WO2019051397A1 - Nucleolin-targeting aptamers and methods of using the same - Google Patents

Abstract

Provided herein are compositions including aptamers capable of binding to and/or inhibiting the activity of nucleolin. Methods of treating cancer in a subject by administering such compositions are also provided. Further provided are methods of screening aptamers via systematic evolution of ligands by exponential enrichment (SELEX) using a modified RNA library comprising a random 2'Fluoropyrimidine RNA pool of sequences having 5'-constant region (SEQ ID NO: 491 )-A Variable Region-3'constant region (SEQ ID NO: 492).

Description

NUCLEOLIN-TARGETING APTAMERS AND METHODS OF USING THE SAME

CROSS-REFERENCE TO RELATED APPLICATIONS

This patent application claims the benefit of priority of United States Provisional Patent Application No. 62/555,745, filed September 8, 2017, which is incorporated herein by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support by the National Institutes of Health under Award Number CA159826. The government has certain rights in the invention.

SEQUENCE LISTING

This application is being filed electronically via EFS-Web and includes an electronically submitted Sequence Listing in .txt format. The .txt file contains a sequence listing entitled "2018-09-10_5667-00448_ST25.txt" created on September 10, 2018 and is 101,860 bytes in size. The Sequence Listing contained in this .txt file is part of the specification and is hereby incorporated by reference herein in its entirety.

INTRODUCTION

The protein nucleolin plays a critical role in repair of DNA double- stranded breaks (DSB) (Goldstein et al, PNAS, 2013). Mechanistically, nucleolin functions as a histone chaperone at the DSB, escorting the histone proteins H2A and H2B away from the nucleosome at the DNA break. This nucleosome disruption is required for the recruitment of repair enzymes and the repair of the DNA breaks. Therefore, inhibition of nucleolin results in sensitization of cells to DNA damaging agents. Importantly, the majority of human tumors overexpress nucleolin on the cell surface relative to normal cells, thus making nucleolin a tumor-preferential target. A nucleolin inhibitor would have the unique ability to specifically sensitize only tumor cells to DNA damaging agents as it should only target and internalize into cancerous cells.

Aptamers, small artificial RNA or DNA oligonucleotide ligands, can be selected to inhibit protein function and are also emerging as important tumor-targeting molecules. Additionally, they have many advantages over traditional antibody targeting agents, including ease of synthesis and amenability to chemical modification (Keefe et al, Nat Rev Drug Discov, 2010). Moreover, they exhibit antibody-like target affinities and specificities at a fraction of the size, allowing more efficient tumor penetration while maintaining the ability to discriminate between proteins that differ by only a few amino acids (reviewed in Conrad et al, Methods Enzymol, 1996; Obsorne et al, Chem Rev, 1997).

There is a need in the art for new aptamers that may bind to and/or inhibit the nucleolin protein. Such aptamers may be useful not only as new cancer treatments but also may facilitate the delivery of agents to the nucleus of a cell.

SUMMARY

In one aspect of the present invention, aptamers are provided. The aptamer may include a polynucleotide having at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOS: 1-490, 494-515, or any one of the sequences described in the Tables or Figures disclosed herein (for example, Tables 1-4, 6-8 or FIGS. 11A-11B, 12A-12B, 13A-13C, 14A-14D, 15A-15B, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28A-28B, 29, 30, 31, 32, 33, 34, 35, 36 or 37A-37B). In another aspect, the present invention relates to dimers, trimers, and tetramers including any one of the aptamers described herein.

In a further aspect of the present invention, pharmaceutical compositions including any of the aptamers described herein are provided. The pharmaceutical compositions may include a pharmaceutical carrier, excipient, or diluent.

In a still further aspect, the present invention relates to methods for treating cancer in a subject. The methods may include administering to the subject a therapeutically effective amount of any one of the aptamers, dimers, trimers, tetramers, or pharmaceutical compositions described herein.

In a still further aspect, methods of labeling or inhibiting nucleolin are provided. The methods include contacting nucleolin with any one of the compositions described herein to allow binding and possibly inhibition of the activity of the nucleolin. This contacting can be in vitro by adding the nucleolin to cells or may be in vivo by administering the compositions described herein to a subject. The compositions and aptamers provided herein are capable of binding to and possibly inhibiting the function of nucleolin.

BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 shows the work flow demonstrating the selection of aptamer families capable of relocating into the nucleus after binding to nucleolin on cell surface. A random 2'Fluoro- pyrimidine RNA pool of sequences GGGAGAGAGGAAGAGGGAUGGG (SEQ ID NO: 491)- N40-CAUAACCCAGAGGUCGAUAGUACUGGAUCCCCCC (SEQ ID NO: 492) (where N₄₀ represents 40 random nucleotides) was incubated for 20min at 37°C with nucleolin protein (in 20mM Hepes, 150mM NaCl, 2mM CaCl₂ and 0.01% bovine serum albumin) at ratios of RNA:protein varying from 187: 1 to 133: 1. RNA bound to protein was isolated by filtration through a 0.45μιη nitrocellulose membrane before RNA extraction, reverse transcription, PCR amplification and transcription to complete 1 round of selection. Each subsequent round of selection used the RNA pool transcribed from the previous round of selection, for a total of 7 rounds of SELEX against the nucleolin protein. The Round 6 RNA pool was also used to perform 2 Cell-SELEX rounds against both MCF-7 and Panc-1 cells. For the Cell-SELEX rounds, the Round 6 RNA pool was incubated with either MCF-7 or Panc- 1 cells for 2hrs at 37°C / 5% C0₂ before using a high salt wash to remove non-internalized RNA. Cells were then tryspinized, washed again with high salt, and RNA extracted from the cell nuclei using the Invitrogen™ PARIS™ kit. RNA pools from Rounds 3, 5, 7 and 9 (Panc-1) were reverse transcribed, PCR amplified and analyzed by High-Throughput Sequencing.

FIGS. 2A-2D show binding of the SELEX and Cell-SELEX rounds to the nucleolin protein (NCL). RNA pools from SELEX rounds 3, 6, and 7 or from Cell-SELEX Rounds 7-8

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MCF-7 or Rounds 7-8 Panc-1 were end-labeled with P. Nucleolin protein was serially diluted in 20mM Hepes, 150mM NaCl, 2mM CaCl₂ and 0.01% bovine serum albumin and incubated

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with a trace amount of the P-labeled RNA pools. After incubation at 37°C, unbound RNA was captured on a nylon membrane and RNA-nucleolin complexes captured on a nitrocellulose membrane. The fraction of protein-bound RNA was determined via phosphorimaging of the nitrocellulose and nylon membranes.

FIGS. 3A-3B show nucleolin- specific RNA aptamers bind to the RBD domain of nucleolin. (FIG. 3A) Map of truncated nucleolin mutants. From Chen et al. 2011, JBC. (FIG. 3B) Southwestern blot showing the binding of the initial RNA aptamer library (Sell) versus SELEX round 6 (R6 NCL) to truncated nucleolin mutants expressed in MCF7 cells.

FIG. 4 shows binding analysis of the nucleolin (NCL) aptamers identified through high

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throughput sequencing. Aptamers were end-labeled with P. Nucleolin protein was serially diluted in 20mM Hepes, 150mM NaCl, 2mM CaCl₂ and 0.01% bovine serum albumin and

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incubated with a trace amount of the P-labeled RNA pools. After incubation at 37°C, unbound RNA was captured on a nylon membrane and RNA-nucleolin complexes captured on a nitrocellulose membrane. The fraction of protein-bound RNA was determined via phosphorimaging of the nitrocellulose and nylon membranes.

FIGS. 5A-5F show binding of nucleolin aptamer truncates to the nucleolin protein.

Aptamers were end-labeled with 32 P. Nucleolin protein was serially diluted in 20mM Hepes, 150mM NaCl, 2mM CaCl₂ and 0.01% bovine serum albumin and incubated with a trace amount of the 32 P-labeled RNA pools. After incubation at 37°C, unbound RNA was captured on a nylon membrane and RNA-nucleolin complexes captured on a nitrocellulose membrane. The fraction of protein-bound RNA was determined via phosphorimaging of the nitrocellulose and nylon membranes.

FIGS. 6A-6B show nucleolin specific RNA aptamer EV3 sensitizes colon cancer cells to ionizing radiation. HCT 116 p53 -/- colon cancer cells were treated with 5μg of indicated aptamers and exposed to 2Gy IR 48h later. Cells were cultivated for lOd and survival was assessed by MTT assay.

FIG. 7 shows EV3 does not sensitize HFF (human foreskin fibroblasts), that do not express nucleolin on cell surface, to radiation. hTERT-immortalized HFF cells that do not express nucleolin on cell surface were treated with 5μg of indicated aptamers and exposed to 2Gy IR 48h later. Cells were cultivated for lOd and survival was assessed by MTT assay.

FIG. 8 shows EV3 and EV5 bind to nucleolin expressed on the cell surface in a concentration dependent manner. Flow cytometry analysis of MFI (mean fluorescence intensity) of DL650-labeled EV3 and EV5 after incubation of HCT116 p53-/- cells with the indicated aptamer concentrations.

