C, and the reaction was then held at 4°C.
  • bradykinin-linked column selection were obtained in two 100 ⁇ l fractions that contained 0.07% of the total counts loaded. Recovery of three 100 ⁇ l fractions from the second round selection yielded 0.26% of the total counts loaded therein, indicating that an increased proportion of the aptamers loaded onto the column had bound to bradykinin.
  • This high affinity aptamer pool was eluted, amplified by PCR, cloned, and sequenced (about 20 to 40 clones). From these clones, several homologous batches of aptamers and/or individual clones are prepared by solid phase DNA synthesis and tested for bradykinin binding affinity and specificity.
  • An initial oligonucleotide pool (0.5 nmole, 3 ⁇ 10 14 unique sequences) of synthetic 96-mer prepared as in Example 1-B is amplified approximately 30-fold by largescale PCR using known techniques. Assuming 10-20% readthrough of synthetic DNA and possible preferential amplification by the Taq polymerase, the estimated actual complexity is reduced to about 1 ⁇ 10 13 unique sequences.
  • bradykinin-linked column and control support column are prepared as in Example 1-B.
  • the pool is heated to 94°C for 3 minutes in selection buffer, cooled to room temperature, then
  • the aptamer pellet is taken up in 100 ⁇ l of dd H 2 O and transferred to a 0.5 ml siliconized eppendorf tube for PCR.
  • One aptamer PCR reaction and one control (without template) reaction are then run as described in
  • PGF2 ⁇ derivatized ToyopearlTM AF-amino 650M (Toso Haas, Inc., Woburn, MA) support charged with 10 ⁇ moles PGF2 ⁇ /ml matrix was used for all selections described. The support was coupled through the free carboxyl group of PGF2o; according to the manufacturer's instructions.
  • PGF2 ⁇ was purchased from Sigma Chemical Co. (Cat. No. P 3023) and tritiated PGF2 ⁇ was purchased from New England Nuclear.
  • PGF2 ⁇ Tris salt
  • 10 mg of PGF2 ⁇ was dissolved in 1 ml H 2 O/methanol and converted to the sodium salt by passage over an ion exchange column.
  • the column eluent was then evaporated, dissolved in dioxane and converted to the N-hydroxy-succinimide (NHS) ester by treatment with NHS and diisopropyl carbodiimide for 24 hrs.
  • NHS N-hydroxy-succinimide
  • This mixture was then added to l ml of the settled support Toyopearl washed previously with 200 mM NaHCO 3 .
  • the mixture was shaken for 24 hrs., and washed with a NaHCO 3 solution.
  • the coupling yield was determined by the amount of tritium associated with the support.
  • the support was then capped by treatment with acetic acid (NHS-ester) in dioxane/200 mM NaHCO 3 buffer (1:1).
  • Example 1-B 0.5 nmoles of the oligonucleotide pool prepared in Example 1-B (doped with tracer amounts of 5'- 32 P-end-labeled species) was resuspended in 400 ⁇ l of selection buffer and heat denatured for 2 min at 95°C.
  • denatured DNA was immediately transferred to wet ice for 10 min. This material was applied to the control support (underivatized Toyopearl), flow initiated, and eluent collected. Flow-through was reapplied three times. At the end of the third application, the column was rinsed with 200 ⁇ l selection buffer (1 bed volume). The flow-through was pooled and applied for a fourth time. A column profile was established using 32P quantification via Cerenkov counting. Flow-through material was then pooled for application to the PGF2 ⁇ support.
  • oligonucleotides were eluted with 20mM EDTA/60%
  • Example 2-B The DNA selected in Example 2-B above was amplified via PCR using known techniques under the following conditions: 1 nmole of 5' and 3' primer
  • the matrix was extensively washed to remove contaminants and single-stranded aptamer eluted with 600 ⁇ l washes of 0.15N NaOH (2X), yielding 40-48% recovery of input 32P DNA.
  • the aptamer solution was brought to pH 6 with acetic acid and concentrated via n-butanol extraction to 40% of the initial volume.
  • the material was precipitated with absolute ethanol (3 vols) on dry ice for 15 minutes.
  • the DNA was pelleted, washed with 70% ethanol and dried under vacuum. The material was resuspended in selection buffer as described above. Subsequent rounds of selection were carried out using the same protocol: removal of aptamer by binding to the control support column; followed by binding to the PGF2 ⁇ column.
  • the aptamers obtained after 6 rounds of PGF2 ⁇ selection were a pool of molecules that resulted from competition among aptamer species for a limited number of PGF2 ⁇ binding sites.
  • PGF2 ⁇ :oligonucleotide molar ratio compared to the binding ratio used to generate the PGF2 ⁇ aptamer pool This indicated that specific binding of oligonucleotides involves structural features that required the presence of Mg ++ ion.
  • the use of EDTA in the elution buffer efficiently removes Mg ++ ion from solution and thus prohibits specific binding of oligonucleotides to the PGF2or matrix.
  • the round 6 pool is characterized by determining the elution profile obtained after washing a PGF2 ⁇ column (200 ⁇ l support volume) saturated with the round 6 pool.
  • the washes are carried out using 0.4 ml of selection buffer containing 1.0 mM solutions of a series of compounds that resemble PGF2 ⁇ more closely than HP does.
  • the elution with a molecule similar to PGF2 ⁇ will be followed by elution with 0.4 ml of selection buffer containing 1.0 mM PGF2 ⁇ to determine the efficiency of PGF2 ⁇ elution.
  • the compounds that are tested include hydroxydecanoic acid, arachidonic acid, prostaglandin A, prostaglandin B, and other eicosanoids.
