HK1119179B

HK1119179B - Methods for the selection of aptamers

Info

Publication number: HK1119179B
Application number: HK08111122.0A
Authority: HK
Inventors: Tomasz Heyduk; Ewa Heyduk
Original assignee: Saint Louis University
Priority date: 2005-06-10
Filing date: 2006-05-16
Publication date: 2012-11-23

Description

FIELD OF THE INVENTION

The present invention relates to methods for selecting aptamers. More specifically, the invention provides methods for the selection of aptamers for use in combination with another epitope binding agent such as another aptamer, an antibody, or a double stranded nucleic acid. The invention also encompasses methods for simultaneously selecting at least two aptamers that each recognize distinct epitopes on a target molecule.

BACKGROUND OF THE INVENTION

The ability to detect, label, and track a molecular target is a powerful research tool. To date, antibodies are the typical reagents used for such research. Antibodies have high specificity for their target, and often can be used for in vivo as well as in vitro applications. Producing antibodies, however, is a sensitive, expensive, and time-consuming endeavor. Polyclonal antibodies, although highly specific, are limited in supply. Monoclonal antibodies, while extremely useful for molecular biology techniques, require labor intensive, diligent cell culture work. Furthermore, if a specific antibody will be used for in vivo human studies, the antibody may require modification to avoid triggering an unwanted immune response. Despite these drawbacks, antibodies have remained the state of the art in many biological research fields.

Aptamers, or target specific nucleic acid sequences, offer an alternative to antibodies. The advent of in vitro selection of aptamers was key to demonstrating their utility. Aptamers can be selected to recognize virtually any target, and they can be synthetically engineered, greatly reducing cost and time when compared to producing antibodies. The most common method for selecting aptamers is referred to as Selex (Systematic Evolution of Ligands by Experimental Enrichment). In general, the Selex process selects target specific aptamers from a pool of randomly generated nucleic acid oligonucleotides through several rounds of selection and amplification. Despite the fact that aptamers are less expensive to make, do not require animal facilities to produce, and can be selected with simple molecular biology techniques, they remain in the background of biological research. A need exists for better aptamer selection methods, which will further increase the advantage of aptamers relative to antibodies. Moreover, although the Selex method has advanced the field of aptamer selection with respect to the selection of one aptamer, a need exists for methods involving the simultaneous selection of two or more aptamers that recognize distinct epitopes on a target molecule.

SUMMARY OF THE INVENTION

Among the several aspects of the invention, therefore, is a method for simultaneously selecting at least two aptamers comprising a first aptamer sequence and a second aptamer sequence, wherein the first aptamer sequence binds to a first epitope on a target molecule and the second aptamer sequence binds to a second epitope on the target molecule; the method comprising:

(a) contacting a plurality of pairs of nucleic acid constructs comprising a first nucleic acid construct and a second nucleic acid construct with the target molecule to form a mixture of nucleic acid constructs and target molecules, the first nucleic acid construct comprising:
1. i. A-B-C-D; the second nucleic acid construct comprising:
2. ii. E-F-G-H;
wherein:
- A, C, E, and G are each different DNA sequences from about 10 to about 30 nucleotides in length, A and C together comprising a sequence to prime a polymerase chain reaction for amplifying a first aptamer sequence, and E and G together comprising a sequence to prime a polymerase chain reaction for amplifying a second aptamer sequence;
- B is a single-stranded random nucleotide sequence from about 20 to about 110 nucleotides in length that contains specific sequences binding to a first epitope of the target molecule;
- D and H are a pair of complementary nucleotide sequences from about 2 to about 20 nucleotides in length, wherein D and H have a free energy for association from about 5.5 kcal/mole to about 8.0 kcal/mole at a temperature from approximately 21 ° C to about 40° C and at a salt concentration of approximately 1 mM to about 100 mM; and
- F is a single-stranded random nucleotide sequence from about 20 to about 110 nucleotides in length that contains specific sequences binding to a second epitope of the target molecule;
(b) isolating from the mixture a complex comprising the target molecule having the first nucleic acid construct bound to a first epitope and the second nucleic acid construct bound to the second epitope; and
(c) purifying the first nucleic acid construct and the second nucleic acid construct from the complex.

Another aspect of the invention provides a method to select at least one aptamer in the presence of an epitope binding agent construct. Alternatively, the invention encompasses a method for simultaneously selecting at least two aptamers.

Other aspects and features of the invention will be in part apparent and in part pointed out hereinafter.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 depicts a series of schematics illustrating molecular biosensors for detecting target molecules. (A) Variant of the design for target molecules lacking natural DNA binding activity. The biosensor in this case will be composed of two aptamers developed to recognize two different epitopes of the target molecule. (B) Variant of the design for a target molecule exhibiting natural DNA binding activity. The biosensor in this case will be composed of a short double-stranded DNA fragment containing the DNA sequence corresponding to the DNA-binding site and an aptamer developed to recognize a different epitope of the target molecule.

FIG. 2 depicts a series of schematics illustrating methods for preparing aptamers according to the invention. (A) Selection of an aptamer in the presence of a known aptamer construct. The process is initiated with a nucleic acid construct, an aptamer construct (composed of an known aptamer (thick black line), a linker, and a short oligonucleotide sequence (hatched bar)), and the target molecule (grey). The hatched bars depict complementary short oligonucleotide sequences. (B) Simultaneous selection of two aptamers that bind distinct epitopes of the same target molecule (grey). The process is initiated with two types of nucleic acid constructs (the primer1-2 construct and the primer3-4 construct) and the target molecule. The hatched bars depict short complementary sequences at the end of the two types of nucleic acid constructs. (C) Alternative design for simultaneous selection of two aptamers that bind distinct epitopes of the same target molecule (grey). An additional pair of short oligonucleotides (hatched bars) connected by a flexible linker is present during the selection process. These oligonucleotides will be complementary to short oligonucleotide sequences at the end of the nucleic acid constructs (in primer 1 and primer 4). Their presence during selection will provide a bias towards selecting pairs of aptamers capable of simultaneously binding to the target molecule. Before cloning of the selected nucleic acid constructs the pairs of selected sequences will be ligated to preserve the information regarding the preferred pairs between various selected constructs. (D) Selection of an aptamer in the presence of a known antibody construct. The process is initiated with a nucleic acid construct, an antibody construct (composed of a known antibody (thick black line), a linker, and a short oligonucleotide sequence (hatched)), and the target molecule (grey). The hatched bars depict complementary short oligonucleotide sequences. (E) Selection of an aptamer in the presence of a known double-stranded DNA construct. The process is initiated with a nucleic acid construct, a double-stranded DNA construct (composed of an known double-stranded DNA sequence, a linker, and a short oligonucleotide sequence (hatched)), and the target molecule (grey). The hatched bars depict complementary short oligonucleotide sequences.

FIG. 3 is a schematic illustrating various formations of molecular biosensors that can be made utilizing aptamers selected according to the invention.

FIG. 4 is a schematic illustrating the method of the invention.

FIG. 5 summarizes the selection of an aptamer that binds to thrombin at an epitope distinct from the binding site of the G15D aptamer. (A) An illustration of the reagents used to begin the process of selection. (B) The graph indicates the increase in thrombin binding with successive rounds of selection. (C) The sequences represent aptamers developed after 12 rounds of selection.

FIG. 6 The demonstration of the functional thrombin sensor comprising Texas Red-labeled THR27 and fluorescein-labeled THR35 or THR36 (both contain the sequence corresponding to that of clones 20, 21, 24, and 26 of Figure 5C). The fluorescence image represents the specificity of either 20nM (panel A) or 100nM (panel B) of the indicated biosensor.

FIG. 7 summarizes the simultaneous selection of two aptamers that bind to thrombin at distinct epitopes. (A) An illustration of the reagents used to begin the process of selection. (B) The graph indicates the increase in thrombin binding with successive rounds of selection. (C) The sequences represent aptamers developed after 13 rounds of selection.

FIG. 8 summarizes the selection of an aptamer that binds to CRP at an epitope distinct from the DNA-binding site. (A) An illustration of the reagents used to begin the process of selection. (B) The graph indicates the increase in thrombin binding with successive rounds of selection. (C) The sequences represent aptamers developed after 11 rounds of selection.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Methods for efficiently selecting aptamers have been discovered. The invention is directed to methods for simultaneously selecting two or more aptamers that each recognize distinct epitopes on a target molecule. Utilizing the method of simultaneous aptamer selection typically cuts the time of selection in half compared to methods involving sequential selection of two aptamers using Selex. Alternatively, the invention is directed to selecting at least one aptamer in the presence of an epitope binding agent construct. The aptamer and epitope binding agent construct also each recognize distinct epitopes on a target molecule. In each method of the invention, novel nucleic acid constructs are utilized to facilitate selection of aptamers having the desired epitope binding characteristics. In each aspect of the invention, the nucleic constructs comprise the aptamer or aptamers selected by the method of the invention. Advantageously, the methods of the invention may be utilized to select aptamers to construct various molecular biosensors as illustrated in FIG. 3 .