FIGS. 9A-9D show binding of Ev3 aptamer truncates to the nucleolin protein. Aptamers were end-labeled with 32 P. Nucleolin protein was serially diluted in 20mM Hepes, 150mM NaCl,

2mM CaCl₂ and 0.01% bovine serum albumin and incubated with a trace amount of the 32 P- labeled RNA pools. After incubation at 37°C, unbound RNA was captured on a nylon membrane and RNA-nucleolin complexes captured on a nitrocellulose membrane. The fraction of protein- bound RNA was determined via phosphorimaging of the nitrocellulose and nylon membranes.

FIG. 10 shows truncation of EV3 resulted in reduced activity as radio sensitizer. HCT 116 p53 -/- colon cancer cells were treated with 5μg of indicated full-length aptamers or EV3 truncates and exposed to 2Gy IR 48h later. Cells were cultivated for lOd and survival was assessed by MTT assay. FIGS. 11A-11B show predicted secondary structures for a representative Family B aptamer (SEQ ID NO: 8).

FIGS. 12A-12B show predicted secondary structures for a representative Family C aptamer (SEQ ID NO: 9).

FIGS. 13A-13C show predicted secondary structures for a representative Family D aptamer (SEQ ID NO: 10).

FIGS. 14A-14D show predicted secondary structures for a representative Family E aptamer (SEQ ID NO: 11).

FIGS. 15A-15B show predicted secondary structures for a representative Family F aptamer (SEQ ID NO: 12).

FIG. 16 shows predicted secondary structures for Ev3min2 truncate aptamer (SEQ ID NO: 497).

FIG. 17 shows predicted secondary structures for Ev3min3 truncate aptamer (SEQ ID NO: 498).

FIG. 18 shows predicted secondary structures for Ev3min4 truncate aptamer (SEQ ID

NO: 499).

FIG. 19 shows predicted secondary structures for Ev3min5 truncate aptamer (SEQ ID NO: 500).

FIG. 20 shows predicted secondary structures for Ev3min6 truncate aptamer (SEQ ID NO: 501).

FIG. 21 shows predicted secondary structures for Ev3min7 truncate aptamer (SEQ ID NO: 502).

FIG. 22 shows predicted secondary structures for Ev3min8 truncate aptamer (SEQ ID NO: 503).

FIG. 23 shows predicted secondary structures for Ev3min9 truncate aptamer (SEQ ID

NO: 504).

FIG. 24 shows predicted secondary structures for Ev3minl0 truncate aptamer (SEQ ID NO: 505).

FIG. 25 shows predicted secondary structures for Ev3minl l truncate aptamer (SEQ ID NO: 506). FIG. 26 shows predicted secondary structures for Ev3minl2 truncate aptamer (SEQ ID NO: 507).

FIG. 27 shows predicted secondary structures for Ev3minl3 truncate aptamer (SEQ ID NO: 508).

FIGS. 28A-28B show predicted secondary structures for Ev3minl4 truncate aptamer (SEQ ID NO: 509) and Ev3minl5 truncate aptamer (SEQ ID NO: 510).

FIG. 29 shows predicted secondary structures for Ev3minl6 truncate aptamer (SEQ ID NO: 511).

FIG. 30 shows predicted secondary structures for Ev3minl7 truncate aptamer (SEQ ID NO: 512).

FIG. 31 shows predicted secondary structures for Ev3minl8 truncate aptamer (SEQ ID NO: 513).

FIG. 32 shows predicted secondary structures for Ev3minl9 truncate aptamer (SEQ ID NO: 514).

FIG. 33 shows predicted secondary structures for Ev3min20 truncate aptamer (SEQ ID NO: 515).

FIG. 34 shows predicted secondary structures for Ev3min21 truncate aptamer (SEQ ID NO: 486).

FIG. 35 shows predicted secondary structures for Ev3min22 truncate aptamer (SEQ ID NO: 487).

FIG. 36 shows predicted secondary structures for Ev3min23 truncate aptamer (SEQ ID NO: 488).

FIGS. 37A-37B show predicted secondary structures for Ev3min24 truncate aptamer (SEQ ID NO: 489) and Ev3min25 truncate aptamer (SEQ ID NO: 490).

DETAILED DESCRIPTION

Here, in the non-limiting Examples, the present inventors disclose new aptamers that may bind to and/or inhibit the nucleolin protein. The present inventors demonstrate that such aptamers may be useful not only to sensitize cancer cells to cancer treatments including, for example, ionizing radiation and chemotherapeutic agents, but also may facilitate the delivery of agents to the nucleus of a cell. In one aspect of the present invention, aptamers are provided. As used herein, the term "aptamer" refers to single-stranded oligonucleotides that bind specifically to target molecules with high affinity. Aptamers can be generated against target molecules, such as nucleolin, by screening combinatorial oligonucleotide libraries for high affinity binding to the target (See, e.g. , Ellington, Nature 1990; 346: 8 18-22 (1990), Tuerk, Science 249:505-1 0 (1990)). The aptamers disclosed herein may be synthesized using methods well-known in the art. For example, the disclosed aptamers may be synthesized using standard oligonucleotide synthesis technology employed by various commercial vendors including, without limitation, Integrated DNA Technologies, Inc. (IDT), Sigma-Aldrich, Life Technologies, or Bio-Synthesis, Inc.

The aptamer may include a polynucleotide having at least 50%, 60%, 70%, 80%, 85%,

90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOS: 1-490, 494-515, or any one of the sequences described in the Tables or Figures disclosed herein (for example, Tables 1-4, 6-8 or FIGS. 11A-11B, 12A-12B, 13A-13C, 14 A- 14D, 15A-15B, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28A-28B, 29, 30, 31, 32, 33, 34, 35, 36 or 37A-37B). The aptamers described herein (i.e., SEQ ID NOS: 1-490, 494-515) may or may not include a 5' constant region (GGGAGAGAGGAAGAGGGAUGGG (SEQ ID NO: 491)) that may be used, for example, to transcribe or purify the aptamers in vitro. The aptamers described herein (i.e., SEQ ID NOS: 1-490, 494-515) may or may not include a 3' constant region (CAUAACCCAGAGGUCGAUAGUACUGGAUCCCCCC (SEQ ID NO: 492)) that may be used, for example, to transcribe or purify the aptamers in vitro. In some embodiments, the aptamer may include a polynucleotide having at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to the polynucleotide sequence - 5 '-GGGAGAGAGGAAGAGGGAUGGG (SEQ ID NO: 491)-A Variable Region- CAUAACCCAGAGGUCGAUAGUACUGGAUCCCCCC (SEQ ID NO: 492)-3\ wherein the variable region may include any one of SEQ ID NOS: 13-473 or a portion thereof. The portion of the indicated aptamers should be capable of binding to nucleolin. In some embodiments, the aptamer may include a polynucleotide having at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 480 (Ev3 Aptamer).

The terms "polynucleotide," "nucleotide sequence," "polynucleotide sequence," "nucleic acid" and "nucleic acid sequence" refer to a nucleotide, oligonucleotide, polynucleotide (which terms may be used interchangeably), or any fragment thereof. These phrases may refer to DNA or RNA of genomic, natural, or synthetic origin.

Regarding polynucleotide sequences, the terms "sequence identity," "percent identity," and "% identity" refer to the percentage of base matches between at least two nucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences. Sequence identity for a nucleotide sequence may be determined as understood in the art. (See, e.g. , U.S. Patent No. 7,396,664). A suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST), which is available from several sources, including the NCBI, Bethesda, Md., at its website. The BLAST software suite includes various sequence analysis programs including "blastn," that is used to align a known nucleotide sequence with other polynucleotide sequences from a variety of databases. Also available is a tool called "BLAST 2 Sequences" that is used for direct pairwise comparison of two nucleotide sequences. "BLAST 2 Sequences" can be accessed and used interactively at the NCBI website.

Regarding polynucleotide sequences, sequence identity is measured over the length of an entire defined nucleotide sequence, for example, as defined by a particular sequence identified herein. Furthermore, sequence identity, as measured herein, is based on the identity of the nucleotide base in the nucleotide sequence, irrespective of any further modifications to the nucleotide sequence. For example, the polynucleotide nucleotide sequences described herein may include modifications to the nucleotide sequences such 2'flouro, 2'0-methyl, and inverted deoxythymidine (idT) modifications. These modifications are not considered in determining sequence identity. Thus if a base, for example, is a 2'fluoro adenine (or 2'0-methyl, etc.), it is understood to be an adenine for purposes of determining sequence identity with another sequence. Likewise, 3' idT modifications to the polynucleotide sequences described herein also should not be considered in determining sequence identity.

Based on the general aptamer structure presented, for example, in FIGS. 1 1A-11B, 12A- 12B, 13A-13C, 14A-14D, 15A-15B, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28A-28B, 29, 30, 31, 32, 33, 34, 35, 36 or 37A-37B, a person of ordinary skill in the art would readily recognize that several modifications could be made to the sequence while preserving the overall structure and presumably the function of the aptamer. For example, in FIG. 11A, a person of ordinary skill in the art could simply switch the first stem forming region GGGA and the tenth stem forming region UCCC to CCCU and AGGG, respectively, and still retain the stem structure of the aptamer. Additionally, modifications to the stem regions could be made that change the bases within the stem region but conserve the overall pyrimidine and purine base composition so that the stem region hybridizes at a similar melting temperature. A person of ordinary skill would also recognize that changes made to the aptamer that disturbed the general aptamer stem loop structure would likely result in an aptamer incapable of efficiently binding its target.