  • columns made using equimolar amounts of PGF2 ⁇ and 8-iso-PGF2 ⁇ are used to generate a pool of aptamers containing species that bind to one or the other isomer or both. Some of these aptamers presumably bind to regions of the PGF2 ⁇ structure that are unaffected by the isomerization. Chemically modified eicosanoids are used in a similar manner.
  • PGF2 ⁇ derivatized ToyopearlTM Toyo Haas, Inc., Woburn, MA support (charged with 10 ⁇ moles PGF2 ⁇ /mL matrix) was used for all selections described.
  • PGF2 ⁇ was purchased from Sigma Chemical Co. (Cat. No. P 3023) and 3 H-PGF2 ⁇ was purchased from New England Nuclear.
  • PGF2 ⁇ (salt) (10 mg) is dissolved in H 2 O/methanol (1 ml) and converted to the sodium salt by passage over an ion exchange column. The eluent is evaporated, dissolved in dioxane and converted to the NHS-ester by treatment with N-hydroxy-succinimide (NHS) and diisopropyl carbodiimide for 24 hrs. This mixture is then added to a toyopearl AF-amino 650M (Toyo Haas, Inc.) support (1 ml of settled support) which has been washed previously with 200 mM NaHCO 3 ). The mixture is shaken for 24 hours and the support is washed with 200 mM NaHCO 3 solution. To determine the amount of loading the above-described coupling procedure is repeated except that a small amount of tritiated PGF2 ⁇ is added and the coupling yield is determined from the amount of 3 H-label
  • the support is capped by treatment with acetic acid NHS-ester in dioxane/buffer 1:1. (The buffer is 200 mM NaHCO 3 ).
  • the all-capped support is made by treatment of toyopearl AF-amino 650M with acetic acid NHS-ester in the same manner as described above.
  • a pool of aptamers consisting of 60 bases of completely random sequence is synthesized by standard solid phase techniques using phosphoramidite chemistry (Gait M.J., Oligonucleotide Synthesis. IRL Press, 1984;
  • 1.3 ⁇ 10 36 different aptamer sequences are possible in a random 60-mer pool.
  • a standard 1 ⁇ M scale synthesis followed by HPLC purification yields 60 nmoles of single stranded DNA. Assuming that each base residue has an average molecular weight of 350, the synthesis yields 1.26 mg of purified DNA.
  • the aptamers are synthesized with a phosphate group at the 5' end.
  • the biotin residue is linked to primer using a commercially available biotin phosphoramidite conjugate (New England Nuclear, Catalog No. NEF-707) that is incorporated into the strand after solid phase DNA synthesis using standard synthesis conditions. The biotin label is incorporated into DNA according to manufacturer's recommendations.
  • Selection buffer mimics the ion and pH conditions found in the human circulatory system.
  • a control column containing identical support is prepared in the same manner. This support is the parent matrix for attachment of selection ligand but has been capped as the acetamide to mimic the linkage used for attachment to PGF2a.
  • aptamer 1 nmole of aptamer (doped with tracer amounts of 32 P-labeled species) is resuspended in 400 ⁇ l of selection buffer and heat denatured for 2 minutes at 95°C. The denatured DNA is immediately transferred to wet ice for 10 minutes. This material is applied to the control support. Flow is initiated and eluent collected. Flow-through is reapplied up to three times. At the end of the third application the column is rinsed with selection buffer. A column profile is established using
  • PGF2 ⁇ matrix is identical to that described above. After application to the column, the matrix is washed with 200 ⁇ L of selection buffer and the material reapplied to establish a column profile.
  • the support is washed with additional selection buffer until the eluting 32P material reaches a constant low level (less than about 0.2% of input DNA per 200 ⁇ L of flow through).
  • the support then is washed with 1 mL of selection buffer containing increased NaCl (IM) until counts per 200 ⁇ L of wash are less than about 0.2% of input totals.
  • Desired aptamer is eluted with a solution of 20 mM EDTA/60% acetonitrile (elution buffer).
  • Specifically bound aptamers are recovered from the first 2 to 4 column volumes that are obtained after adding elution buffer. The solvent is removed in vacuo and the material is chromatographed on a G50 Sephadex Nick column (Pharmacia, catalog no. 17-0855-02) as per the manufacturer's instructions using 10 mM Tris pH 7.5/0.1 mM
  • Linkers of known sequence that serve as primers for amplification of the aptamer by PCR or other methods are covalently attached to the DNA in the aptamer pool as follows. 1.0 pmole of aptamer obtained as described in
  • Section 1 (about 21 ng of which corresponds to about 6.0
  • linker 1 which contains 40 nucleotide residues
  • Linker 1 which will be ligated to the 5' end of the aptamer and consists of a pool of 256 different species, has the structure shown below. Four random sequence residues at the 5' end of strand A of linker 1 gives rise to the 256 different species. Four random sequence residues at the 3' end of strand C of linker 2 result in a pool of 256 linker 2 species.
  • strand B Linker 2 has the following structure.
  • the linker 1 sequence 5' GAATGC
  • restriction enzyme Bsm I which cuts as follows (x denotes the cut site in each strand):
  • linker 1 Positioning of the BspMI site as shown in linker 1 permits subsequent precise removal of the attached linker from the aptamer after amplification.
  • linker 2 sequence :
  • restriction enzyme Ear I which cuts as follows (x denotes the cut site in each strand):
  • Nucleotide residues labeled N are random A, T, G or C residues and serve to anneal with the terminal four bases at the 5' end, linker 1, and 3' end, linker 2, of each aptamer. Perfect matches between the random linker bases and the terminal four random bases of the aptamer permit annealing and ligation of the linkers to the aptamer.