(A) Method for Selection of an Aptamer in the Presence of an Epitope Binding Agent Construct

One aspect of the invention encompasses a method for selecting an aptamer in the presence of an epitope binding agent construct. The aptamer and epitope binding agent construct are selected so that they each bind to the same target at two distinct epitopes. Typically, the method comprises contacting a plurality of nucleic acid constructs and epitope binding agent constructs with a target molecule to form a mixture. The mixture will generally comprise complexes having target molecule bound with nucleic acid constructs and epitope binding agent constructs. According to the method, the complex is isolated from the mixture and the nucleic acid construct is purified from the complex. The aptamer selected by the method of the invention will comprise the purified nucleic acid construct.

In this method of selection, a plurality of nucleic acid constructs is utilized in the presence of the epitope binding agent construct to facilitate aptamer selection. The nucleic acid constructs comprise: A-B-C-D

The epitope binding agent construct comprises: P-Q-R wherein:

A and C are each different DNA sequences from about 10 to about 30 nucleotides in length, A and C together comprising a sequence to prime a polymerase chain reaction for amplifying the aptamer sequence;
B is a single-stranded random nucleotide sequence from about 20 to about 110 nucleotides in length that contains specific sequences binding to a first epitope of the target molecule;
D and R are a pair of complementary nucleotide sequences from about 2 to about 20 nucleotides in length, wherein D and R have a free energy for association from about 5.5 kcal/mole to about 8.0 kcal/mole at a temperature from approximately 21° C to about 40° C and at a salt concentration of approximately I mM to about 100 mM;
P is an epitope binding agent that binds to a second epitope on the target molecule. The epitope binding agent will vary depending upon the embodiment, but is selected from the group comprising an aptamer, an antibody, an antibody fragment, a double-stranded DNA sequence, a ligand, a ligand fragment, a receptor, a receptor fragment, a polypeptide, a peptide, a coenzyme, a coregulator, an allosteric molecule, and an ion; and
Q is a flexible linker.

Generally speaking, A and C are each different DNA sequences ranging from about 7 to about 35 nucleotides in length and function as polymerase chain reaction primers to amplify the nucleic acid construct. In another embodiment, A and C range from about 15 to about 25 nucleotides in length. In yet another embodiment, A and C range from about 15 to about 20 nucleotides in length. In still another embodiment, A and C range from about 16 to about 18 nucleotides in length. In an exemplary embodiment, A and C are 18 nucleotides in length. Typically, A and C have an average GC content from about 53% to 63%. In another embodiment, A and C have an average GC content from about 55% to about 60%. In a preferred embodiment, A and C will have an average GC content of about 60%.

B is typically a single-stranded oligonucleotide synthesized by randomly selecting and inserting a nucleotide base (A, C, T, G in the case of DNA, or A, C, U, G in the case of RNA) at every position of the oligonucleotide. In one embodiment, B encodes an aptamer sequence that binds to the first epitope on the target. In another embodiment B is comprised of DNA bases. In yet another embodiment, B is comprised of RNA bases. In another embodiment, B is comprised of modified nucleic acid bases, such as modified DNA bases or modified RNA bases. Modifications may occur at, but are not restricted to, the sugar 2' position, the C-5 position of pyrimidines, and the 8-position of purines. Examples of suitable modified DNA or RNA bases include 2'-fluoro nucleotides, 2'-amino nucleotides, 5'-aminoallyl-2'-fluoro nucleotides and phosphorothioate nucleotides (monothiophosphate and dithiophosphate). In a further embodiment, B is about 20 to 110 nucleotides in length. In another embodiment, B is from about 25 to about 75 nucleotides in length. In yet another embodiment, B is from about 30 to about 60 nucleotides in length.

In one embodiment, D and R are complementary nucleotide sequences from about 2 to about 20 nucleotides in length. In another embodiment, D and R are from about 4 to about 15 nucleotides in length. In a preferred embodiment, D and R are from about 5 to about 7 nucleotides in length. In one embodiment, D and R have a free energy for association from about 5.2 kcal/mole to about 8.2 kcal/mole as measured in the selection buffer conditions, defined below. In another embodiment, D and R have a free energy for association from about 6.0 kcal/mole to about 8.0 kcal/mole as measured in the selection buffer conditions defined below. In yet another embodiment, D and R have a free energy for association from about 7.0 kcal/mole to 8.0 kcal/mole in the selection buffer conditions. In a preferred embodiment, D and R have a free energy for association of 7.5 kcal/mole in the selection buffer conditions described below.

Q may be a nucleotide sequence from about 10 to about 100 nucleotides in length. In one embodiment, Q is from 10 to about 25 nucleotides in length. In another embodiment, Q is from about 25 to about 50 nucleotides in length. In a further embodiment, Q is from about 50 to about 75 nucleotides in length. In yet another embodiment, Q is from about 75 to about 100 nucleotides in length. In each embodiment, the nucleotides may be any of the nucleotide bases in DNA or RNA (A, C, T, G in the case of DNA, or A, C, U, G in the case of RNA). In one embodiment Q is comprised of DNA bases. In another embodiment, Q is comprised of RNA bases. In yet another embodiment, Q is comprised of modified nucleic acid bases, such as modified DNA bases or modified RNA bases. Modifications may occur at, but are not restricted to, the sugar 2' position, the C-5 position of pyrimidines, and the 8-position of purines. Examples of suitable modified DNA or RNA bases include 2'-fluoro nucleotides, 2'-amino nucleotides, 5'-aminoallyl-2'-fluoro nucleotides and phosphorothioate nucleotides (monothiophosphate and dithiophosphate). In a further embodiment, B may comprise nucleotide mimics. Examples of nucleotide mimics include locked nucleic acids (LNA), peptide nucleic acids (PNA), and phosphorodiamidate morpholino oligomers (PMO). Alternatively, Q may be a polymer of bifunctional chemical linkers. In one embodiment the bifunctional chemical linker is heterobifunctional. Suitable heterobifunctional chemical linkers include sulfoSMCC (Sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate), and Ic-SPDP( N-Succinimidyl-6-(3'-(2-PyridylDithio)-Propionamido)-hexanoate). In another embodiment the bifunctional chemical linker is homobifunctional. Suitable homobifunctional linkers include disuccinimidyl suberate, disuccinimidyl glutarate, and disuccinimidyl tartrate. Additional suitable linkers are illustrated in the Examples, such as the phosphoramidate form of Spacer 18 comprised of polyethylene glycol. In one embodiment, Q is from 0 to about 500 angstroms in length. In another embodiment, Q is from about 20 to about 400 angstroms in length. In yet another embodiment, Q is from about 50 to about 250 angstroms in length.

In a preferred embodiment, A and C are approximately 18 nucleotides in length and have an average GC content of about 60%; B is about 30 to about 60 nucleotides in length; Q is a linker comprising a nucleotide sequence that is from about 10 to 100 nucleotides in length or a bifunctional chemical linker; and D and R range from about 5 to about 7 nucleotides in length and have a free energy of association of about 7.5 kcal/mole.

As will be appreciated by those of skill in the art, the choice of epitope binding agent, P, can and will vary depending upon the particular target molecule. By way of example, when the target molecule is a protein P may be an aptamer, peptide, or antibody. By way of further example, when P is double stranded nucleic acid the target molecule is typically a macromolecule that binds to DNA or a DNA binding protein. Suitable epitope binding agents, depending upon the target molecule, include agents selected from the group consisting of an aptamer, an antibody, an antibody fragment, a double-stranded DNA sequence, a ligand, a ligand fragment, a receptor, a receptor fragment, a polypeptide, a peptide, a coenzyme, a coregulator, an allosteric molecule, and an ion. In an exemplary embodiment, P is an aptamer sequence ranging in length from about 20 to about 110 bases. In another embodiment, P is an antibody selected from the group consisting of polyclonal antibodies, ascites, Fab fragments, Fab' fragments, monoclonal antibodies, and humanized antibodies. In a preferred embodiment, P is a monoclonal antibody. In an additional embodiment, P is a double stranded DNA.