In some embodiments, the aptamer may have a dissociation constant (K_D) for the nucleolin protein that is less than 1000, 800, 600, 500, 450, 350, 250, 150, 125, 100, 90, 80, 70, 65, 60, 55, 50, 45, 40, 35, 30, 25, 20, 15, 10, 5, 2.5, 2, 1, 0.5, or 0.1 nanomolar (nM). The K_D of an aptamer may be measured using the methodology used by the inventors in the Examples.

The aptamers may include a polynucleotide (RNA, DNA, or peptide nucleic acid (PNA)) that is in an unmodified form or may be in a modified form including at least one nucleotide base modification. Nucleotide base modifications of polynucleotides to, for example, protect the polynucleotide from nuclease degradation and/or increase the stability of the polynucleotide and are well-known in the art. Common nucleotide base modifications that may be used in accordance with the present invention include, without limitation, deoxyribonucleotides, 2'-0- Methyl bases, 2'-Fluoro bases, 2' Amino bases, inverted deoxythymidine bases, 5' modifications, and 3' modifications. In some embodiments, the aptamer may include a polynucleotide including a modified form including at least one nucleotide base modification selected from the group consisting of a 2'fluoro modification, a 2'O-methyl modification, a 5' modification, and a 3 'modification.

Typical 5' modifications may include, without limitation, inverted deoxythymidine bases, addition of a linker sequence such as C6, addition of a cholesterol, addition of a reactive linker sequence which could be conjugated to another moiety such as a PEG. Typical 3' modifications may include, without limitation, inverted deoxythymidine bases, and inverted abasic residues.

As additional 5' and/or 3' modifications, the aptamer may include a polynucleotide including a 5' linker and/or a 3' linker. Common 5' and/or 3' linkers for polynucleotides are known in the art and may include peptides, amino acids, nucleic acids, as well as homofunctional linkers or heterofunctional linkers. Particularly useful conjugation reagents that can facilitate formation of a covalent bond with an ap tamer may comprise an N-hydroxysuccinimide (NHS) ester and/or a maleimide or using click chemistry. Typical 5' and/or 3' linkers for polynucleotides may include without limitation, amino C3, C4, C5, C6, or C12-linkers.

The aptamer may further include an agent. Suitable agents may include, without limitation, stability agents, detectable agents such as reporter moieties, and/or therapeutic agents.

As used herein, a "stability agent" refers to any substance(s) that may increase the stability and/or increase the circulation time of a polynucleotide in vivo. Typical stability agents are known in the art and may include, without limitation, polyethylene glycol (PEG), cholesterol, albumin, or Elastin-like polypeptide.

As used herein, a "detectable agent" refers to any substance(s) that may be detected using appropriate equipment. Suitable detectable agents may be, without limitation, a fluorophore moiety, an enzyme moiety, an optical moiety, a magnetic moiety, a radiolabel moiety, an X-ray moiety, an ultrasound imaging moiety, a photoacoustic imaging moiety, a nanoparticle-based moiety, or a combination of two or more of the listed moieties.

A "fluorophore moiety" may include any molecule capable of generating a fluorescent signal. Various fluorophore moieties are well-known in the art and/or commercially available. Exemplary fluorophore moieties include, without limitation, fluorescein, FITC, Alexa Fluor 488, Alexa Fluor 660, Alexa Fluor 680, Alexa Fluor 750, and Alexa Fluor 790 (Life Technologies); Cy2, Cy3, Cy3.5, Cy5, Cy5.5 and Cy7 (GE Healthcare); DyLight 350, DyLight 488, DyLight 594, DyLight 650, DyLight 680, DyLight 755 (Life Technologies); IRDye 800CW, IRDye 800RS, and IRDye 700DX (Li-Cor); VivoTag680, VivoTag-S680, and VivoTag-S750 (Perkin Elmer).

An "enzyme moiety" refers to polypeptides that catalyze the production of a detectable signal. Exemplary enzyme moieties may include, without limitation, horseradish peroxidase (HRP), alkaline phosphatase (AP), glucose oxidase, or β-galactosidase.

"Optical moieties" may include, for example, any agents that may be used to produce contrast or signal using optical imaging such as luminescence or acousto-optical moieties.

"Magnetic moieties" may include, for example, a chelating agent for magnetic resonance agents. Chelators for magnetic resonance agents can be selected to form stable complexes with paramagnetic metal ions, such as Gd(III), Dy(III), Fe(III), and Mn(II). Other exemplary detectable agents may include radiolabel moieties. Exemplary radioactive labels may include, without limitation,⁹⁹Mo, ^99mTc, ^Cu, ⁶⁷Ga, ¹⁸⁶Re, ¹⁸⁸Re, ¹⁵³Sm, ¹⁷⁷Lu, ⁶⁷Cu, ¹²³I, ¹²⁴I, ¹²⁵I, ⁿC, ^X3N, ¹⁵0, and ¹⁸F.

"X-ray moieties" may include, for example, any agents that may be used to produce contrast or signal using X-ray imaging such as iodinated organic molecules or chelates of heavy metal ions.

"Photoacoustic imaging moieties" may include photoacoustic imaging-compatible agents such as methylene blue, single-walled carbon nanotubes (SWNTs), and gold nanoparticles.

Ultrasound imaging moieties may include, for example, any agents that may be used to produce contrast or signal using ultrasound imaging such as Levovist, Albunex, or Echovist.

A detectable agent may also be a nanoparticle -based moiety. A nanoparticle-based moiety is a nanoparticle that is capable of generating a signal. For example, silicon containing nanoparticles may be used to produce fluoresecence, luminescence, or another type of signal.

Other exemplary nanoparticle-based moieties include, without limitation, nanospheres such as Kodak X-SIGHT 650, Kodak X-SIGHT 691, Kodak X-SIGHT 751 (Fisher Scientific); metal oxide nanoparticles; and quantum dots such as EviTags (Evident Technologies) or Qdot probes

(Life Technologies).

As used herein, a "therapeutic agent" may be any substance that provides a therapeutic functionality when conjugated to any one of the aptamers described herein. Suitable therapeutic agents may include, without limitation, cytotoxic compounds, and particularly those shown to be effective in other drug conjugates. As used herein, a "cytotoxic compound" refers to any substance that disrupts the functioning of cells and/or causes the death of cells. Various therapeutic cytotoxic compounds are known in the art and may include, without limitation, DNA damaging agents, anti-metabolites, natural products and their analogs. Exemplary classes of cytotoxic compounds include enzyme inhibitors such as dihydrofolate reductase inhibitors, and thymidylate synthase inhibitors, tubulin inhibitors, DNA intercalators, DNA cleavers, topoisomerase inhibitors, the anthracycline family of drugs, the vinca drugs, the mitomycins, the bleomycins, the cytotoxic nucleosides, the pteridine family of drugs, diynenes, the podophyllotoxins, dolastatins, auristatins, maytansinoids, differentiation inducers, and taxols. More specifically, suitable cytoxic compounds may include 5-fluorouracil, aclacinomycin, activated Cytoxan, bisantrene, bleomycin, carmofur, CCNU, cis-platinum, daunorubicin, doxorubicin, DTIC, melphalan, methotrexate, mithromycin, mitomycin, mitomycin C, peplomycin pipobroman, plicamycin, procarbazine, retinoic acid, tamoxifen, taxol, tegafur, VP16, VM25, diphtheria toxin, botulinum toxin, geldanamycin, maytansinoids (including DM1), monomethylauristatin E (MMAE), monomethylauristatin F (MMAF), and maytansinoids (DM4) and their analogues. Exemplary cytotoxic compounds may also include therapeutic radiopharmaceuticals including, without limitation, ¹⁸⁶Re, ¹⁸⁸Re, ¹⁵³Sm, ⁶⁷Cu, ¹⁰⁵Rh, ^mAg, and ¹⁹²Ir.

The aptamer and agent may be "linked" either covalently or non-covalently. Additionally, the aptamer and agent may be linked using the 5' and/or 3' linkers described herein. The aptamer and agent may be linked at the 5' end and/or the 3' end of the aptamer. To link the aptamer and agent non-covalently, the aptamer and the agent may be linked by a tag system. A "tag system" may include any group of agents capable of binding one another with a high affinity. Several tag systems are well-known in the art and include, without limitation, biotin/avidin, biotin/streptavidin, biotin/NeutrAvidin, or digoxigenin (DIG) systems. In some embodiments, the tag system comprises biotin/avidin or biotin/streptavidin. In such embodiments, the aptamer may be modified at either the 5' or 3' end to include bio tin while the agent may be modified to include streptavidin or avidin. Alternatively, the aptamer may be modified at either the 5' or 3' end to include streptavidin or avidin while the agent may be modified to include bio tin.