  • the ligation reaction is carried out in a 300 ⁇ l volume using 1,000 units of T4 DNA ligase (New England Biolabs, Catalog No.
  • linker 1 linker 1 ligated to the 5' end of the aptamer with linker 2 ligated to the 3' end of the aptamer.
  • linker 2 linker 2 ligated to itself to give a dimer.
  • the dimers are removed by adding solid agarose-avidin support (Vector Labs, Inc. Catalog No.
  • linker dimers from the aptamer pool
  • E. coli polymerase I New England Biolabs
  • flanking linker is eluted by heating to 94°C and washing.
  • Protocols for adding linkers to only one end of an aptamer and amplifying it follow.
  • a pool of a very long linkers For example, in a preferred embodiment, a pool of a very long linkers
  • the long linker described above could be a replicon and directly used to generate an aptamer clone bank by transforming a desired host.
  • PCR Technology Principles and Applications for DNA Amplification. Chapter 10, p. 105-111 (Henry A. Erlich, ed. 1989) Stockton Press.
  • a less preferred (because yields are lower) embodiment for attaching a linker to a single stranded aptamer would be ligation of single stranded linker to single stranded aptamer.
  • the selected DNA is amplified via PCR using the following conditions: 1 nmole of each primer, 250 ⁇ M dNTPs (containing 20 ⁇ Ci of dCTP, dGTP and dATP-total 60 ⁇ Ci) in 200 ⁇ L of 10 mM Tris pH 8.3 containing 50 mM KCl and 1.5 mM MgCl 2 .
  • the reaction is sealed with mineral oil. This reaction is put through 15 cycles of
  • One cycle of PCR amplification is carried out by bringing the temperature to 94°C for 1 minute.
  • the denaturation step is 60°C for 1 minute.
  • the hybridization step is 72°C for 1 minute and then back to 94°. After 15 cycles, the temperature is left at 72°C for 2 minutes to completely fill in all primed single stranded regions.
  • the mineral oil is removed by extraction with CHCl 3 . The solution is then vortexed and separated via
  • Linker 2 is removed by digestion with Ear I (New England Biolabs, Catalog No. 528L) under recommended conditions using excess enzyme to insure complete cutting by the enzyme. Following Ear I digestion, the column is heated to 95°C for 3 minutes to denature the aptamer complement-strand molecule followed by washing in TE buffer (10 mM Tris-Hcl, pH 7.5, 1 mM EDTA) to remove all unbound strands.
  • Ear I New England Biolabs, Catalog No. 528L
  • the aptamer is removed from linker 1 strand A, which is bound to the agarose-avidin support, by
  • BsmI restriction buffer 50 mM sodium chloride, 20 mM Tris-HCl, pH 7.4 at 20°C, 10 mM magnesium chloride, 10 mM 2-mercaptoethanol,
  • PGF2 ⁇ molecule The aptamer pool is then radiolabeled by incorporation of 32 P as described in Example 3-B.
  • aptamers are labeled using radiolabeled nucleotide triphosphates during PCR amplification.
  • the DNA is precipitated with ethanol as described in
  • Linkers are covalently coupled to the 5' end of aptamers obtained from column selection as described in Examples 3-A and 3-B.
  • Aptamer DNA is synthesized with a free amine group at the 5' end.
  • Amine phosphoramidite monomers are used to generate the 5' terminal amine- nucleoside residue (using equal amounts of A, T, G and C monomer at the final coupling step).
  • the aptamer DNA is coupled to primer sequences as follows.
  • Linker is coupled to the 3' end using linker 2 described in
  • Example 3-C Linker (carrying biotin at the 5' end) is attached to the aptamer free 5' amine group by chemical coupling between primer oligomer DNA with a free 3' phosphate group.
  • the reaction is carried out for 4 hours at room temperature in 0.1 M methylimidazole, pH 7.0 and 0.1 M 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride.
  • the latter reagent acts as a water soluble condensing agent.
  • the resulting aptamer contains the linkage, 5' X-O-P-O 2 -NH-CH 2 -Z 3', at the aptamer-linker junction; X is the 3' terminal residue of the linker and Z is the 5' terminal aptamer residue.
  • linkers are attached at both ends of the aptamer, as described in the Examples above, PCR amplification is carried out and the DNA is attached to an avidin column.
  • Free aptamer carrying a amino group at the 5' end is obtained by (i) digestion in excess Ear I enzyme, (ii) heat denaturing at 94°C, (iii) washing the column with TE, (iv) release of free aptamer after incubation of the column in 80% acetic acid for 4 hours at room temperature.
  • the aptamers are then recovered by
  • DNA oligomers containing even a single RNA nucleotide residue are sensitive to RNAses such as RNAse T 1 or U 1 .
  • T 1 and U 1 enzymes cleave specifically at guanine residues to yield two oligomers.
  • One oligomer contains the RNA residue at the 3' end the phosphate group linked at the 3' position and the other oligomer contains a hydroxyl group at the 5' end. Cleavage of such an oligomer at the RNA residue is also possible by incubation of the oligomer in 0.1 M NaOH for 30 minutes and yields essentially the same products as the T 1 or U 1 enzymes.
  • RNAse sensitivity of DNA-RNA oligomers may be applied to selection and amplification of aptamers.
  • DNA polymerases have the capacity to initiate DNA synthesis from a free 3' hydroxyl group on either DNA or RNA oligomers.
  • RNA-containing oligomer is synthesized using support bound protected G* monomer (Milligen/Biosearch, Catalog No. GEN 067570) that is used directly in a 1 ⁇ mole scale DNA synthesis using phosphoramidite chemistry according to manufacturer's instructions.