Typically in the method, a plurality of nucleic acid constructs, A-B-C-D, are contacted with the epitope bind agent construct, P-Q-R, and the target molecule in the presence of a selection buffer to form a mixture. Several selection buffers are suitable for use in the invention. A suitable selection buffer is typically one that facilitates non-covalent binding of the nucleic acid construct to the target molecule in the presence of the epitope binding agent construct. In one embodiment, the selection buffer is a salt buffer with salt concentrations from about 1mM to 100mM. In another embodiment, the selection buffer is comprised of Tris-HCl, NaCl, KCl, and MgCl₂. In a preferred embodiment, the selection buffer is comprised of 50mM Tris-HCl, 100mM NaCl, 5mM KCl, and 1mM MgCl₂. In one embodiment, the selection buffer has a pH range from about 6.5 to about 8.5. In another embodiment, the selection buffer has a pH range from about 7.0 to 8.0. In a preferred embodiment, the pH is 7.5. Alternatively, the selection buffer may additionally contain analytes that assist binding of the constructs to the target molecule. Suitable examples of such analytes can include, but are not limited to, protein co-factors, DNA-binding proteins, scaffolding proteins, or divalent ions.

The mixture of the plurality of nucleic acid constructs, epitope binding agent constructs and target molecules are incubated in selection buffer from about 10 to about 45 min. In yet another embodiment, the incubation is performed for about 15 to about 30 min. Typically, the incubation is performed at a temperature range from about 21° C to about 40° C. In another embodiment, the incubation is performed at a temperature range from about 20°C to about 30°C. In yet another embodiment, the incubation is performed at 35°C. In a preferred embodiment, the incubation is performed at 25°C for about 15 to about 30 min. Generally speaking after incubation, the mixture will typically comprise complexes of the target molecule having nucleic acid construct bound to a first epitope and epitope binding agent construct bound to a second epitope of the target molecule. The mixture will also comprise unbound nucleic acid constructs and epitope binding agent constructs.

The complex comprising the target molecule having bound nucleic acid construct and bound epitope binding agent construct is preferably isolated from the mixture. In one embodiment, nitrocellulose filters are used to separate the complex from the mixture. In an alternative embodiment magnetic beads are used to separate the complex from the mixture. In yet another embodiment sepharose beads can be used to separate the complex from the mixture. In an exemplary embodiment, strepavidin-linked magnetic beads are used to separate the complex from the mixture.

Optionally, the target molecules are subjected to denaturation and then the nucleic acid constructs purified from the complex. In one embodiment, urea is used to denature the target molecule. In a preferred embodiment, 7M urea in 1M NaCl is used to denature the target molecule. The nucleic acid constructs may be purified from the target molecule by precipitation. In another embodiment, the nucleic acid constructs are precipitated with ethanol. In yet another embodiment, the nucleic acid constructs are precipitated with isopropanol. In one embodiment, the precipitated DNA is resuspended in water. Alternatively, the precipitated DNA is resuspended in TE buffer.

Generally speaking, the purified, resuspended nucleic acid constructs are then amplified using the polymerase chain reaction (PCR). If the nucleic acid construct contains a B comprised of RNA bases, reverse transcriptase is preferably used to convert the RNA bases to DNA bases before initiation of the PCR. The PCR is performed with primers that recognize both the 3' and the 5' end of the nucleic acid constructs in accordance with methods generally known in the art. In one embodiment, either the 3' or 5' primer is attached to a fluorescent probe. In an alternative embodiment, either the 3' or the 5' primer is attached to fluorescein. In another embodiment, either the 3' or 5' primer is biotinylated. In a preferred embodiment, one primer is labeled with fluorescein, and the other primer is biotinylated.

In addition to primers, the PCR reaction contains buffer, deoxynucleotide triphosphates, polymerase, and template nucleic acid. In one embodiment, the PCR can be performed with a heat-stable polymerase. In a preferred embodiment, the concentrations of PCR reactants are outlined in the examples section as follows: 80uL ofdd H2O, 10uL of 10x PCR buffer, 6uL of MgCl₂, 0.8uL 25mM dNTPs, 1uL 50uM primer 1 (modified with fluorescein), 1uL 50uM primer 2 (biotinylated), 0.5uL Taq polymerase, and 1uL of template.

In another embodiment, the PCR consists of a warm-up period, where the temperature is held in a range between about 70°C and about 74°C. Subsequently, the PCR consists of several cycles (about 8 to about 25) of 1) incubating the reaction at a temperature between about 92°C and about 97°C for about 20sec to about 1min; 2) incubating the reaction at a temperature between about 48°C and about 56°C for about 20sec to about 1min; and 3) incubating the reaction at a temperature between about 70°C and about 74°C for about 45sec to about 2min. After the final cycle, the PCR is concluded with an incubation between about 70°C and about 74°C for about 3min to about 10min. In an alternative embodiment, the reaction consists of 12-18 cycles. A preferred embodiment of the PCR, as outlined in the examples section, is as follows: 5 min at 95°C, sixteen cycles of 30s at 95°C, 30s at 50°C, and 1min at 72°C, and then an extension period of 5min at 72°C.

Typically after PCR amplification, the double-stranded DNA PCR product is separated from the remaining PCR reactants. One exemplary embodiment for such separation is subjecting the PCR product to agarose gel electrophoresis. In another embodiment, the PCR product is separated in a low melting point agarose gel. In a preferred embodiment, the gel is a native 10% acrylamide gel made in TBE buffer. In one embodiment, the band(s) having the double-stranded DNA PCR product are visualized in the gel by ethidium bromide staining. In another embodiment, the band(s) are visualized by fluorescein fluorescence. Irrespective of the embodiment, the bands are typically excised from the gel by methods generally known in the art.

Generally speaking, the double-stranded gel-purified PCR product is separated into single-stranded DNA in accordance with methods generally known in the art. One such embodiment involves using a basic pH to denature the double helix. In another embodiment, 0.15N NaOH is used to denature the helix. In still another embodiment, streptavidin linked beads are used to separate the denatured DNA strands. In a preferred embodiment, magnetic streptavidin beads are used to separate the denatured DNA strands.

The method of the invention typically involves several rounds of selections, separation, amplification and purification in accordance with the procedures described above until nucleic acid constructs having the desired binding affinity for the target molecule are selected. In accordance with the method, the single-stranded DNA of estimated concentration is used for the next round of selection. In one embodiment, the cycle of selection, separation, amplification, purification, and strand separation is performed from about 4 to about 20 times. In another embodiment, the said cycle is performed from about 12 to about 18 times. In yet another embodiment, the said cycle is performed until the measured binding-activity of the selected nucleic acid constructs reaches the desired strength.

Alternatively, the single DNA strand attached to the strepavidin-linked beads is used as a template for RNA polymerase. In this embodiment, after the RNA polymerase is finished, the supernatant contains the RNA nucleic acid construct that can be used in another round of RNA aptamer selection.

In an alternative method, if a RNA aptamer is being selected, the double-stranded, gel-purified PCR DNA product is transcribed with RNA polymerase to produce a single-stranded RNA construct. In such a case, A will typically contain a sequence encoding a promoter recognized by RNA polymerase. In one embodiment, double-stranded, gel-purified PCR DNA product attached to strepavidin-linked beads is used as a template for RNA polymerase. In this embodiment, after the RNA polymerase reaction, the supernatant containing the RNA nucleic acid construct can be used in another round of RNA aptamer selection.

Generally speaking, after the nucleic acid constructs have reached the desired binding specificity, the nucleic acid constructs are cloned, and the cloned DNA is sequenced. In one embodiment, the sequences are used in aptamer constructs either alone or as part of a molecular biosensor.

(B) Method for Simultaneous Selection of Two or More Aptamers

Another aspect of the invention is a method for simultaneously selecting two or more aptamers. The aptamers selected by the method each bind to the same target molecule at two distinct epitopes. Typically, the method comprises contacting a plurality of pairs of nucleic acid constructs with a target molecule to form a mixture. The mixture will generally comprise complexes having target molecule bound with a pair of nucleic acid constructs at distinct epitope sites. According to the method, the complex is isolated from the mixture and the nucleic acid constructs are purified from the complex. The aptamers selected by the method of the invention will comprise the pair of purified nucleic acid constructs.

In the method of the invention, the first nucleic acid constructs comprises: A-B-C-D

The second nucleic acid construct comprises: E-F-G-H. wherein:

A, C, E, and G are each different DNA sequences from about 10 to about 30 nucleotides in length, A and C together comprising a sequence to prime a polymerase chain reaction for amplifying a first aptamer sequence, and E and G together comprising a sequence to prime a polymerase chain reaction for amplifying a second aptamer sequence;
B is a single-stranded random nucleotide sequence from about 20 to about 110 nucleotides in length that contains specific sequences binding to a first epitope of the target molecule;
D and H are a pair of complementary nucleotide sequences from about 2 to about 20 nucleotides in length, wherein D and H have a free energy for association from about 5.5 kcal/mole to about 8.0 kcal/mole at a temperature from approximately 21 °C to about 40°C and at a salt concentration of approximately 1 mM to about 100 mM; and
F is a single-stranded random nucleotide sequence from about 20 to about 110 nucleotides in length that contains specific sequences binding to the second epitope of the target molecule.