In another aspect, the present invention relates to dimers, trimers, and tetramers including any one of the aptamers described herein. A "dimer" refers to the linking together of two aptamer molecules in order to, for example, to increase the stability and/or increase the circulation time of a polynucleotide in vivo. A "trimer" refers to the linking together of three aptamer molecules in order to, for example, to increase the stability and/or increase the circulation time of a polynucleotide in vivo. A "tetramer" refers to the linking together of four aptamer molecules in order to, for example, to increase the stability and/or increase the circulation time of a polynucleotide in vivo. The aptamer molecules may be linked together covalently, noncovalently, or a combination of both. The aptamer molecules may be linked at their 5' or 3' ends. To link the aptamers noncovalently, the aptamers may be linked by a tag system or through a scaffold system. In a further aspect of the present invention, pharmaceutical compositions including any of the aptamers described herein are provided. The pharmaceutical compositions may include a pharmaceutical carrier, excipient, or diluent (i.e., agents), which are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often a pharmaceutical composition may include an aqueous pH buffered solution. Examples of pharmaceutical carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™ brand surfactant, polyethylene glycol (PEG), and PLURONICS™ surfactant. In some embodiments, the pharmaceutical carrier may include a buffer including about 20 mM Hepes, pH 7.4; 150 mM NaCl; 1 mM CaCl₂; ImM MgCl₂; 5 mM KC1.

In a still further aspect, the present invention relates to methods for treating cancer in a subject. The methods may include administering to the subject a therapeutically effective amount of any one of the aptamers, dimers, trimers, tetramers, or pharmaceutical compositions described herein. The subject may be any mammal, suitably a human, domesticated animal such as a dog or cat, or a mouse or rat. Optionally, the present methods may further include administering a chemotherapeutic agent or radiation therapy to the subject.

Exemplary cancers in accordance with the present invention include, without limitation, colon, primary and metastatic breast, ovarian, liver, pancreatic, prostate, bladder, lung, osteosarcoma, pancreatic, gastric, esophageal, skin cancers (basal and squamous carcinoma; melanoma), testicular, colorectal, urothelial, renal cell, hepatocellular, leukemia, lymphoma, multiple myeloma, head and neck, and central nervous system cancers or pre-cancers.

Treating cancer includes, but is not limited to, reducing the number of cancer cells or the size of a tumor in the subject, reducing progression of a cancer to a more aggressive form, reducing proliferation of cancer cells or reducing the speed of tumor growth, killing of cancer cells, reducing metastasis of cancer cells or reducing the likelihood of recurrence of a cancer in a subject. Treating a subject as used herein refers to any type of treatment that imparts a benefit to a subject afflicted with a disease or at risk of developing the disease, including improvement in the condition of the subject (e.g., in one or more symptoms), delay in the progression of the disease, delay the onset of symptoms or slow the progression of symptoms, etc.

Optionally, the present methods may further include administering a chemotherapeutic agent and/or radiation therapy to the subject. Without being limited by theory, the present inventors conjecture (and demonstrate in the Examples) that aptamers that block nucleolin function in cancer cells can sensitize cancer cells to DNA-damaging agents such as chemotherapeutic agents and radiation therapy. In some embodiments, the aptamer-containing composition described herein is administered prior to, simultaneously with, or after the chemotherapeutic agent and/or radiation therapy. In some embodiments, the aptamer-containing composition is administered prior to the administration of the optional chemotherapeutic agent and/or radiation therapy.

Chemotherapeutic agents are compounds that may be used to treat cancer. Suitable chemotherapy agents may include, without limitation, 5-fluorouracil, aclacinomycin, activated Cytoxan, bisantrene, bleomycin, carmofur, CCNU, cis-platinum, daunorubicin, doxorubicin, DTIC, melphalan, methotrexate, mithromycin, mitomycin, mitomycin C, peplomycin pipobroman, plicamycin, procarbazine, retinoic acid, tamoxifen, taxol, tegafur, VP 16, or VM25. In some embodiments, the chemotherapeutic agent may be a DNA-damaging agent including, without limitation, cisplatin, carboplatin, picoplatin, oxaliplatin, methotrexate, doxorubicin, or daunorubicin, 5-fluorouracil, capecitabine, floxuridine, and gemcitabine, and the purine analogs 6-mercaptopurine, 8-azaguanine, fludarabine, and cladribine. The optional radiation therapy in the present methods may include one or more doses of between 1 Gy and 30 Gy. Suitably, the radiation therapy includes a single fraction dose of 12, 15, 18, 20, 21, 23, 25, or 28 Gy.

The chemotherapeutic agent and/or radiation therapy may be administered in any order in relation to the aptamer-containing compositions described herein, at the same time or as part of a unitary composition. The aptamer-containing composition and chemotherapeutic agent and/or radiation therapy may be administered such that one composition or therapy is administered before the other with a difference in administration time of 1 hour, 2 hours, 4 hours, 8 hours, 12 hours, 16 hours, 20 hours, 1 day, 2 days, 4 days, 7 days, 2 weeks, 4 weeks or more.

An "effective amount" or a "therapeutically effective amount" as used herein means the amount of a composition that, when administered to a subject for treating a state, disorder or condition is sufficient to effect a treatment (as defined above). The therapeutically effective amount will vary depending on the composition, formulation or combination, the disease and its severity and the age, weight, physical condition and responsiveness of the subject to be treated.

The compositions (i.e., those including the aptamers described herein) described herein may be administered by any means known to those skilled in the art, including, but not limited to, intratumoral, oral, topical, intranasal, intraperitoneal, parenteral, intravenous, intramuscular, subcutaneous, intrathecal, transcutaneous, nasopharyngeal, or transmucosal absorption. Thus the compositions may be formulated as an ingestable, injectable, topical or suppository formulation. Within broad limits, administration of larger quantities of the aptamer-containing compositions is expected to achieve increased beneficial biological effects than administration of a smaller amount. Moreover, efficacy is also contemplated at dosages below the level at which toxicity is seen.

It will be appreciated that the specific dosage administered in any given case will be adjusted in accordance with the aptamer-containing compositions being administered, the disease to be treated or inhibited, the condition of the subject, and other relevant medical factors that may modify the activity of the compositions or the response of the subject, as is well known by those skilled in the art. For example, the specific dose for a particular subject depends on age, body weight, general state of health, diet, the timing and mode of administration, the rate of excretion, medicaments used in combination and the severity of the particular disorder to which the therapy is applied. Dosages for a given patient can be determined using conventional considerations.

The maximal dosage for a subject is the highest dosage that does not cause undesirable or intolerable side effects. The number of variables in regard to an individual prophylactic or treatment regimen is large, and a considerable range of doses is expected. The route of administration will also impact the dosage requirements. It is anticipated that dosages of the compound will reduce symptoms of the condition at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% compared to pre-treatment symptoms or symptoms is left untreated. It is specifically contemplated that pharmaceutical preparations and compositions may palliate or alleviate symptoms of the disease without providing a cure, or, in some embodiments, may be used to cure the disease or disorder. The effectiveness of the aptamer-containing composition in treating the cancer or reducing the likelihood of resistance can be measured by tracking the growth of the tumor or the growth rate of the tumor or cancer cells. A decrease in tumor size or in the rate of tumor growth is indicative of treatment of the cancer.

The aptamers disclosed herein may also be used in methods of labeling or inhibiting nucleolin. As disclosed herein the aptamers provided bind to nucleolin and may be used to inhibit nucleolin. In some instances the aptamers are trafficked with the nucleolin to the nucleus of the cell when the aptamer is contacts the cell. The aptamers may be combined with an agent as described above and if the agent is a reporter moiety the agent may allow nucleolin to be labeled within the cell or to bring the agent in contact with nucleolin. Nucleolin may be contacted with the aptamer directly or indirectly in vivo, in vitro, or ex vivo. Contacting encompasses administration to a cell, a culture of cells, tissue, mammal, patient, or human expressing nucleolin. Further, contacting a cell includes adding an agent to a cell culture. Other suitable methods may include introducing or administering an agent to a cell, tissue, mammal, or patient using appropriate procedures and routes of administration as defined above.

The present disclosure is not limited to the specific details of construction, arrangement of components, or method steps set forth herein. The compositions and methods disclosed herein are capable of being made, practiced, used, carried out and/or formed in various ways that will be apparent to one of skill in the art in light of the disclosure that follows. The phraseology and terminology used herein is for the purpose of description only and should not be regarded as limiting to the scope of the claims. Ordinal indicators, such as first, second, and third, as used in the description and the claims to refer to various structures or method steps, are not meant to be construed to indicate any specific structures or steps, or any particular order or configuration to such structures or steps. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., "such as") provided herein, is intended merely to facilitate the disclosure and does not imply any limitation on the scope of the disclosure unless otherwise claimed. No language in the specification, and no structures shown in the drawings, should be construed as indicating that any non-claimed element is essential to the practice of the disclosed subject matter. The use herein of the terms "including," "comprising," or "having," and variations thereof, is meant to encompass the elements listed thereafter and equivalents thereof, as well as additional elements. Embodiments recited as "including," "comprising," or "having" certain elements are also contemplated as "consisting essentially of and "consisting of those certain elements.

Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if a concentration range is stated as 1% to 50%, it is intended that values such as 2% to 40%, 10% to 30%, or 1% to 3%, etc., are expressly enumerated in this specification. These are only examples of what is specifically intended, and all possible combinations of numerical values between and including the lowest value and the highest value enumerated are to be considered to be expressly stated in this disclosure. Use of the word "about" to describe a particular recited amount or range of amounts is meant to indicate that values very near to the recited amount are included in that amount, such as values that could or naturally would be accounted for due to manufacturing tolerances, instrument and human error in forming measurements, and the like. All percentages referring to amounts are by weight unless indicated otherwise.

No admission is made that any reference, including any non-patent or patent document cited in this specification, constitutes prior art. In particular, it will be understood that, unless otherwise stated, reference to any document herein does not constitute an admission that any of these documents forms part of the common general knowledge in the art in the United States or in any other country. Any discussion of the references states what their authors assert, and the applicant reserves the right to challenge the accuracy and pertinence of any of the documents cited herein. All references cited herein are fully incorporated by reference in their entirety, unless explicitly indicated otherwise. The present disclosure shall control in the event there are any disparities between any definitions and/or description found in the cited references.

Unless otherwise specified or indicated by context, the terms "a", "an", and "the" mean "one or more." For example, "a protein" or "an RNA" should be interpreted to mean "one or more proteins" or "one or more RNAs," respectively.

The following examples are meant only to be illustrative and are not meant as limitations on the scope of the invention or of the appended claims.

EXAMPLES Example 1 - Development of Nucleolin-binding Aptamers

With the goal of developing an aptamer that binds and/or inhibits the nucleolin protein, we performed a dual protein and cell selection via systematic evolution of ligands by exponential enrichment (SELEX) using a modified RNA library (FIG. 1). First, SELEX was performed against a recombinant nucleolin protein (SEQ ID NO: 493) resulting in an RNA library enriched in clones specific for nucleolin after 6 rounds of selection (FIG. 2A). As a 7^th round of SELEX did not improve the aptamer pool's affinity for the nucleolin protein (FIG. 2B), we moved forward with the pool of RNA from the 6^th round of SELEX (R6 NCL). To identify nucleolin- specific RNAs capable of binding to nucleolin on cell surface and subsequently transporting to the nucleus, the R6 NCL RNA pool was incubated with either MCF-7 or Panc-1 cells (FIG. 1). The nuclei were then isolated and the aptamer pool that reached this compartment was amplified. After 2 rounds of cellular selection with either MCF-7 or Panc-1 cells, the RNA library was further enriched for aptamers capable of binding to the nucleolin protein (FIGS. 2C & 2D).

We previously demonstrated that nucleolin interacts with Rad50, a member of the MRN complex, through its C-terminal RGG domain and that this interaction is essential for recruitment of nucleolin to the DNA damage site and repair of the DSB (Goldstein et al. 2013, PNAS). Thus, we estimated that in order to achieve a disruption of the nucleolin-Rad50 interaction and the inhibition of DSB repair required for radiosensitization, our nucleolin aptamer would need to bind to either the RGG domain itself or to the RBD domain in the proximity of the C-terminus. In fact, we found that the R6 NCL RNA aptamer pool binds to the RBD domain (FIGS. 3A-3B), suggesting that these aptamers may be able to inhibit the nucleolin-Rad50 interaction that is crucial for DSB repair.

High throughput sequencing of the SELEX pools from various selection rounds (rounds 3, 5, 7, and 9 - Panc-1 round 2), resulted in almost 8000 unique RNA families plus 78 ambiguous sequences, where RNA families are RNA sequences that differ by 4 nucleotides or less and ambiguous sequences are single RNA sequences that do not fit into a RNA family. The most representative sequence from each of the top 6 abundant families, designated Families A-F (FAM-A, etc., Tables 1-4), were transcribed to test their ability to bind to the nucleolin protein. Families B-F demonstrated specific binding to nucleolin while Family A did not appear to significantly bind the protein, suggesting that it may be an artifact resulting from PCR amplification (FIG. 4, Table 5). To make it easier to chemically synthesize the nucleolin aptamers, we sought to shorten their length. Thus, we designed truncates of the Families B-F aptamers (Tables 6-8). Several of these truncations resulted in improved affinity for nucleolin over the parent aptamers, with truncations Bvl, Dv2, Ev3, Ev5, and Fv3 demonstrating the best affinity (FIGS. 5A-5F). To further truncate the Ev3 aptamer, we designed 24 additional truncates of Ev3 (Tables 7 and 8). Several of these truncations, primarily Ev3.min21, Ev3.min22, and Ev3.min24 demonstrated a similar affinity for nucleolin compared to their parent Ev3 aptamer (FIGS. 9A-9D).

Table 1: Nucleolin Aptamer Sequences without 5' and 3' Constant Regions

FAM-E GGGAGAGAGGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCUG CUGUGCCACCCACCGCAUAACCCAGAGGUCGAUAGUACUGGAUCCCCC

C (SEQ ID NO: 11)

FAM-F GGGAGAGAGGAAGAGGGAUGGGACCACGCGCCAACGUGUCAGCUACA

CGCCGUGUUCCCCGGCAUAACCCAGAGGUCGAUAGUACUGGAUCCCCC

C (SEQ ID NO: 12)

Table 3: Representative Nucleolin Aptamer Sequences without 5' and 3' Constant Regions from All Families

AD CACCAGGUUCUGCUGUCCCCAAGCGCUGACCCAUCCUUCC 42

AE AAGAUCCGGUAACUCCCCACCGCAAUCACCGUCGACUACU 43

AF CCAUCUAGAUCUCCGUAGAUUCCCCCCGGCUCU UUCUCGC 44

AG CCAUCUGAACCCACAGAUUCCCCCAUCAUCAGCCACAGUG 45

AH CACUAAGUUGGUAGCCCCAACUGCCCCGACACGAGGAUGU 46

Al UUGUGCUCCGUGGCUCCCCGGACCAACCGCUUCCAGCAGU 47

AJ CAAUCACGCGUAGUACGUCGCGGAAGAUCCCCAUGCCGA 48

AK CACAUGGUACGCCCAAAAGCGAGGCCCGCUGCGUAGUGC 49

AL UGCCAUACGCGGUUCGAAGUCGAAGCCCGACAACCCGGCA 50

AM GUUAUUCACAUGCCUCCCGUGAAUCAACAAGAAU UCCUUG 51

AN AAAGAUCUAGACUGUAAGUCUCCAAUCGCCCAGUUAAUUC 52

AO GCCCAAUCGCCAGUGGAACGCGCUGAAGGAUCUGCACCC 53

AP UGCAACGUAAAAGAGAGUCAUCUCAGGCUAGUCGUCUACC 54

AQ GUGUACGCCAAGUCGAGGCCCGACCGUACCCAUACGCGAC 55

AR UUAGCUCUACUUUCCUCUUCAGUAAGACUAACCGCUUCUU 56

AS UCCAAGCGGAGGCCCCGCACCCACCCUCCAACGGGCACGG 57

AT UAUCGCUCCACAACGACUCCCGUGGACUACCCAAUUCCAA 58

AU GUCGUGCCCAAGUGAAGGCCUCACGCACGCAUCCUAACCU 59

AV AAGAUCUGCGCCAGCACAAUCACCAUCGUCCUGAGAAUGG 60

AW AUGCCAAGCAGUGGCCCUGCCACCCACCUAUCACUGUCGA 61

AX AACAGACCAAGCAGCGGCCCUGCUCUGCCAUCAUACGCCU 62

AY GUCAUUCGCUGACGAAUCAACAUGAAUUCCUAACUGCUGA 63

AZ ACACGCCAAGCUGGUAGCCCCAGCCGUGCCCAUUACGGCC 64

BA UAGCCAAGCAGCAGCCCUGCCAACCCAUCCUACCCGGGCG 65

BB GCCCAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGGG 66

BC AAGAUCUCGUCAUGCUUUGACGUCAAUCACCAUUGUUCCC 67

BD AUCCCCCAGGAUGAGCACGUUGCCAUGGACUGGCUAUCC 68

BE CUGUUACAGUCUCGCGUAACCCCCCCAUCGAUGUCCUCGA 69

BF AGCCAGCUUUCGGCAAACCGAAUUCACUCCACCCUGCUCA 70

BG CACGGUAUAACCUCCUCAUAUACCUGCUGUGCCACCCGCG 71

BH CCGGAAGAUCUGCUCGCACUAGCCGGAGCCCAAUCACGGC 72

Bl CCUGCCGAACGGCUAAGUCGCAGCCCGACCCGCGGCAGGG 73

BJ CUCCGACCCGCGGACGAAGUCAACUUCCACAGUCCCACAC 74

BK ACAUUAGGAUCUGCGUGAUGGGGAUCACCCGCUACAUGUC 75

BL UCUAAGAUGGGGAAGAUCUCCGGAGCACCGGGCAAUCACC 76

BM CUAUUCGAGUUCCCACGAAUCCCCCAUCGAGAACCUAC 77

BN UGCCAAGCCGAGGCCCGGCCAGCAUCCCUCACGAGAGAGG 78

BO GCCAAGCACGUAGCCCGUGCCCCCACCCGCCUGUGUGCUG 79

BP UGCCAAGCACGAAGCCCGUGCCCCCAUCCAGAGUGUGAGA 80 BQ AGCCAGCUUU UGCAUACCACGUGCAAUUCACUCCACCCGUCA 81

BR CUUUGUAAACCCGGCAAACAAAAUCAACUUCCAUCAUCAA 82

BS CCAU UGUAGCGACCACACAAUUCCCCAUCGGACAGCAUGG 83

BT CUCUCGCCGU UCCCAGGCACGACAAAAUCAACUUCCCGCU 84

BU AAGCCAAGCCGCGGCCCGGCCUUCCCAUGUGCUACUAGAG 85

BV CCAAAUGCCAAAGCCGUAGCCCGGCCAGUAGCCCACACGUC 86

BW CCAU UACGCGACGUAAU UCCCCCAUCGUUUCCUCGUUAAG 87

BX CCAUCUAGAUCUCCGUAGAUUCCCCGGCUCUUUCUCGC 88

BY ACUGUCUGCAUACACGGUAUGCCCAACGCCAUCCAAACCG 89

BZ ACCUGCGGCUAUUGCCAGCGCCAUAAGACCCUCCACAGUA 90

Table 4: Variant Nucleolin Aptamer Sequences without 5' and 3' Constant Regions from