  • Aptamer strands have the following structure.
  • G* denotes the position of the guanine RNA residue.
  • DNA primers (strands B and C as described in Example 3-C) are attached to aptamer DNA eluted from the column and amplification using strand B of linker 1 with a ribosyl G residue at the 3' end is used as primer for synthesis of the aptamer strand containing an RNA residue in
  • RNA containing strand has 5' biotin attached.
  • the aptamer thus obtained is then used in a subsequent round of selection on a PGF2 ⁇ column.
  • DNA obtained in elution buffer washes is precipitated, and resuspended in buffer for kinase reaction and then ligated to flanking primer sequences as described.
  • the kinase reaction prior to ligation of linkers is necessary to replace the 5' terminal phosphate group that is lost from the aptamer when T 1 digestion (or NaOH treatment) is carried out.
  • amplification are carried out with linker left on the 3' end during a subsequent round of selection.
  • the population of aptamers thus obtained bind to the PGF2 ⁇ target regardless of the presence of linker at the 3' end. This population is a subset of all aptamers that bind to
  • Aptamer DNA is synthesized as described in Example 3-B except that the 5' terminal four bases have a known sequence to generate a pool of aptamers with the following sequence 5' PO 3 -AATTCN 55 3'.
  • a linker similar to linker 1 with the following structure is ligated to the 5' end of the aptamer,
  • linker 2 of Example 3-C is ligated to the 3' end of the aptamer pool after elution from target molecules.
  • restriction enzymes such as EcoRI
  • 5' linker because cutting occurs on short double stranded regions that carry the recognition site (such as the double stranded region that occurs when aptamer is removed from the avidin column by restriction enzyme cutting after removal of the 3' linker and complementary strand).
  • Other restriction sites such as that for Hind III, or Xba I which leave a four base 5' overhang may be created and used at the 5' end to leave 5 bases of known sequence. Creation of a site for enzymes that leave either 2 (Cla I) or 0 (Pvu II) base 5' overhangs, respectively, will generate aptamers with 4 or 3 bases of known sequence at the 5' end of the aptamer. Sites created and used in this manner at the 3' end require the use of enzymes that leave a 0 (Sma I), 2 (Pvu I) or 4 (Apa I) base 3' overhang after cutting to
  • aptamers with 3, 4 or 5 bases respectively at the 3' end with known sequence. If both ends of the aptamers have known sequences that constitute part of a restriction enzyme site, then the sites at the ends must differ from each other so that the linkers can be removed separately after amplification.
  • Eleven pools of aptamers of random sequence are synthesized which vary in length from 50 to 60 bases for each pool. Equal molar amounts of each pool is mixed and the variable length pool is then used to select for aptamers that bind to PGF2 ⁇ as described in Examples 3-B through 3-E or 3-1 above.
  • the human lung fibroblast-like cell line, CCD-18LU (American Type Culture Collection No. CCL205), is transfected with the human CD4 gene cloned into an
  • CD4 + A pool of aptamers consisting of 60 bases of random
  • the recovered aptamer in medium is added to 2 confluent plates of CD4 + cells previously washed twice in 5 ml per wash of medium lacking serum. The plates are left at 37°C for 30 min. After incubation, the plates are washed two times in medium and one time in saline using 5 ml per wash. The CD4 + cells are then treated with trypsin (1.5 ml trypsin 0.01% solution in 10 mM EDTA) for 30 minutes at 37°C. The medium containing cells is briefly spun to pellet out the cells. The aptamers are recovered by ethanol precipitation and amplified. The procedure is repeated 3 to 6 times to enrich for aptamers that specifically bind to the CD4 cell surface protein.
  • Radiolabeled aptamers are obtained by a standard kinase reaction using ⁇ - 32 P-ATP to label the 5' end of aptamer after
  • radiolabeled nucleoside triphosphates can be obtained by using PCR amplification to label the aptamer pool.
  • the binding assay (positive selection) uses 0.1 nmole of labeled aptamer
  • CD4 + cells for 30 min at 37°C, followed by two washes in medium and one saline wash. The retained radioactivity is determined by scintillation counting of cells lysed in
  • aptamers may be tested for their capacity to block the binding of HIV to T-cell lines such as SupTI or HUT-78
  • aptamer isolates or small pools consisting of 10 to 50 individual aptamer species that reduce HIV infectivity are used to identify optimal species for blocking HIV infectivity by interfering with the binding interaction between gpl20 and CD4.
  • HeLa cells stably transfected and expressing the gene for the HER2 oncogene referred to herein as the HER2 cell line are grown to confluency and washed two times with phosphate-buffered saline.
  • Single-stranded oligonucleotide is generated by the random incorporation of 60 nucleotides between two primer binding sites using standard solid-phase synthesis techniques essentially as described in "Oligonucleotide Synthesis- -a Practical Approach" (IRL Press 1984, ed. M.J. Gait).
  • oligonucleotides which have binding specificity for any cell surface proteins, and structure including the target HER2 glycoproteins, are then released from the cell by cleavage with trypsin (or other protease which is capable of cleaving, and thereby dissociating from cells, the protein target of interest) in buffered saline.
  • Aptamers and cell proteins released by protease cleavage are then digested for an additional 30 minutes at 37°C with protease to extensively degrade all cellular proteins. This process may be aided by a brief heat step (80°C for 3 minutes) followed by readdition of fresh protease such a pronase (Sigma Chemical Company, catalog no. P4914). Alternatively, a protease from the thermophilic bacterium (Sigma Chemical Company, catalog no.
  • P1512 may be used to aid recovery of aptamers from cell proteins.