In another embodiment, A, C, E and G are each different DNA sequences ranging from about 7 to about 35 nucleotides in length. In another embodiment, A, C, E, and G range from about 15 to about 25 nucleotides in length. In yet another embodiment, A, C, E, and G range from about 15 to about 20 nucleotides in length. In still another embodiment, A, C, E and G range from about 16 to about 18 nucleotides in length. In an exemplary embodiment, A, C, E and G are 18 nucleotides in length. Generally speaking, A, C, E and G have an average GC content from about 53% to 63%. In another embodiment, A, C, E and G have an average GC content from about 55% to about 60%. In a preferred embodiment, A, C, E and G will have an average GC content of about 60%.

In one embodiment, B and F are single-stranded oligonucleotides synthesized by randomly selecting and inserting a nucleotide base (A, C, T, G in the case of DNA, or A, C, U, G in the case of RNA) at every position of the oligonucleotide. In a preferred embodiment, B and F encode an aptamer sequence, such that B binds to the first epitope on the target molecule and F binds to the second epitope on the target molecule. In one embodiment B and F are comprised of DNA bases. In another embodiment, B and F are comprised of RNA bases. In yet another embodiment, B and F are comprised of modified nucleic acid bases, such as modified DNA bases. Modifications may occur at, but are not restricted to, the sugar 2' position, the C-5 position of pyrimidines, and the 8-position of purines. Examples of suitable modified DNA or RNA bases include 2'-fluoro nucleotides, 2'-amino nucleotides, 5'-aminoallyl-2'-fluoro nucleotides and phosphorothioate nucleotides (monothiophosphate and dithiophosphate). In typical embodiments, B and F are about 20 to 110 nucleotides in length. In another embodiment, B and F are from about 25 to about 75 nucleotides in length. In yet another embodiment, B and F are from about 30 to about 60 nucleotides in length.

D and H are complementary nucleotide sequences from about 2 to about 20 nucleotides in length. In another embodiment, D and H are from about 4 to about 15 nucleotides in length. In a preferred embodiment, D and H are from about 5 to about 7 nucleotides in length. In one embodiment, D and H have a free energy for association from about 5.2 kcal/mole to about 8.2 kcal/mole as measured in the selection buffer conditions, defined below. In another embodiment, D and H have a free energy for association from about 6.0 kcal/mole to about 8.0 kcal/mole as measured in the selection buffer conditions. In yet another embodiment, D and H have a free energy for association from about 7.0 kcal/mole to 8.0 kcal/mole in the selection buffer conditions. In a preferred embodiment, D and H have a free energy for association of 7.5 kcal/mole in the selection buffer conditions.

In a preferred embodiment, A, C, E and G are approximately 18 nucleotides in length and have an average GC content of about 60%, B and F are about 30 to about 60 nucleotides in length, and D and H range from about 5 to about 7 nucleotides in length and have a free energy of association of about 7.5 kcal/mole.

The method for simultaneous selection is initiated by contacting a plurality of pairs of the nucleic acid constructs A-B-C-D and E-F-G-H with the target molecule in the presence of a selection buffer to form a complex. Generally speaking, suitable selection buffers allow non-covalent simultaneous binding of the nucleic acid constructs to the target molecule. The method for simultaneous selection then involves the same steps of selection, separation, amplification and purification as described in section (a) above involving methods for the selection of an aptamer in the presence of an epitope binding agent construct, with the exception that the PCR is designed to amplify both nucleic acid constructs (A-B-C-D and E-F-G-H), using primers to A, C, E, and G. Typically several rounds of selection are performed until pairs of nucleic acid constructs having the desired affinity for the target molecule are selected. In one embodiment, the cycle of selection, separation, amplification, purification, and strand separation is performed from about 4 to about 20 times. In another embodiment, the cycle is performed from about 12 to about 18 times.

After the pair of nucleic acid constructs has reached the desired binding specificity, the nucleic acid constructs are cloned, and the cloned DNA is sequenced. The resulting nucleic acid constructs comprise a first aptamer that binds to a first epitope on the target molecule and a second aptamer that binds to a second epitope on the target molecule.

In another aspect of the invention, two aptamers can be simultaneously selected in the presence of a bridging construct comprised of S-T-U. In one embodiment, S and U are complementary nucleotide sequences from about 2 to about 20 nucleotides in length. In another embodiment, S and U are from about 4 to about 15 nucleotides in length. In a preferred embodiment, S and U are from about 5 to about 7 nucleotides in length. In one embodiment, S and U have a free energy for association from about 5.2 kcal/mole to about 8.2 kcal/mole as measured in the selection buffer conditions, defined below. In another embodiment, S and U have a free energy for association from about 6.0 kcal/mole to about 8.0 kcal/mole as measured in the selection buffer conditions. In yet another embodiment, S and U have a free energy for association from about 7.0 kcal/mole to 8.0 kcal/mole in the selection buffer conditions. In a preferred embodiment, S and U have a free energy for association of 7.5 kcal/mole in the selection buffer conditions.

T may be a nucleotide sequence from about 10 to about 100 nucleotides in length. In one embodiment, T is from 10 to about 25 nucleotides in length. In another embodiment, T is from about 25 to about 50 nucleotides in length. In a further embodiment, T is from about 50 to about 75 nucleotides in length. In yet another embodiment, T is from about 75 to about 100 nucleotides in length. In each embodiment, the nucleotides may be any of the nucleotide bases in DNA or RNA (A, C, T, G in the case of DNA, or A, C, U, G in the case of RNA). In one embodiment T is comprised of DNA bases. In another embodiment, T is comprised of RNA bases. In yet another embodiment, T is comprised of modified nucleic acid bases, such as modified DNA bases or modified RNA bases. Modifications may occur at, but are not restricted to, the sugar 2' position, the C-5 position of pyrimidines, and the 8-position of purines. Examples of suitable modified DNA or RNA bases include 2'-fluoro nucleotides, 2'-amino nucleotides, 5'-aminoallyl-2'-fluoro nucleotides and phosphorothioate nucleotides (monothiophosphate and dithiophosphate). In a further embodiment, B may comprise nucleotide mimics. Examples of nucleotide mimics include locked nucleic acids (LNA), peptide nucleic acids (PNA), and phosphorodiamidate morpholino oligomers (PMO). Alternatively, T may be a polymer of bifunctional chemical linkers. In one embodiment the bifunctional chemical linker is heterobifunctional. Suitable heterobifunctional chemical linkers include sulfoSMCC (Sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate), and Ic-SPDP(N-Succinimidyl-6-(3'-(2-PyridylDithio)-Propionamido)-hexanoate). In another embodiment the bifunctional chemical linker is homobifunctional. Suitable homobifunctional linkers include disuccinimidyl suberate, disuccinimidyl glutarate, and disuccinimidyl tartrate. Additional suitable linkers are illustrated in the Examples, such as the phosphoramidate form of Spacer 18 comprised of polyethylene glycol. In one embodiment, T is from 0 to about 500 angstroms in length. In another embodiment, T is from about 20 to about 400 angstroms in length. In yet another embodiment, T is from about 50 to about 250 angstroms in length.

In one embodiment, S is complementary to D and U is complementary to H. In another embodiment, S and U will not bind to D and H unless S, U, D, and H are brought in close proximity by the A-B-C-D construct and the E-F-G-H construct binding to the target.

In this embodiment of the invention utilizing the bridging construct, the method is initiated in the presence of nucleic acid constructs A-B-C-D and E-F-G-H, and the bridging construct S-T-U. Generally speaking, the method is performed as described with the same steps detailed above. In one embodiment, after the final round of selection, but before cloning, the bridging construct is ligated to the A-B-C-D construct and the E-F-G-H construct. This embodiment allows the analysis of pairs of selected nucleic acid sequences that are best suited for use in a molecular biosensor.

DEFINITIONS

As used herein, the term "analyte" refers generally to a ligand, chemical moiety, compound, ion, salt, metal, enzyme, secondary messenger of a cellular signal transduction pathway, drug, nanoparticle, environmental contaminant, toxin, fatty acid, steroid, hormone, carbohydrate, amino acid, peptide, polypeptide, protein or other amino acid polymer, microbe, virus or any other agent which is capable of binding to a polypeptide, protein or macromolecular complex in such a way as to create an epitope or alter the availability of an epitope for binding to an aptamer.