All Families

AAGAUCCUCGCGCAUCUGCCGAGCAAUCACCAUCGGACU 115

AAAGAUCCUCGCGCAUCUGCCGAGCAAUCACCAUCGGACG 116

AAGAUCCUCGCGCACCUGCCGAGCAAUCACCAUCGGACG 117

H CCA A A U G CC A AG CCG UAGCCCGGCCAGUAGCCCACACGUC 118

CCAAAAUGCCAAGCCGUAGCCCGGCCAGUAGCCCACACGUC 119

CCAAAUGCCAAGCCGUAGCCCGGCCAGUAGCCCACACGAC 120

CCAAAUGCCAAGCCGUAGCCCGGCCAGUAGCCCACACGUA 121

1 UGCCAAGCCGAGGCCCGGCCACCAUCCACUGAUAGUGGGC 122

UGCCAAGCCGAGGCCCGGCCACCAUCCACUGAUAGUGGGA 123

UGCCAAGCCGAGGCCCGGCCACCAUCCACUGAUAGUGGG 124

UGCCAAGCCGAGGCCCGGCCACCAUCCACUGAUAGUGGGU 125

J AAGAUCCUGACGCGACACAGCAAUCACCAUCGAACCAGCU 126

AAGAUCCUGACGCGACACAGCAAUCACCAUCGAACCAGCC 127

K AAGAUCUGCGGCAACGCACAAUCACCAUCGAUUCCGAAUU 128

AAGAUCUGCGGCAACGCACAAUCACCAUCGAUUCCGAAUG 129

AAGAUCUGCGGCAACGCACAAUCACCAUCGAUUCCGAAUC 130

AAGAUCUGCGGCAACGCACAAUCACCAUCGAUUCCGAACU 131

AAGAUCUGCGGCAACGUACAAUCACCAUCGAU UCCGAAUU 132

L GAGCUCUCGAUUUCCUCCGCGACACCCAUCCAAACCUCA 133

AGCUCUCGAU UUCCUCCGCGACACCCAUCCAAACCUCA 134

GAGCUCUCGAUUUCCUCCGCGACACCCAUCCAAACCUCG 135

M CUCUCCGGUCUACCAUCCGGACCGGCGACAAAGUCAACUU 136

CUCUCCGGUCUACCACCCGGACCGGCGACAAAGUCAACUU 137

N AAGAUCUGCUAUGCACAAUCACCAUCGGGCGCUCCGGGGAA 138

AAGAUCUGCUAUGCACAAUCACCAUCGGGCGCUCCGGGAA 139

AAGAUCUGCUACGCACAAUCACCAUCGGGCGCUCCGGGGAA 140

0 UUGACUCUGCUGCGUAGUUCGCACCAAGAUCAACCACUUC 141

UUGACUCUGCUGCGUAGUUCGCACCAAGAUCAACCACUUCC 142

UUGACUCUGCUGCGUAGCUCGCACCAAGAUCAACCACUUC 143

UUGACUCUGCUGCGCAGUUCGCACCAAGAUCAACCACUUC 144

UUGACUCUGCUGCGUAGUCCGCACCAAGAUCAACCACUUC 145

P UACCAAGUCGUGGCCCGACUACCCAGCACGAUGCGCAA 146

U ACC AAAG U CG U G G CCCG AC U ACCCAG C ACG AU G CG CAA 147

UACCAAGUCGUGGCCCGACUACCCAGCACGGUGCGCAA 148

UACCAAGUCGUGGCCCGACUACCCAGCACGAUGCGCAG 149

UACCAAGUCGUGGCCCGACUACCCAGCACAAUGCGCAA 150

UACCAAGUCGCGGCCCGACUACCCAGCACGAUGCGCAA 151

Q CUAUUCGAGUUCCCACGAAUCCCCCCAUCGAGAACCUAC 152

CUAUUCGAGUUCCCACGAAUCCCCCCAUCGAGAACCUA 153 CUAUUCGAGUUCCCACGAAUCCCCCCAUCGAGAACCUAU 154

CUAUUCGAGUUCCCACGAAUCCCCCCAUCGAGAACCUAA 155

R UGCCAAGCCGAGGCCCGGCCACCGUCCCCGCGGCUGAUGA 156

UGCCAAAGCCGAGGCCCGGCCACCGUCCCCGCGGCUGAUGA 157

UGCCAAGCCGAGGCCCGGCCACCGUCCCCGCGGCUGAUCGA 158

UGCCAAGCCGAGGCCCGGCCACCGUCCCCGCGGCUGAUGG 159

UGCCAAGCCGAGGCCCGGCCACCGUCCCCGCGGCUGACGA 160

S AAUGAUCUCGCCAAUGGGCGACAAUCACCAUGUCUUCACA 161

AACGAUCUCGCCAAUGGGCGACAAUCACCAUGUCUUCACA 162

AAUGAUCUCGCCAAUGGGCGACAAUCACCAUGUCUUCACG 163

AAUGAUCUCGCCAAUGUGCGACAAUCACCAUGUCUUCACA 164

T UCAGUGCGCCAAGUGGAGGCCCCACCGCAGCCCAUCAA 165

UCAGUGCGCCAAGUGGAGGCCCCACCGCAGCCCAUCGA 166

UCAGUGCGCCAAGUGGAGGCCCCACCGCAGCCCAUCAG 167 u UGUAUGCCAGCUUUGACGAUAACUGUCGCGCGUCAAUUCA 168

V UACGCCAAAGUGGAGCCCACUCGUACCCCAUCAUGAGCUG 169

UACGCCAAAGUGGAGCCCACUCGUACCCCAUCAUGAGCCUG 170

UACGCCAAAGUGGAGCCCACUCGUACCCCAUCAUGAGCUC 171

UACGCCAAAGUGGAGCCCACUCGUACCCCAUCAUGGGCUG 172

UACGCCAAAGUGGAGCCCACUCGUAUCCCAUCAUGAGCUG 173

UACGCCAAAGUGGAGCCCACUCGUACCCCAUCGUGAGCUG 174

UACGCCAAAGUGGAGCCCACUCGUACUCCAUCAUGAGCUG 175

CACGCCAAAGUGGAGCCCACUCGUACCCCAUCAUGAGCUG 176

UACGCCAAAGUGGAGCCCACUCGCACCCCAUCAUGAGCUG 177

UACGCCAAAGUGGAGCCCACUCGUACCCCAUCAUGAGCUA 178 w CCGCCAGCUU UGGGUACCCUGACCAAUUCACGGCCAUCCA 179

CCGCCAGCUU UGGGUACCCUGACCAAUUCACGGCCAUCCG 180

CCGCCCAGCUUUGGGUACCCUGACCAAUUCACGGCCAUCCA 181

X GUAAUUGUCUGAGACCACCGGACAAUCAACAAGAAAUCCU 182

GUAAUUGUCUGAGACCACCGG AC A A U C A AC A AG A A A A U CC U 183

UAAUUGUCUGAGACCACCGGACAAUCAACAAGAAAUCCU 184

Y UCAGGCCAAAGUGUGAUAGCCACACCCGCACCCAUCAGGA 185

UCAGGCCAAAGUGUGAUAGCCACACCCGCACCCAUCAGA 186

UCAGGCCAAAGUGUGAUAGCCACACCCGCACCCAUCAGG 187 z CCGACCGCCGACCAGGGUGCCACUCGUACCCCUGUCCGCC 188

CCGACCGCCGACCAGGGUGCCACUCGUACCCCUGUCCGCCC 189

CCGACCGCCGACCAGGGUGCCACUCGUACCCCUGUCCCGCC 190

CCGACCGCCGACCAGGGUGCCACUCGUACCCCUGUCCGC 191

AA UGCCAAGUCGAAGCCCGACCACGCCAUCCCUAACAGUGCC 192 UGCCAAAGUCGAAGCCCGACCACGCCAUCCCUAACAGUGCC 193

UGCCAAGUCGAAGCCCGACCACGCCAUCCCUAACAGUGC 194

UGCCAAGUCGAAGCCCGACCACGCCAUCCCUAACGGUGCC 195

UGCCAAGUCGAAGCCCGACCACGCCAUCCCUAACAGUGCA 196

UGCCAAGUCGAGGCCCGACCACGCCAUCCCUAACAGUGCC 197

UGCCAAGCCGAAGCCCGACCACGCCAUCCCUAACAGUGCC 198

AB ACUUGUGCUGAGUCGCCAAAGUGAGGCCCACUCGCCAGCA 199

GCU UGUGCUGAGUCGCCAAAGUGAGGCCCACUCGCCAGCA 200

ACCUGUGCUGAGU CG CCA A AG UGAGGCCCACUCGCCAGCA 201

AC CCGCCAGCUCCUCUGAGGCACAAGAGGUUCACGGUGAUCC 202

CCGCCAGCUCCUCUGAGGCACAAGAGGUUCACGGUGAUCCC 203

AD CACCAGGUUCUGCUGUCCCCAAGCGCUGACCCAUCCUUCC 204

CACCAGGUUCUGCUAUCCCCAAGCGCUGACCCAUCCUUCC 205

CACCAGGUUCUGCUGUCUCCAAGCGCUGACCCAUCCUUCC 206

CACCAGGUUCUGCUGUUCCCAAGCGCUGACCCAUCCUUCC 207

CACCAGGUCCUGCUGUCCCCAAGCGCUGACCCAUCCUUCC 208