  • the aptamers recovered from binding to HER2 cells are recovered by precipitation with ethanol using glycogen as a carrier.
  • the aptamers are then resuspended in medium (3 ml) and incubated with 5 ⁇ 10 6 HeLa cells for about 60 minutes.
  • Cellular supernatants are recovered, and the oligonucleotides precipitated from the serum-free culture medium after adding 200 to 800 ⁇ g glycogen (Boehringer Mannheim) followed by the addition of two volumes of ethanol.
  • the human HeLa cell line is transfected with two different genes to generate two lines that express the inserted gene.
  • the first gene is the human IL-1 receptor (Sims et al., Proc. Natl. Acad. Sci. (1989)
  • Transfected clones expressing each receptor are identified by immuno-precipitation using polyclonal antibodies against the IL-1R protein.
  • Aptamers that specifically bind to the IL-lRm molecule at the cell surface are obtained by selection using the IL-1Rm cell line. The procedure starts with a pool of aptamers containing 60 random bases flanked by 18 base primer sequences as described above. Two confluent plates containing about 8,000,000 IL-1R cells are
  • 0.1 nmole of aptamer pool is estimated to contain
  • molecule numbers is based on the estimated molecular weight of 33,600 for a 96-mer. Each base residue in the aptamer has an average molecular weight near 350 da.
  • the aptamer pool size may be reduced by as much as 10-fold if the initial DNA synthesis does not provide fully random sequences due to uncharacterized biases in the synthesis and purification steps.
  • the cells are washed three times in medium lacking serum prior to adding the aptamer pool.
  • the IL-1R cells are incubated for 30 minutes at 37°C followed by recovery of the medium containing aptamers from the cells.
  • the aptamers in solution are then added to washed IL-1Rm cells and incubated for 30 minutes at 37°C, followed by three washes in medium lacking serum followed by three washes in buffered saline.
  • the cells are then trypsinized for 30 minutes at 37°C and intact cells are pelleted by a brief spin. Aptamers are recovered from the supernatant after enzyme digestion or heating by precipitation and amplified by standard PCR methods. The process is repeated using 0.1 nmole of amplified aptamer pools at the start of each round of selection.
  • Enrichment for aptamers that specifically bind to the IL-1Rm protein is monitored by measuring the binding of selected aptamer pools to IL-1Rm cells by the following method.
  • Aptamers obtained after 6 rounds of selection and amplification are modified according to methods disclosed herein.
  • Biotin is covalently attached at the 5' end via linkage to N-ethyl-diethanolamine linked to the 5' nucleotide of each aptamer in the amplified pool.
  • aptamers labeled for chemiluminescent detection may be synthesized and used for in situ detection of bound aptamers (Bronstein et al., Clin. Chem. (1989) 15:1856; Bronstein et al., Anal. Biochem. (1989) 180:95).
  • Aptamers attached to target IL- 1Rm molecules on IL-1Rm cells are then assayed by
  • aptamers that specifically bind to the IL-1Rm target are detected by incubating a washed, confluent IL-1Rm tissue culture plate containing about 5
  • Aptamers that bind IL-1Rm efficiently but that do not bind to IL-1R are binding to structures in IL-1Rm that are present due to the mutation engineered into the parent IL-1R molecule.
  • This type of selection procedure can be adapted to naturally occurring mutations, such as translocations that are correlated with pathological conditions. Protein structures uniquely associated with a mutation may be used to generate aptamers that
  • Aptamers which bind to IL-1R can be obtained by following a protocol as described in Example 15 above except that HeLa is used as the control cell line and the target is the IL-1R molecule on the IL-1R cell line.
  • Nonradioactive methods can be used to detect bound aptamers.
  • aptamer recovered from the HeLa control cells is incubated with IL-1R cells in serum-free medium for 15 minutes at 37°C, then prewarmed calf serum is added to give a final concentration of 10% and incubate an additional
  • the serum contains enzymes that degrade aptamers that are not tightly bound to target molecules.
  • the serum will enhance selection for aptamers that are not nuclease sensitive due to their tight association with IL-1R.
  • the cells are washed twice in medium without serum and once in saline, and aptamers are recovered and amplified.
  • DNA oligonucleotides containing a randomized sequence region were synthesized using standard solid phase techniques and phosphoramidite chemistry
  • DNA 19-mers with the following sequences were used as primers for PCR amplification of oligonucleotide sequences recovered from selection columns.
  • the 5' primer sequence was 5' TCTCCGGATCCAAGCTTAT 3' and the 3' primer sequence was 5' biotin-O-TCTAGACTCGAGGAATTCG 3'.
  • biotin residue was linked to the 5' end of the 3' primer using commercially available biotin
  • biotin phosphoramidite is incorporated into the strand during solid phase DNA synthesis using standard synthesis conditions.
  • a pool of aptamer DNA 68 bases in length was synthesized as described in Example 5-A, and then PCR-amplified to construct the initial pool.
  • An aliquot of the enzymatically-synthesized DNA was further amplified in the presence of ⁇ - 32 P-dNTPs to generate labeled aptamer to permit quantitation from column fractions.
  • a Factor X column was prepared by washing 1 mL (58 nmole) agarose-bound concanavalin A ("Con-A") (Vector Laboratories, cat. no. AL-1003) with 20 mM Tris-acetate buffer (pH 7.4) containing 1 mM MgCl 2 , 1 mM CaCl 2 , 5 mM KCl and 140 mM NaCl (the "selection buffer”) (4 ⁇ 10 ml). 1 mi of settled support was then incubated overnight at 4°C in 10 mL selection buffer containing 368 ⁇ g (6.24 nmole) Factor X (Haematologic Technologies Inc, Cat No. HCXA-0060).