The term "aptamer" refers to a polynucleotide, generally a RNA, modified RNA, DNA, or modified DNA that has a useful biological activity in terms of biochemical activity, molecular recognition or binding attributes. Usually, an aptamer has a molecular activity such as binding to a target molecule at a specific epitope (region).

The term "epitope" refers generally to a particular region of a target molecule. Examples include an antigen, a hapten, a molecule, a polymer, a prion, a microbe, a cell, a peptide, polypeptide, protein, or macromolecular complex. An epitope may consist of a small peptide derived from a larger polypeptide. An epitope may be a two or three-dimensional surface or surface feature of a polypeptide, protein or macromolecular complex that comprises several non-contiguous peptide stretches or amino acid groups.

The term "epitope binding agent" refers to a substance that is capable of binding to a specific epitope of an antigen, a polypeptide, a protein or a macromolecular complex. Non-limiting examples of epitope binding agents include aptamers, thioaptamers, double-stranded DNA sequence, peptides and polypeptides, ligands and fragments of ligands, receptors and fragments of receptors, antibodies and fragments of antibodies, polynucleotides, coenzymes, coregulators, allosteric molecules, peptide nucleic acids, locked nucleic acids, phosphorodiamidate morpholino oligomers (PMO), and ions.

The term "epitope binding agent construct" refers to a construct that contains an epitope-binding agent and can serve in a "molecular biosensor" with another epitope binding agent construct. Preferably, an epitope binding agent construct also contains a "linker," and a "signaling oligo". Epitope binding agent constructs can be used to initiate the aptamer selection methods of the invention. An aptamer construct is a special kind of epitope binding agent construct wherein the epitope binding agent is an aptamer.

The term "molecular biosensor" refers to a construct comprised of at least two epitope binding agent constructs. The molecular biosensor can be used for detecting or quantifying the presence of a target molecule.

The term "nucleic acid construct" refers to a molecule comprising a random nucleic acid sequence flanked by two primers. Preferably, a nucleic acid construct also contains a signaling oligo. Nucleic acid constructs are used to initiate the aptamer selection methods of the invention.

The term "signaling oligo" means a short (generally 2 to 15 nucleotides, preferably 5 to 7 nucleotides in length) single-stranded polynucleotide. Signaling oligos are typically used in pairs comprising a first signaling oligo and a second signaling oligo. Preferably, the first signaling oligo sequence is complementary to the second signaling oligo. Preferably, the first signaling oligo and the second signaling oligo can not form a stable association with each other through hydrogen bonding unless the first and second signaling oligos are brought into close proximity to each other through the mediation of a third party agent.

As used herein, the term "linker" or "linker molecule" refers to a polymer attached to an epitope binding agent construct. The attachment may be covalent or non-covalent. It is envisioned that the linker can be a polymer of amino acids or nucleotides. A preferred linker molecule is flexible and does not interfere with the binding of a nucleic acid binding factor to the set of nucleic acid components.

As used herein, the term "macromolecular complex" refers to a composition of matter comprising a macromolecule. Preferably, these are complexes of one or more macromolecules, such as polypeptides, lipids, carbohydrates, nucleic acids, natural or artificial polymers and the like, in association with each other. The association may involve covalent or non-covalent interactions between components of the macromolecular complex. Macromolecular complexes may be relatively simple, such as a ligand bound polypeptide, relatively complex, such as a lipid raft, or very complex, such as a cell surface, virus, bacteria, spore and the like. Macromolecular complexes may be biological or non-biological in nature.

EXAMPLES

The following examples illustrate the invention.

Example 1-Methods for selecting aptamers for use in molecular sensors

Figure 2 summarizes five possible methods for selecting aptamers useful in the practice of the invention. Panel A depicts the selection of an additional aptamer in the presence of a target bound to a known aptamer. The nucleic acid construct is comprised of a signaling oligo, represented by the hatched bar, and two primers flanking a random DNA sequence. In practice, the signaling oligo is treated as a specific subpart of the primer in the nucleic acid construct. A complimentary signaling oligo is attached to the preselected aptamer via a long flexible linker. Here, the process begins by combining the nucleic acid construct, the target, and the known aptamer construct. Selection of aptamers using such a random sequence construct will be biased towards aptamers capable of binding to the target at an epitope distinct from the epitope of the known aptamer construct, and that will function in molecular biosensors depicted in Fig. 3A.

An alternative scenario is depicted in panel B, which describes the simultaneous selection of two aptamers binding two distinct epitopes of the target. The nucleic acid constructs are comprised of signaling oligos (represented by the hatched bars at the end of primer 1 and primer 4) and two primers flanking either side of a random-sequence. There are at least two different types of nucleic acid constructs, each type containing unique primer sequences. In panel B, one type contains primers 1 and 2, and the second contains primers 3 and 4. In this example, the process begins with combining both types of nucleic acid constructs, and the target. Selection of aptamers using such random sequence constructs will be biased towards aptamers capable of binding to the target simultaneously at two distinct epitopes of the protein, and that will function in sensors depicted in Fig. 3A.

Panel C depicts an alternative design for simultaneous selection of two aptamers binding two distinct epitopes of the target. In addition to the two different types of nucleic acid constructs, a third bridging construct is used. The bridging construct comprises an additional pair of short oligonucleotides (hatched bars) connected by a flexible linker. These oligonucleotides will be complementary to the short oligonucleotides at the end of the nucleic acid constructs. The presence of the bridging construct during selection will provide a bias towards selecting pairs of aptamers capable of simultaneously binding the target. Before cloning of the selected aptamers (after the last selection) the pairs of selected sequences will be enzymatically ligated using T4 ligase to preserve the information regarding the preferred pairs between various selected aptamers.

In a fourth alternate embodiment, a second aptamer can be selected in the presence of a target bound by an antibody (Figure 2 D). The signaling oligo in the nucleic acid construct, depicted by the hatched bar, is complementary to the signaling oligo attached to the antibody via a long flexible linker. The process begins by combining the nucleic acid construct, the target, and the antibody construct. Selection of an aptamer using such a random sequence construct will be biased towards aptamers able to bind to the protein at an epitope distinct from the antibody epitope and will function in sensors depicted in Fig. 3C.

In a fifth alternate embodiment, a second aptamer can be selected in the presence of the target bound to a double-stranded DNA fragment (Figure 2E). The signaling oligo in the nucleic acid construct, depicted by the hatched bar, is complementary to the signaling oligo attached to the double-stranded DNA construct via a long flexible linker. The process begins by combining the nucleic acid construct, the target, and the double-stranded DNA construct. Selection of an aptamer using such a random sequence construct will be biased towards aptamers able to bind to the target at a site distinct from the double-stranded DNA binding site and will function in sensors depicted in Fig. 3B.

Example 2-Sequential selection of aptamers that bind to thrombin for use in making a thrombin sensor

The results of selecting an aptamer in the presence of a known aptamer construct are depicted in Figure 5. The in vitro evolution procedure was initiated using a selection construct containing a 33 nt random sequence (THR11)(Table 1) in the presence of the known THR22 aptamer construct (THR22)(Table 1) and the target, in this case thrombin (Figure 5A). Five µM of THR11 were added to 5µM THR22 in a total of 1 mL of buffer (50mM Tris-HCl (pH 7.5), 100mM NaCl, 5mM KCl and 1mM MgCl₂). The mixture was boiled for approximately 1min, and allowed to cool to room temperature (RT). Thrombin (200nM) was added, and the mixture was incubated for 15-30 min at RT. Next, the mixture was spun through a nitrocellulose filter (NCF), followed by 2 washes of 1mL and a single wash of 0.5mL. Pre-warmed urea (200µl of 7M solution containing 1M NaCl) was loaded on the NCF, and incubated for 15min at 37°C. The DNA/urea mixture was eluted, and the DNA was precipitated with ethanol (added cold ethanol (2.5x the volume of eluted DNA) and incubated for at least two hours at -20°C). The precipitated DNA was centrifuged, the supernatant removed, and the subsequent pellet was dried in a speed-vac. The pellet was redissolved in 20µL of water, and used as a template for the PCR reaction.

Each PCR reaction contained 80µL of dd H2O, 10µL of 10xPCR buffer, 6µL of MgCl₂, 0.8µL 25mM dNTPs, 1µL 50uM primer 1(modified with fluorescein), 1 uL 50µM primer 2 (biotinylated), 0.5µL Taq polymerase, and 1µL of template. The reaction cycle consisted of 5 min at 95°C, sixteen cycles of 30s at 95°C, 30s at 50°C, and 1 min at 72°C, and 5min at 72°C. The pooled samples were allowed to cool, and subsequently separated on a polyacrylamide gel. The band(s) of interest were visualized by utilizing the fluorescein tag, and were excised from the gel. The gel pieces were transferred to a microtube and crushed using a pipet tip. The gel pieces were covered with diffusion buffer (100mM Tris (pH 8.0), 0.5 M NaCl, 5mM EDTA) and the mixture was incubated for at least two hours at 50°C. After centrifugation the supernatant was filtered through an empty Bio-Rad microspin column. The gel pieces were washed with fresh diffusion buffer, and the process repeated for a second time. The supernatants from the first and second procedures were combined.