CACCAGGCUCUGCUGUCCCCAAGCGCUGACCCAUCCUUCC 209

CACCAGGUUCUGCUGUCCUCAAGCGCUGACCCAUCCUUCC 210

AE AAGAUCCGGUAACUCCCCACCGCAAUCACCGUCGACUACU 211

AAGAUCCGGUGACUCCCCACCGCAAUCACCGUCGACUACU 212

AAGAUCCGGUAACUCCCUACCGCAAUCACCGUCGACUACU 213

AAAGAUCCGGUAACUCCCCACCGCAAUCACCGUCGACUACU 214

AF CCAUCUAGAUCUCCGUAGAUUCCCCCCGGCUCU UUCUCGC 215

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUCGU 216

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUCGA 217

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUCG 218

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUCGC 219

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUCAC 220

CCAUCUAGAUCUCCGUAGAUUUCCCCCGGCUCUUUCUCGC 221

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUUCCUCGC 222

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUCUCUCGC 223

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUUGC 224

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCCCUUUCUCGC 225

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUCUC 226

CCAUCUAGAUCUCCGUAGAUUCCCCCGGCCUCU UUCUCGC 227

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUCCC 228

CCAUCUAGAUCUCCGUAGAUUCCCCCGGGCUCUU UCUCGUC 229

AG CCAUCUGAACCCACAGAUUCCCCCAUCAUCAGCCACAGUG 230

CCAUCUGAACCCACAGAUUCCCCCAUCAUCAGCCACAGUA 231 CCAUCUGAACCCACAGAUUCCCCCAUCAUCAGCCACAGCG 232

CCAUCUGAACCCACAGAUUCCCCCAUCAUCAGCCACAGUC 233

CCAUCUGAACCCACAGAUUCCCCCAUCAUCAGCCACGGUG 234

AH CACUAAGUUGGUAGCCCCAACUGCCCCGACACGAGGAUGU 235

CACUAAGUUGGUAGCCCCAACUGCCCCGACACGAGGAUGUC 236

CACUAAGUUGGUAGCCCCAACUGCCCCGACACGAGGAUGC 237

Al UUGUGCUCCGUGGCUCCCCGGACCAACCGCUUCCAGCAGU 238

UUGUGUUCCGUGGCUCCCCGGACCAACCGCUUCCAGCAGU 239

UUGUGCUCCGUGGCUCCCCGGACCAACCGCUUCCAGCAGC 240

UUGCGCUCCGUGGCUCCCCGGACCAACCGCUUCCAGCAGU 241

AJ CAAUCACGCGUAGUACGUCGCGGAAGAUCCCCAUGCCGA 242

CAAUCACGCGUAGUACGUCGCGGAAGAUCCCCAUGCCGG 243

CAAUCACGCGUAGUACGUCGCGGAAGAUCCCCAUGCCAA 244

CAAUCACGCGUAGUACGUCGCGGAAGAUCCCCAUGCCGU 245

CAAUCACGCGUAGCACGUCGCGGAAGAUCCCCAUGCCGA 246

CAAUCACGCGUAGUACGUCGCGGAGGAUCCCCAUGCCGA 247

AK CACAUGGUACGCCCAAAAGCGAGGCCCGCUGCGUAGUGC 248

CACAUGGUACGCCCCAAAGCGAGGCCCGCUGCGUAGUGC 249

CACAUGGUACGCCCAAAGCCGAGGCCCGCUGCGUAGUGC 250

CACAUGGUACGCCCAAAAGCGAGGCCCGCUGCGUAGUG 251

AL UGCCAUACGCGGUUCGAAGUCGAAGCCCGACAACCCGGCA 252

UGCCAUACGCGGUUCGAAGUCGAAGCCCGACAACCCCGGCA 253

UGCCAUACGCGGUUCGAAGUCGAGGCCCGACAACCCGGCA 254

AM GUUAUUCACAUGCCUCCCGUGAAUCAACAAGAAU UCCUUG 255

UUAUUCACAUGCCUCCCGUGAAUCAACAAGAAUUCCUUG 256

GUUAUUCACAUGCCUCCCGUGAAUCAACAAGAAU UCCUCG 257

GUUAUUCACAUGCCUCUCGUGAAUCAACAAGAAUUCCUUG 258

259

AN AAAGAUCUAGACUGUAAGUCUCCAAUCGCCCAGUUAAUUC 260

AAAAGAUCUAGACUGUAAGUCUCCAAUCGCCCAGUUAAUUC 261

AAAGAUCUAGACUGUAAGUCUCCAAUCGCCCAGUAAUUC 262

AO GCCCAAUCGCCAGUGGAACGCGCUGAAGGAUCUGCACCC 263

GCCCAAUCGCCAGUGGAACGCGCUGAAGGAUCUGCACC 264

GCCCAAUCGCCAGUGGAACGCACUGAAGGAUCUGCACCC 265

GCCCAAUCGCCAGUGGAACGCGCUGAAGGAUCUGCACCCC 266

CCCAAUCGCCAGUGGAACGCGCUGAAGGAUCUGCACCC 267

GCCCAAUCGCCAGCGGAACGCGCUGAAGGAUCUGCACCC 268

AP UGCAACGUAAAAGAGAGUCAUCUCAGGCUAGUCGUCUACC 269

UGCAACGUAAAAGAGAGUCAUCUCAGGCUAGUCGUCUAC 270 AQ GUGUACGCCAAGUCGAGGCCCGACCGUACCCAUACGCGAC 271

UGUACGCCAAGUCGAGGCCCGACCGUACCCAUACGCGAC 272

GUGUACGCCAAGUCGAGGCCCGACCGUACCCAUACGCGGC 273

GUGUACGCCAAGUCGAGGCCCGACCGUACCCAUACGCGAU 274

AR UUAGCUCUACUUUCCUCUUCAGUAAGACUAACCGCUUCUU 275

UUAGCUCUACUUUCCUCUUCAGUAAGACUAACCGCUUCCU 276

UUAGCUCUACUUUCCUCUUCAGUAAGACUAACCGCUUCUC 277

UUAGCUCUACUUUCCUCUUCAGUAAGACUAACCGCUCCUU 278

AS UCCAAGCGGAGGCCCCGCACCCACCCUCCAACGGGCACGG 279

UCCAAGCGGAGGCCCCGCACCCACCCUCCAACGGGCACGC 280

UCCAAGCGGAGGCCCCGUACCCACCCUCCAACGGGCACGG 281

UCCAAGCGGAGGCCCCGCACCCACCCCCCAACGGGCACGG 282

UCCAAGCGGAGGCCCCGCACCCACCCUCCAACGGGCACGA 283

UCCAAAGCGGAGGCCCCGCACCCACCCUCCAACGGGCACGG 284

UCCAAGCGGAGGCCCCGCACCCACCCUCCAACGGGCACAG 285

AT UAUCGCUCCACAACGACUCCCGUGGACUACCCAAUUCCAA 286

UAUCGCUCCACAACGACUCCCGUGGACUACCCAAUUCCAG 287

UAUCGCUCCACAACGACUCCCGUGGACUACCCAAUUCCAAA 288

UAUCGCUCCACAACGACUCCCGUGGACUACCCAAUUCCAU 289

AU GUCGUGCCCAAGUGAAGGCCUCACGCACGCAUCCUAACCU 290

U CG U GCCCAAG UGAAG G CC U CACG CACGC AU CCU AACC U 291

GUCGUGCCCAAGUGAAGGCCUCACGCACGCAUCCUAACCC 292

AV AAGAUCUGCGCCAGCACAAUCACCAUCGUCCUGAGAAUGG 293

AAGAUCUGCGCCAGCACAAUCACCAUCGUCCUGAGAAUGC 294

AAGAUCUGCGCCAGCACAAUCACCAUCGUCCUGAGAAUGA 295

AAGAUCUGCGCCAGCACAAUCACCAUCGUCCUGAGAGUGG 296

AAGAUCUGCGCCAGCACAAUCACCAUCGUCCUGGGAAUGG 297

AW AUGCCAAGCAGUGGCCCUGCCACCCACCUAUCACUGUCGA 298