  • a column containing 1 mL of settled beads had a void volume of approximately 300 ⁇ L.
  • a control Con-A column was prepared by adding 1 mL of settled support to a column followed by 5 washes of 1 mL of selection buffer.
  • the DNA Prior to application of the aptamer DNA pool to Con-A columns, the DNA was heated in selection buffer at 95°C for 3 minutes and then cooled to room temperature for 10 minutes. The pool, consisting of 100 pmole DNA in 0.5 mL selection buffer, was then pre-run on the control Con-A column at room temperature to remove species that bound to the control support. Three additional 0.5 mL aliquots of selection buffer were added and column fractions 2, 3 and 4 (0.5 mL each) were pooled and then reapplied to the column twice. The DNA in 1.5 mL
  • the recovered DNA was then applied to a Con-A- Factor X column as a 0.5 mL aliquot followed by a 1.0 mL aliquot. Flow-through was retained and reapplied to the column twice. DNA added to the column on the final application was left on the column for 1 hour at room temperature. The column was then eluted with 0.5 mL aliquots of selection buffer. 0.5 mL fractions were collected and radioactivity was determined in each fraction. Radioactivity in eluted fractions 7 through 12 were low and relatively constant. After recovery of fraction 12, the column was washed with 0.5 mL aliquots of 0.1 M ⁇ -methyl-mannoside (Sigma Cat. no.
  • Aptamer DNA (Round 1 DNA) was recovered from the Factor X by phenol extraction (2 ⁇ 0.5 mL). The aqueous phase volume was reduced to about 250 ⁇ L by n- butanol extraction. Aptamer DNA was precipitated on dry ice using 3 volumes of ethanol and 20 ⁇ g of glycogen as a carrier. The DNA was pelleted, washed once in 70% ethanol and then dried.
  • reaction consisted of the following: 100 ⁇ L template 96-mer DNA (approximately 0.01 pmoles); 20 ⁇ L 10X buffer
  • reaction lasted 1 minute. Primer annealing occurred at 56°C for 1 minute, and elongation of primed DNA strands using the Taq polymerase ran at 72°C for 2 minutes, with 5-second extensions added at each additional cycle. The final elongation reaction to completely fill in all strands ran for 10 minutes at 72°C, and the reaction was then held at 4°C.
  • nitrocellulose filters (1 cm diameter) pre-soaked in selection buffer overnight at 4°C and DNA in 100 ⁇ L of selection buffer was incubated at room temperature for 10 minutes with: (1) An unselected 68-mer oligonucleotide DNA pool, (2) unselected DNA with Factor X (1 ⁇ M), (3) Round 11 aptamer DNA and Factor X (1 ⁇ M), and (4) Round 11 aptamer DNA alone. The filters were then washed 3 times with 3.0 mL of selection buffer at 37° and
  • DNA oligonucleotides containing a randomized sequence region were synthesized using standard solid phase techniques and phosphoramidite chemistry
  • DNA 18-mers with the following sequences were used as primers for PCR amplification of oligonucleotide
  • the 5' primer sequence was 5' HO-CGTACGGTCGACGCTAGC-OH 3' and the 3' primer sequence was 5' biotin-O- GGATCCGAGCTCCACGTG-OH 3'.
  • the biotin residue was linked to the 5' end of the 3' primer using commercially
  • biotin phosphoramidite New England Nuclear, Cat. No. NEF-707.
  • the biotin phosphoramidite is
  • DNA 19-mers with the following sequences can also be used as primers for PCR amplification of oligonucleotides recovered from selection columns.
  • the 3' primer sequence is 5' biotin-O-CTATAGGGCGAATTCAGGT-OH 3' and the 5' primer sequence is
  • a pool of aptamer DNA 96 bases in length was synthesized as described in Example 6-A, and then PCR- amplified to construct the initial pool. A small amount of the enzymatically-synthesized DNA was further
  • a thrombin column was prepared by washing 1 ml (58 nmole) agarose-bound concanavalin A ("Con-A") (Vector
  • a control Con-A column was prepared by adding 1 m. of settled support to a column followed by 5 washes of 1 ml of selection buffer.
  • the pool consisting of 100 pmole DNA in 0.5 ml selection buffer, was then pre-run on the control Con-A column at room temperature to remove species that bound to the control support. Three additional 0.5 ml aliquots of selection buffer were added and column fractions 2, 3 and 4 (0.5 ml each) were pooled and then reapplied to the column twice. The DNA in 1.5 ml selection buffer was then recovered. Approximately 1% of total input cpm were retained on the column.
  • the recovered DNA was then applied to a Con-A-thrombin column as a 0.5 mf aliquot followed by a 1.0 ml aliquot. Flow-through was retained and reapplied to the column twice. DNA added to the column on the final application was left on the column for 1 hour at room temperature. The column was then eluted with 0.5 ml aliquots of selection buffer. 0.5 ml fractions were collected and radioactivity was determined in each fraction. Radioactivity in eluted fractions 7 through 12 were low and relatively constant. After recovery of fraction 12, the column was washed with 0.5 ml aliquots of 0.1 M ⁇ -methyl-mannoside (Sigma Cat. no. M-6882) in selection buffer to elute the bound thrombin along with thrombin-bound aptamers. Fractions 14 and 15 showed a significant peak of thrombin enzyme activity, as
  • Aptamer DNA (Round 1 DNA) was recovered from the thrombin by phenol extraction (2 ⁇ 0.5 ml) . The aqueous phase volume was reduced to about 250 ⁇ l by n-butanol extraction. Aptamer DNA was precipitated on dry ice using 3 volumes of ethanol and 20 ⁇ g of glycogen as a carrier. The DNA was pelleted, washed once in 70% ethanol and then dried. C. Amplification of Selected Thrombin Aptamers
  • reaction consisted of the following: 100 ⁇ l template 96- mer DNA (approximately 0.01 pmoles); 20 ⁇ l 10X buffer
  • reaction lasted 1 minute. Primer annealing occurred at 60°C for 1 minute, and elongation of primed DNA strands using the Taq polymerase ran at 72°C for 2 minutes, with 5-second extensions added at each additional cycle. The final elongation reaction to completely fill in all strands ran for 10 minutes at 72°C, and the reaction was then held at 4°C.