Pre-equilabrated (1 M NaCl, 50mM Tris (pH 8.0), and I mM EDTA) DYNAL magnetic streptavidin beads were mixed with the gel-purified DNA, and incubated at RT for 30min with constant shaking. The supernatant was removed, and the beads were washed once with 500µL, once with 250µL, and once with 100µL of buffer. Next, the beads were incubated for 30min at 37°C with 50µL of 0.15N NaOH. The supernatant containing the fluorescein labeled DNA was removed and filtered through a G-25 Sephadex microspin column pre-equilibrated with buffer. The estimated concentration of the recovered DNA was calculated by comparison to a known amount of fluorescein-labeled primer.

The second round of selection began by combining 50nM of the recovered DNA and 50-1000nM of THR22 in a total of 50µL of selection buffer. The DNA mixture was boiled for 1min, and allowed to cool to RT. Subsequently, the DNA mixture was filtered through a pre-equilibrated NCF to remove DNA sequences with affinity for the NCF. Thrombin (20nM) was added to the filtered DNA and the mixture was incubated for 15-10 min at RT. Next, the mixture was spun through another pre-equilibrated NCF, followed by two washes of 100µL. After incubation with 100µL of urea (7M in a buffer of 1M NaCl) for 15min at 37°C, the DNA-thrombin complexes were eluted from the NCF. The DNA in the eluted solution was precipitated with alcohol (see above) and re-suspended in 20µL of water. This was used as a template for the PCR reaction. PCR products were purified by electrophoresis on polyacrylamide gel and the single-stranded DNA was obtained from purified PCR products as described above for the first selection. Subsequent selections were repeated until the detected thrombin-binding activity reached a maximum (Figure 5B).

Panel B depicts the thrombin-binding activity of single-stranded DNAs obtained after each indicated round of selection. Measurable thrombin-binding activity appeared after the 4th selection and reached maximum binding activity after the 12th selection. Binding was measured in the presence of excess THR22. DNA obtained after the 12th selection was cloned and the DNA from individual clones was sequenced. Panel C depicts the sequence alignment (using ClustalX) of the individual clones. Clones obtained from 4 independent selection experiments are shown. These selections were performed using the following pairs of aptamer constructs and selection constructs: THR22 and THR 11; THR25 and THR 11; THR42 and THR11; THR43 and THR 11 (Table 1). Several families of highly conserved sequences are easily visible in panel C.

One sequence, which appeared in 4 clones (clones 20, 21, 24, and 26) shown in Figure 5, was used to create a functional thrombin biosensor (Figure 6). The cloned sequence was used in two separate aptamer constructs. Each construct (THR 35 and THR 36) was comprised of the aptamer sequence, a linker, and a fluorescein-labeled signaling oligo. As shown in Figure 6, THR 35 and THR 36 differ in the nucleotides flanking the cloned sequence. The other half of the thrombin biosensor (THR27, Table 1) contained the same aptamer sequence as the THR22 aptamer construct used in the selection, a linker, and a Texas Red-labeled complementary signaling oligo. Panels A and B depict the fluorescence image (sensitized acceptor emission) of microtiterplate wells containing 20 nM (panel A) or 100 nM (panel B) of the indicated thrombin sensor and the indicated concentrations of thrombin. For comparison, a sensor comprising aptamer constructs containing previously described thrombin aptamers (THR21 and THR27, Table 1) is shown.

Example 3-Simultaneous selection of aptamers that bind to thrombin

Figure 7 depicts the results of simultaneously selecting two aptamers that bind to a target at distinct epitopes. The selection procedure began with two types of selection constructs, each containing a 30 nt random sequence (THR49 and THR50) (Table 1), and the target thrombin (panel A). The process proceeds as outlined above, with the exception that two sets of PCR reactions were performed, corresponding to the two different types of nucleic acid constructs initially used. The thrombin-binding activity of the mixture of single-stranded DNAs obtained after each indicated round of selection is shown in panel B. Measurable thrombin-binding activity appeared after the 6th selection and reached a maximum after the 14th selection. DNA obtained after the 14th selection was cloned and the DNA from individual clones was sequenced. Panel C depicts the sequence alignment (using ClustalX) of the clones. Several families of highly conserved sequences are easily visible.

Example 4-Selection of an aptamer for use in a CRP sensor with double-strandedDNA

Figure 8 depicts the selection of an aptamer in the presence of a double-stranded DNA molecular recognition construct. Aptamers to the cAMP binding protein ("CRP") were selected to bind at sites distinct from the DNA-binding site of the protein. Selection was initiated with a nucleic acid construct containing a 33 nt random sequence (MIS12)(Table 1). Additionally, a double-stranded DNA construct comprised of the CRP DNA binding site sequence (MIS10X3 hybridized with MIS11), a linker, and a signaling oligo was used for the process. (Figure 8A). The selection process was essentially the same as outlined above for the thrombin aptamer. The only difference was that the buffer used in the selection contained 200µl c-AMP, which is required for the double-stranded DNA construct to bind to CRP. In the first selection ∼ 5uM MIS12 was combined with 400nM MIS10X3/MIS11, 400nM CRP, and 0.2 mM c-AMP. In subsequent selections 100 nM MIS10X3/MIS11, 50 nM selected single-stranded DNA constructs and 100 nM CRP were combined.

CRP binding activity of single-stranded DNA obtained after the indicated round of selection is depicted in Figure 8B. Measurable CRP binding activity appeared after the 6th selection and reached a maximum after the 12th selection. Binding was measured in the presence of excess MIS10X3/MIS11. DNA obtained after the 12th selection was cloned and the DNA obtained from individual clones was sequenced. The sequence alignment (using ClustalX) of the clones is depicted in panel C. A conserved core sequence or ∼16 nucleotides could be identified.



THR11	SEQ ID NO:1	Construct containing 33 nt random DNA sequence for thrombin aptamer selection
THR22	SEQ ID NO:2	Co-aptamer for thrombin aptamer selection
THR25	SEQ ID NO:3	Co-aptamer for thrombin aptamer selection
THR42	SEQ ID NO:4	co-aptamer for thrombin aptamer selection
THR43	SEQ ID NO:5	Construct containing 33 nt random DNA sequence for thrombin aptamer selection
THR27	SEQ ID NO:6	G15D aptamer connected via 5 Spacer18 linkers to 7 nt "signaling" oligonucleotide containing amino-dT (near its 5' end)
THR35	SEQ ID NO:7	Thrombin sensor component
THR36	SEQ ID NO:8	Thrombin sensor component
THR21	SEQ ID NO:9	7 nt "signaling" oligonucleotide labeled at 5' with fluorescein connected to 60-18 [29] aptamer via 5 Spacer18 linkers
THR49	SEQ ID NO:10	Construct containing 30 nt random DNA sequence for simultaneous selection of two thrombin aptamers
THR50	SEQ ID NO:11	Construct containing 30 nt random DNA sequence for simultaneous selection of two thrombin aptamers
MIS12	SEQ ID NO:12	Construct containing 33 nt random DNA sequence for CRP aptamer selection
MIS10X3	SEQ ID NO:13	co-aptamer for CRP aptamer selection
MIS11	SEQ ID NO:14	Complement to MIS10X3
Clone 1	SEQ ID NO:15
Clone 2	SEQ ID NO:16
Clone 3	SEQ ID NO:17
Clone 4	SEQ ID NO:18
Clone 5	SEQ ID NO:19
Clone 6	SEQ ID NO:20
Clone 7	SEQ ID NO:21
Clone 8	SEQ ID NO:22
Clone 9	SEQ ID NO:23
Clone 10	SEQ ID NO:24
Clone 11	SEQ ID NO:25
Clone 12	SEQ ID NO:26
Clone 13	SEQ ID NO:27
Clone 14	SEQ ID NO:28
Clone 15	SEQ ID NO:29
Clone 16	SEQ ID NO:30
Clone 17	SEQ ID NO:31
Clone 18	SEQ ID NO:32
Clone 19	SEQ ID NO:33
Clone 20	SEQ ID NO:34
Clone 21	SEQ ID NO:35
Clone 22	SEQ ID NO:36
Clone 23	SEQ ID NO:37
Clone 24	SEQ ID NO:38
Clone 25	SEQ ID NO:39
Clone 26	SEQ ID NO:40
Clone 27	SEQ ID NO:41
Clone 28	SEQ ID NO:42
Clone 29	SEQ ID NO:43
Clone 30	SEQ ID NO:44
Clone 31	SEQ ID NO:45
Clone 32	SEQ ID NO:46
Clone 33	SEQ ID NO:47
Clone 34	SEQ ID NO:48
Clone 35	SEQ ID NO:49
Clone 1-1	SEQ ID NO:50
Clone 1-2	SEQ ID NO:51
Clone 1-3	SEQ ID NO:52
Clone 1-4	SEQ ID NO:53
Clone 1-5	SEQ ID NO:54
Clone 1-6	SEQ ID NO:55
Clone 1-7	SEQ ID NO:56
Clone 1-8	SEQ ID NO:57
Clone 1-9	SEQ ID NO:58
Clone 1-10	SEQ ID NO:59
Clone 2-1	SEQ ID NO:60
Clone 2-2	SEQ ID NO:61
Clone 2-3	SEQ ID NO:62
Clone 2-4	SEQ ID NO:63
Clone 2-5	SEQ ID NO:64
Clone 2-6	SEQ ID NO:65
Clone 2-7	SEQ ID NO:66
Clone 2-8	SEQ ID NO:67
Clone 2-9	SEQ ID NO:68
Clone 2-10	SEQ ID NO:69
Clone 2-11	SEQ ID NO:70
Clone 2-12	SEQ ID NO:71
Clone 2-13	SEQ ID NO:72
Clone 2-14	SEQ ID NO:73
Clone 1	SEQ ID NO:74
Clone 2	SEQ ID NO:75
Clone 3	SEQ ID NO:76
Clone 4	SEQ ID NO:77
Clone 5	SEQ ID NO:78
Clone 6	SEQ ID NO:79
Clone 7	SEQ ID NO:80
Clone 8	SEQ ID NO:81
Clone 9	SEQ ID NO:82
Clone 10	SEQ ID NO:83
Clone 11	SEQ ID NO:84
Clone 12	SEQ ID NO:85
Clone 13	SEQ ID NO:86
Clone 14	SEQ ID NO:87
Clone 15	SEQ ID NO:88
Clone 16	SEQ ID NO:89
Clone 17	SEQ ID NO:90
Clone 18	SEQ ID NO:91
Clone 19	SEQ ID NO:92
Clone 20	SEQ ID NO:93
Clone 21	SEQ ID NO:94
Clone 22	SEQ ID NO:95
Clone 23	SEQ ID NO:96

SEQUENCE LISTING

<110> Saint Louis University Heyduk, Tomasz Heyduk, Ewa
<120> METHODS FOR THE SELECTION OF APTAMERS
<130> 108284
<150> US 60/689,470 <151> 2005-06-10
<160> 96
<170> PatentIn version 3.3
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<220> <223> BASED ON MAMMALIAN
<400> 24 gggggtacta ggtattaatg ggtagggtgg tgt 33
<210> 25 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 25 cagcagggaa cggaacggtt agggtgggta ggg 33
<210> 26 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<220> <221> misc_feature <222> (5)..(5) <223> n is a, c, g, or t
<400> 26 gcggngatag gtcgcgtaag ttgggtaggg tgg 33
<210> 27 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 27 caggatgggt agggtggtca gcgaagcagt agg 33
<210> 28 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 28 caacggttgg gtgaactgta gtggcttggg gtg 33
<210> 29 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 29 caggatgggt agggtggtca gcgaagcagt agg 33
<210> 30 <211> 32 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 30 caggatgggt agggtggtca gcgaagcagt ag 32
<210> 31 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 31 ggcgagagca gcgtgatagg gtgggtaggg tgg 33
<210> 32 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 32 cagggtcagg gctagatgat gcgattaacc atg 33
<210> 33 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 33 caggatgggt agggtggtca gcgaagcagt agg 33
<210> 34 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 34 gggggtacta ggtatcaatg ggtagggtgg tgt 33
<210> 35 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 35 gggggtacta ggtatcaatg ggtagggtgg tgt 33
<210> 36 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<220> <221> misc_feature <222> (27)..(27) <223> n is a, c, g, or t
<400> 36 ggagacgtaa tgggttggtt gggaagngga tcc 33
<210> 37 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 37 gcatacgtaa tggtccggtt ggggcgggta tgt 33
<210> 38 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 38 gggggtacta ggtatcaatg ggtagggtgg tgt 33
<210> 39 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 39 gaggggactt aggatgggta gggtggtagg ccc 33
<210> 40 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 40 gggggtacta ggtatcaatg ggtagggtgg tgt 33
<210> 41 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 41 ggtcggggca tagtaatgct ggattgggca gct 33
<210> 42 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 42 gggtaggagc agtacacgct ggaatgggtc act 33
<210> 43 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 43 gcagtaggta ctatattggc tagggtggtc tgc 33
<210> 44 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 44 gggtagggtg acagggagga cggaatgggc act 33
<210> 45 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 45 gcagtaggta ctatattggc tagggtggtc tgc 33
<210> 46 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 46 gcagtaggta ctatattggc tagggtggtc tgc 33
<210> 47 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 47 gcagtaggta ctatattggc tagggtggtc tgc 33
<210> 48 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 48 gggggtgcta ggtattaaag ggtagggtgg tgt 33
<210> 49 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 49 gcagtaggta ctatgtcggg tcgggtggtc tgc 33
<210> 50 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 50 gggtagggtg gttgtaatag ggattgcgat 30
<210> 51 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 51 gggtagggtg gttgtaatag ggattgcgat 30
<210> 52 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 52 ggcacaaccc gatatggcta tgaatctgcc 30
<210> 53 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 53 gggtagggtg gttgtaatag ggattgcgat 30
<210> 54 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 54 gggtagggtg gttgtaatag ggattgcgat 30
<210> 55 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 55 ggtgtgggtg gttattggtg tagagcgggt 30
<210> 56 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 56 aatggggagg ttggggtgcg ggagagtggt 30
<210> 57 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 57 acgcgtagga tgggtagggt ggtcgcgtta 30
<210> 58 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 58 gggtagggtg gttgtaatag ggattgcgat 30
<210> 59 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 59 gggcgaaggt acgaagacgg atgcacgtgc 30
<210> 60 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 60 aaggccgcca tctgggtccg acgagtacca 30
<210> 61 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 61 tagggtgggt agggtggtca actatggggg 30
<210> 62 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 62 gggtggctgg tcaaggagat agtacgatgc 30
<210> 63 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 63 ggtagggtgg ttaaaatagg ggaatggcag 30
<210> 64 <211> 30 <212> DNA <213> Artificia
l<220> <223> BASED ON MAMMALIAN
<400> 64 cacaagaagg gcgagcgctg agcatagtgc 30
<210> 65 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 65 ccaacgacac atagggtaca cgccgcctcc 30
<210> 66 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 66 ggtagggtgg ttaaaatagg ggaatggcag 30
<210> 67 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 67 taggatgggt agggtggtcc caggaatggc 30
<210> 68 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 68 taggatgggt agggtggccc caggaatggc 30
<210> 69 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 69 ggtagggtgg ttaaaatagg ggaatggcag 30
<210> 70 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 70 gatgtggccc agaagcataa cacgacgtac 30
<210> 71 <211> 30 <212> DNA <213> Artificial<220> <223> BASED ON MAMMALIAN
<400> 71 taggatgggt agggtggtcc caggaatggc 30
<210> 72 <211> 30 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 72 ggagatgcag gtactgagta gggagtgtgc 30
<210> 73 <211> 30 <212> DNA <213> Artificial<220> <223> BASED ON MAMMALIAN
<400> 73 taggatgggt agggtggtcc caggaatggc 30
<210> 74 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 74 aatcaagggc tggtgttaaa ggtgatcgac tag 33
<210> 75 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 75 aaggggagcc atcacacagg aggtcgcttc gct 33
<210> 76 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 76 aaaggcatca cctagagttg ccgccgatac ttg 33
<210> 77 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 77 ggggatgtgc gaaactggtg actatgcggg tgc 33
<210> 78 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 78 cgaaaggagc catcaacctt gaaacgcccg tcc 33
<210> 79 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 79 cagacgggag ccatcgacat agaggtgatt gcc 33
<210> 80 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 80 agggaaagcc atcacctaga cacatacagc atg 33
<210> 81 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 81 ataagaagcc atcataggga cctagctagc ccc 33
<210> 82 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 82 ccaacagacg gtagcacaac actagtactc tgg 33
<210> 83 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 83 acagacgccc ctagtaaaca ataaccgatg gcc 33
<210> 84 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 84 atagctactc gccaagggtg acttctgcta ttg 33
<210> 85 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 85 atggggcaac gcggagacct gtcggtactg cct 33
<210> 86 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 86 gcaatatagc actaagcctt aactccatgg tgg 33
<210> 87 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 87 gcaaggaaaa acaagcaagc catcacgacc tag 33
<210> 88 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 88 caggcatccc aagaagtgtc agccgtttcg tgg 33
<210> 89 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 89 caacaggaga gcccgacaca cagatctggc ccc 33
<210> 90 <211> 33 <212> DNA <213> Artificial
<220>
<223> BASED ON MAMMALIAN
<400> 90 acaagccatc acgtgaatgc cgaccggtac tgt 33
<210> 91 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 91 accgacaaac aagtcaatac gggacacgat cct 33
<210> 92 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 92 cagtgggtcg ggtcacagcc atgagtgttg ctg 33
<210> 93 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 93 aacgggaaag ccatcaccat atttatcgtc ctg 33
<210> 94 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 94 acgggcgcaa acaagatgta caaaagcatg gtg 33
<210> 95 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 95 agcgggatag ggaactatcg gacaatcgtc gtg 33
<210> 96 <211> 33 <212> DNA <213> Artificial
<220> <223> BASED ON MAMMALIAN
<400> 96 gaggataaaa gccatcaact agaatgcgca tgg 33