  • the amplified aptamer pool (100 ⁇ L) was run over a Nick column (G-50 Sephadex, washed with 3 mL TE buffer (10 mM Tris ⁇ HCl (pH 7.6), 0.1 mM EDTA)) to remove unincorporated NTP's, primers, and salt. 400 ⁇ L of TE buffer was then added to the column and the DNA pool was eluted from the column with an additional 400 ⁇ L using TE buffer. (A sample may be removed from the eluent for quantitation and analytical PAGE.) The eluent (400 ⁇ L) was loaded on an avidin agarose column (Vector Laboratories, Cat. No. A-2010) (500 ⁇ L settled support, washed with 3 ⁇ 1 mL Tris/NaCl buffer (0.1 M Tris, 0.1 M NaCl, pH 7.5)).
  • 0.1 M ⁇ -methyl-mannoside in selection buffer was added as fraction 13 in each elution, and fractions 14 and 15 were retained and the DNA amplified. Due to slow leeching of thrombin from the column, DNA bound to thrombin could also be seen in earlier fractions in rounds 3-5.
  • round 5 aptamer DNA was analyzed for specificity in a filter binding assay.
  • nitrocellulose filters (1 cm diameter) prebound with salmon sperm DNA were used to bind either: (1) An unselected 96-mer oligonucleotide DNA pool, (2) unselected DNA with thrombin (60 pmole), (3) Round 5 aptamer DNA and thrombin (60 pmole), (4) Round 5 aptamer DNA alone, or (5) Round 5 aptamer DNA and ovalbumin (60 pmole).
  • 3.5 pmole of DNA was used and the incubation was in 200 ⁇ L selection buffer at room temperature for 1 hour.
  • the filters were then washed 3 times with 3.0 mf of selection buffer and radioactivity was counted to determine the amount of DNA that was retained as a thrombin complex. The results are shown in Table 6. Table 6
  • Unselected DNA did not show significant binding to the thrombin while selected aptamer DNA bound to thrombin.
  • Binding results show specific thrombin binding with no detectable ovalbumin binding.
  • nitrocellulose filters (0.2 micron, 2.4 cm diameter) that were pretreated with salmon sperm DNA (1 mg/ml DNA in selection buffer) and washed twice with 1 ml selection buffer. After application of thrombin mixture, the filters were washed three times with 1 ml selection buffer The radioactivity retained on the filters was then determined. K D values for the individual clones ranged from 50 to >2000 nM.
  • the DNA sequence of the 60-nucleotide randomly- generated region from 32 clones was determined in order to examine both the heterogeneity of the selected
  • 28 clones contain the consensus sequence 5' GGNTGG(N) z GGNTGG 3' where z is an integer from 2 to 5.
  • the remaining 4 clones contain a "close variant sequence" (a sequence differing by only a single base).
  • this consensus sequence contains a sequence which is responsible either wholly or in part, for conferring thrombin affinity to the aptamers.
  • Clotting time for the thrombin-catalyzed conversion of fibrinogen (2.0 mg/mL in selection buffer) to fibrin at 37°C was measured using a precision
  • coagulation timer apparatus Becton-Dickinson, Cat. nos. 64015, 64019, 64020.
  • thrombin incubated with fibrinogen and P1 nuclease Boehringer-Mannheim, Indianapolis, IN
  • thrombin incubated with fibrinogen and aptamer clone #5 200 nM
  • thrombin clotting time in this experiment was 24 sec using thrombin alone (10 nM), 26 sec with thrombin and the control sequence at 20 ⁇ M and 38 sec with thrombin plus the consensus sequence at 20 ⁇ M, indicating
  • the inhibitory aptamers were active at physiological temperature under physiologic ion
  • aptamers for the most part contain the identical nucleotide sequences, bases, sugars and phosphodiester linkages as conventional nucleic acids, but substitute one or more modified linking groups (thioate or MEA), or modified bases
  • uracil or 5-(1-pentynyl-2'-deoxy)uracil The aptamers containing 5-(1-pentynyl)-2'-deoxyuridine were generated by replacing thymidine in the parent aptamers. Thrombin aptamers containing 5-(1-pentynyl)-2'-deoxyuridine were also obtained by selection as described in Examples 13 and 14 below.
  • GGTTGGTGTGGTU'GG 20 * indicates a thioate (i.e., P(O)S) linkage # indicates a MEA linkage
  • the pentynyl compound was obtained by reacting 5-iodo-2'-deoxyuridine with 1-pentyne in the presence of palladium catalyst. 5-(1-pentynyl)-2'-deoxyuridine triphosphate was then used as a replacement for thymidine triphosphate in the standard PCR reaction.
  • N 4 -position of cytidine and deoxycytidine are synthesized using methods described above. Each compound is
  • This procedure may also be performed with
  • deoxyadenine and the 7-position alkylated analogs of deazaguanine, deazadeoxyguanine, deazaadenine and
  • phosphodiester linkage (O-PO(O-)-O) were synthesized and assayed for thrombin inhibition as described above.