Claims

A method for simultaneously selecting at least two aptamers comprising a first aptamer sequence and a second aptamer sequence, wherein the first aptamer sequence binds to a first epitope on a target molecule and the second aptamer sequence binds to a second epitope on the target molecule; the method comprising:
(a) contacting a plurality of pairs of nucleic acid constructs comprising a first nucleic acid construct and a second nucleic acid construct with the target molecule to form a mixture of nucleic acid constructs and target molecules, the first nucleic acid construct comprising:
i. A-B-C-D; the second nucleic acid construct comprising:

ii. E-F-G-H;
wherein:
A, C, E, and G are each different DNA sequences from about 10 to about 30 nucleotides in length, A and C together comprising a sequence to prime a polymerase chain reaction for amplifying a first aptamer sequence, and E and G together comprising a sequence to prime a polymerase chain reaction for amplifying a second aptamer sequence;

B is a single-stranded random nucleotide sequence from about 20 to about 110 nucleotides in length that contains specific sequences binding to a first epitope of the target molecule;

D and H are a pair of complementary nucleotide sequences from about 2 to about 20 nucleotides in length, wherein D and H have a free energy for association from about 5.5 kcal/mole to about 8.0 kcal/mole at a temperature from approximately 21 ° C to about 40° C and at a salt concentration of approximately 1 mM to about 100 mM; and

F is a single-stranded random nucleotide sequence from about 20 to about 110 nucleotides in length that contains specific sequences binding to a second epitope of the target molecule;

(b) isolating from the mixture a complex comprising the target molecule having the first nucleic acid construct bound to a first epitope and the second nucleic acid construct bound to the second epitope; and

(c) purifying the first nucleic acid construct and the second nucleic acid construct from the complex.
The method of claim 1, wherein the target molecule is selected from the group consisting of an analyte, a prion, a protein, a nucleic acid, a lipid, a carbohydrate, a biomolecule, a macromolecular complex, a fungus, a virus, and a microbial organism.
The method of claim 2, wherein the target molecule is a protein.
The method of claim 1, wherein the plurality of nucleic acid constructs are contacted with the target molecule by incubation in a salt buffer, having a pH range from about 6.5 to about 8.5 at a temperature ranging from about 21°C to about 40°C.
The method of claim 1, wherein the complex is isolated from the mixture using a process selected from the group consisting of nitrocellulose filters, magnetic beads, and sepharose beads.
The method of claim 1, further comprising separating the first and second nucleic acid constructs from the complex to form a mixture comprising the target molecule, the first nucleic acid construct and the second nucleic acid construct.
The method of claim 6, wherein the first nucleic acid construct and the second nucleic acid construct are separated from the target molecule by denaturing the target molecule or incubating the complex with an excess of competitor.
The method of claim 7, wherein the first nucleic acid construct and the second nucleic acid construct are purified from the mixture by precipitating the nucleic acid.
The method of claim 8, further comprising amplifying the first nucleic acid construct and the second nucleic acid construct by the polymerase chain reaction to form a polymerase chain reaction product.
The method of claim 9, wherein the first nucleic acid construct and the second nucleic acid construct are purified from the polymerase chain reaction product by agarose gel separation and purification of the nucleic acid from the gel.
The method of claim 9, further comprising repeating the selection, separation, amplification and purification steps of the method from about 4 to about 20 times, wherein at the end of each cycle the first nucleic acid construct and the second nucleic acid construct comprising double-stranded nucleotide sequence have the double-stranded nucleotide sequence separated to form single stranded nucleotide sequence prior to the beginning of each cycle.
The method of claim 11, wherein the double stranded nucleotide sequence is separated to single stranded nucleotide sequence by binding the nucleic acid to strepavidin linked beads and denaturing the nucleic acid.
The method of claim 1, wherein A, C, E, and G are from about 15 to about 25 nucleotides in length, or from about 15 to about 20 nucleotides in length, or from about 16 to about 18 nucleotides length, or 18 nucleotides in length.
The method of claim 1, wherein A, C, E, and G have an average GC content from about 55% to about 60%, for example about 60%.
The method of claim 1, wherein B and F comprise nucleotide bases selected from the group consisting of DNA bases, RNA bases, modified DNA bases, and modified RNA bases.
The method of claim 1, wherein B and F are from about 25 to about 75 nucleotides in length, or from about 30 to about 60 nucleotides in length.
The method of claim 1, wherein D and H are from about 4 to about 15 nucleotides in length, or about 5 to about 7 nucleotides in length.
The method of claim 1, wherein D and H have a free energy of association of about 6.0 kcal/mole to about 8.0 kcal/mole, for example about 7.5 kcal/mole.
The method of claim 1, wherein A, C, E and G are approximately 18 nucleotides in length; B and F are from about 30 to about 60 nucleotides in length; and D and H are from about 5 to about 7 nucleotides in length.
The method of claim 19, wherein D and H have a free energy of association of about 7.5 kcal/mole.
The method of claim 20, wherein A, C, E, and G have an average GC content of about 60%.
A method for selecting at least one aptamer in the presence of an epitope binding agent construct, wherein the aptamer sequence binds to a first epitope on a target molecule and the epitope binding agent construct binds to a second epitope on the target molecule; the method comprising:
(a) contacting a plurality of nucleic acid constructs and the epitope binding agent construct with the target molecule to form a mixture of nucleic acid constructs, epitope binding agent constructs, and target molecules, the nucleic acid construct comprising:
iii. A-B-C-D; the epitope binding agent construct comprising:

iv. P-Q-R;
wherein:
A and C are each different DNA sequences from about 10 to about 30 nucleotides in length, A and C together comprising a sequence to prime a polymerase chain reaction for amplifying the aptamer sequence;

B is a single-stranded random nucleotide sequence from about 20 to about 110 nucleotides in length that contains specific sequences binding to a first epitope of the target molecule;

D and R are a pair of complementary nucleotide sequences from about 2 to about 20 nucleotides in length, wherein D and R have a free energy for association from about 5.5 kcal/mole to about 8.0 kcal/mole at a temperature from approximately 21 ° C to about 40° C and at a salt concentration of approximately 1 mM to about 100 mM;

P is an epitope binding agent selected from the group comprising an aptamer, an antibody, an antibody fragment, a double-stranded DNA sequence, a ligand, a ligand fragment, a receptor, a receptor fragment, a polypeptide, a peptide, a coenzyme, a coregulator, an allosteric molecule, and an ion;

Q is a flexible linker; and

(b) isolating from the mixture a complex comprising the target molecule having the nucleic acid construct bound to the first epitope and the epitope binding agent construct bound to the second epitope; and

(c) purifying the nucleic acid construct from the complex.
The method of claim 22 wherein the epitope binding agent is an antibody selected from the group comprising polyclonal antibodies, ascites, Fab fragments, Fab' fragments, monoclonal antibodies, and humanized antibodies.
The method of claim 23 wherein the epitope binding agent comprises a monoclonal antibody.
The method of claim 22 wherein Q is from 0 to about 500 angstroms in length, or from about 50 to about 250 angstroms in length.
The method of claim 22 wherein Q is comprised of a polymer of bifunctional chemical linkers.
The method of claim 22 wherein Q is comprised of poly ethylene glycol Spacer 18.