  • the H-phosphonate dimer synthon was synthesized as described in Matteucci, M.D., Tet. Lett. (1990) 31:2385-2387.
  • the formacetal dimer, 5' T-O-CH 2 -O-T 3', was then used in solid phase synthesis of aptamer DNA. Control unmodified aptamer DNA was used as a positive control.
  • H-phosphonate were prepared as described in DeClercq, E., et al, J. Med. Chem. (1983) 26:661-666; Froehler, B.C., et al, Nucleosides and Nucleotides (1987) 6:287-291; and Froehler, B.C., et al, Tet. Lett. (1986) 27:469. This analog residue was substituted at the indicated positions and the aptamer assayed for inhibition of thrombin. The results that were obtained are shown in Table 10.
  • 5-(1-pentynyl)-2'-deoxyuridine was synthesized and converted to the triphosphate as described in Otvos, L., et al., Nucleic Acids Res (1987) 1763-1777.
  • the pentynyl compound was obtained by reacting 5-iodo-2'-deoxyuridine with 1-pentyne in the presence of a
  • 5-(1-pentynyl)-2'-deoxyuridine triphosphate was then used as a replacement for thymidine triphosphate in the standard PCR reaction.
  • a pool of 60-mer single-stranded DNA was synthesized, each strand consisting of specific 18-mer PCR primer sequences at both the 5' and 3' ends and a random 20-mer sequence in the center of the oligomer. Details of synthesis of the pool of single-stranded DNA is disclosed in Example 1.
  • VENTTM thermostable polymerase (New England Biolabs, Cat. No. 254) was employed. Amplification was performed as per the manufacturers instructions. Pentynyl dUTP was included in the reaction as a substitute for dTTP. The single-stranded 60-mer was isolated by a modification of standard procedures. The 200 ⁇ L PCR amplification reaction was divided into two samples which were applied to two NICKTM columns equilibrated (5 mL) as described. The eluent was collected, pooled and applied to avidin- agarose as described.
  • the pool of aptamer DNA 60 bases in length was used essentially as described in Example 13.
  • the aptamer pool sequence was 5' TAGAATACTCAAGCTTCGACG-N 20 -AGTTTGGATCCCCGGGTAC 3', while the 5' primer sequence was
  • Thrombin immobilized on a Con-A lectin column served as the target as described.
  • aptamer DNA was recovered and amplified using thymidine triphosphate (dTTP) in place of 5-(1-pentynyl)-2'-deoxyuridine in order to facilitate subsequent cloning and replication of aptamer DNA in E . coli.
  • dTTP thymidine triphosphate
  • the presence of a thymidine nucleotide at a given location in an aptamer corresponded to the location of a 5-(1-pentynyl)-2'-deoxyuridine nucleotide in each original round five aptamer.
  • dTTP served to mark the location of 5- (1-pentynyl)-2'-deoxyuridine residues in the original selected DNA pools.
  • the round five amplified DNA containing dTTP was digested with BamHI and HindIII and cloned into the corresponding sites of pGEM 3Z (Promega Biotech) and transformed into E. coli. DNA from 21 clones was
  • One of these two clones (#17) and the original unselected pool was analyzed for thrombin binding by nitrocellulose filter assay described above using DNA labeled with 32 P to permit analysis of thrombin binding characteristics.
  • the labeled DNA was synthesized by PCR and contained 5-(1-pentynyl)-2'-deoxyuridine in order to retain the original selected DNA structures.
  • the DNA was incubated with thrombin at various concentrations between 10 nM and 10 ⁇ M to obtain the K D values for thrombin binding.
  • the K D of the unselected pool was >10 ⁇ M while the K D of clone 17 was 300 nM.
  • Radiolabeled clone 17 DNA was synthesized using thymidine in place of 5-(1-pentynyl)-2'-deoxyuridine and the resulting DNA had a K D of >10 ⁇ M, demonstrating that the 5-(1-pentynyl)-2'-deoxyuracil heterocycle could not be replaced by thymine in the selected aptamer without loss of binding affinity.
  • 5-methyl-2'-deoxycytidine triphosphate was obtained commercially (Pharmacia, Cat. No. 27-4225-01) and used to synthesize DNA containing random sequences 60 bases in length flanked by primers 19 bases in length.
  • the pool of aptamer DNA 98 bases in length was used essentially as described in Example 6.

Abstract

Procédé d'identification de séquences d'oligomères se liant spécifiquement à des molécules cibles telles que des protéines de sérum, des kinines, des eicosanoïdes, ainsi que des protéines extracellulaires. On utilise le procédé afin de générer des aptamères se liant au facteur X du sérum, à la thrombine, à la bradykinine, au PGF2alpha ainsi qu'à des molécules de surface cellulaires. La technique consiste à transformer en complexe la molécule cible avec un mélange d'oligonucléotides contenant des séquences aléatoires et des séquences servant d'amorce à l'amplification enzymatique du génome dans des conditions dans lesquelles un complexe est formé avec les séquences de liaison spécifique, mais pas avec les autres membres du mélange d'oligonucléotides. Le complexe est ensuite séparé des oligonucléotides non complexés, et les membres complexés du mélange d'oligonucléotides sont récupérés du complexe séparé par amplification enzymatique du génome. Les oligonucléotides récupérés peuvent être séquencés, et l'on peut procéder à des sélections successives par transformation en complexe, séparation, amplification et récupération. On peut utiliser les oligonucléotides à des fins thérapeutiques et diagnostiques.
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CA2104698A1 (fr) 1992-08-22
AU1435492A (en) 1992-09-15

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