A U G CCA AG CAGUCGGCCUGCCACCCACCUAUCACUGUCGA 299

AUGCCAAGCAGUGGCCCUGCCACCCACCUAUCACUAUCGA 300

AUGCCAAGCAGUGGCCCUGCCACCCACCUACCACUGUCGA 301

AUGCCAAGCAGCGGCCCUGCCACCCACCUAUCACUGUCGA 302

AX AACAGACCAAGCAGCGGCCCUGCUCUGCCAUCAUACGCCU 303

GACAGACCAAGCAGCGGCCCUGCUCUGCCAUCAUACGCCU 304

AACAGACCAAGCAGUGGCCCUGCUCUGCCAUCAUACGCCU 305

AACAGACCAAGCAGCGGCCCUGCUCUGCCAUCAUACGCCC 306

AACAGACCAAGCAGCGGCCCUGCUCUGCCAUCAUACACCU 307

ACAGACCAAGCAGCGGCCCUGCUCUGCCAUCAUACGCCU 308

AACAGACCAAGCAGCGGCCCUGCUCUGCCAUCAUACGCCCU 309 AY GUCAUUCGCUGACGAAUCAACAUGAAUUCCUAACUGCUGA 310

UCAUUCGCUGACGAAUCAACAUGAAUUCCUAACUGCUGA 311

GUCAUUCGCUGACGAAUCAACAUGAAUUCCUAACUGCCGA 312

GUCAUUCGCUGACGAAUCAACAUGAAUUCCUAACUGCUGG 313

AZ ACACGCCAAGCUGGUAGCCCCAGCCGUGCCCAUUACGGCC 314

ACACGCCAAGCUGGUAGCCCCAGCCGUGCCCAUUACGGC 315

ACACGCCAAGCUGGUAGCCCCAGCCGUGCCCAUUACGGUC 316

ACACGCCAAGCUGGUAGCCCCAGCCGUACCCAUUACGGCC 317

BA UAGCCAAGCAGCAGCCCUGCCAACCCAUCCUACCCGGGCG 318

UAGCCAAGCAGCAGCCCUGCCAACCCAUCCUACCCGGCG 319

UAGCCAAGCAGCAGCCCUGCCAACCCAUCCUACCCGGGCA 320

UAGCCAAGCAGCAGCCCUGCCAACCCAUCCUACCCGGGUG 321

UAGCCAAGCAGCGGCCCUGCCAACCCAUCCUACCCGGGCG 322

BB GCCCAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGGG 323

GCCCAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGG 324

CCCAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGGG 325

CCCAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGG 326

GCCCAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGGC 327

GCCCAAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGGG 328

GCCCAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGGA 329

GCCCCAAGGCGAGGCCCGCCGCUCCAUCCAGACGCUGAGGG 330

BC AAGAUCUCGUCAUGCUUUGACGUCAAUCACCAUUGUUCCC 331

AAGAUCUCGUCAUGCUUUGACGUCAAUCACCAUUGUUCC 332

AAGAUCUCGUCAUGCUUUGACGCCAAUCACCAUUGUUCCC 333

AAGAUCUCGUCAUGCUUUGACGUCAAUCACCAUUGUUCCA 334

AAGAUCUCGUCAUGCUUUGACGUCAAUCACCAUUGUUCCU 335

AAGAUCUCGUCAUGCUUUGACGUCAAUCACCAUUGUUCCCC 336

AAAGAUCUCGUCAUGCUUUGACGUCAAUCACCAU UGUUCCC 337

AAGAUCUCGUCAUGCCU UGACGUCAAUCACCAUUGUUCCC 338

BD AUCCCCCAGGAUGAGCACGUUGCCAUGGACUGGCUAUCC 339

AUCCCCAGGAUGAGCACGUUGCCAUGGACUGGCUAUCC 340

BE CUGUUACAGUCUCGCGUAACCCCCCCAUCGAUGUCCUCGA 341

CUGUUACAGUCUCGCGUAACCCCCCCAUCGAUGUCCUCGG 342

CUGUUACAGUCUCGAGUAACCCCCCCAUCGAUGUCCUCGA 343

CUGUUACAGUCUCGCGUAACCCCUCCAUCGAUGUCCUCGA 344

CUGUUACAGCCUCGCGUAACCCCCCCAUCGAUGUCCUCGA 345

CUGUUACAGUCUCCCGUAACCCCCCCAUCGAUGUCCUCGA 346

BF AGCCAGCUUUCGGCAAACCGAAUUCACUCCACCCUGCUCA 347

AGCCAGCUUUCGGCAAACCGAAUUCACUCCACCCUCCUCA 348 AGCCAGCUUUCGGCAAACCGAAUUCACUCCGCCCUGCUCA 349

AGCCAGCUUUCGGCAAACCGAAUUCACUCCACCCUGCU 350

AGCCAGCUUUCGGCGAACCGAAUUCACUCCACCCUGCUCA 351

AGCCAGCUUUCGGCAAACCGAAUUCACUCCACCCUGCUCG 352

AGCCAGCUUUCGGCAAACCGAAUUCACUCCACCCUGCUC 353

AGCCAGCUUUCGGCAAACCGAAUUCACUCCACCCUGCACA 354

BG CACGGUAUAACCUCCUCAUAUACCUGCUGUGCCACCCGCG 355

CACGGUAUAACCUCCUCAUAUACCUGCUGUGCCACCCGCA 356

CACGGUAUAACCUCCUCAUAUACCUGCUGUGCCACCCACCG 357

CACGGUAUAACCUCCUCAUAUACCUGCUGUGCCACCCGCU 358

CACGGUAUAACCUCCUCAUAUACCUGCUGUGCCACCCACG 359

CACGGUAUAACCUCCUCAUAUACCUGCUGUGCCACCCGUG 360

CACGGUAUAACCUCCUCAUAUACCUGCUGUGCCGCCCGCG 361

BH CCGGAAGAUCUGCUCGCACUAGCCGGAGCCCAAUCACGGC 362

CCGGAAGAUCUGCUCGCACUAGUCGGAGCCCAAUCACGGC 363

CCGGAGGAUCUGCUCGCACUAGCCGGAGCCCAAUCACGGC 364

CCGGAAGAUCUGCUCGCAUUAGCCGGAGCCCAAUCACGGC 365

Bl CCUGCCGAACGGCUAAGUCGCAGCCCGACCCGCGGCAGGG 366

CCUGCCGAACGGCUAAGUCGCAGCCCGACCCGCGGCAGG 367

CCUGCCGAACGGCUAAGUCGCAGCCCGACCCGCGGCAGGA 368

CCUGCCGAACGGCCAAGUCGCAGCCCGACCCGCGGCAGGG 369

CCUGCCGAACGGCUAAGUCGCGGCCCGACCCGCGGCAGGG 370

BJ CUCCGACCCGCGGACGAAGUCAACUUCCACAGUCCCACAC 371

CUCCGACCCGCGGACGAAGUCAACUUCCACAGUCCCACAA 372

CUCCGACCCGCGGACGAAGUCAACUUCCACAGUCCCACACAC 373

CUCCGACCCGCGGACGAAGUCAACUUCCACAGUCUCACAC 374

CUCCGACCCGCGGACGAAGUCAACUUCCACAGUCCCACAU 375

CUCCGACCCGCGGACGAAGUCAACUUCCACAGUCCCGCAC 376

CUCCGACCCGCGGACGAAGUCAACUUCCACGGUCCCACAC 377

CUCCGACCCGCGGACGAAGUCAACUUCCACAGUCCCAUAC 378

BK ACAUUAGGAUCUGCGUGAUGGGGAUCACCCGCUACAUGUC 379

ACAUUUAGGAUCUGCGUGAUGGGGAUCACCCGCUACAUGUC 380

GCAUUAGGAUCUGCGUGAUGGGGAUCACCCGCUACAUGUC 381

ACAUUAGGAUCUGCGCGAUGGGGAUCACCCGCUACAUGUC 382

BL UCUAAGAUGGGGAAGAUCUCCGGAGCACCGGGCAAUCACC 383

UCUAAGAUGGGGAAGAUCUCCGGAGCACCGGGCAAUCACCC 384

CCUAAGAUGGGGAAGAUCUCCGGAGCACCGGGCAAUCACC 385

UCUAAGGUGGGGAAGAUCUCCGGAGCACCGGGCAAUCACC 386

UCUAAGAUGGGGAAGAUCUCCGGAGCGCCGGGCAAUCACC 387 BM CUAUUCGAGUUCCCACGAAUCCCCCAUCGAGAACCUAC 388

CUAUUCGAGUUCCCACGAAUCCCCCCAUCAGAACCUAC 389

CUACUCGAGU UCCCACGAAUCCCCCAUCGAGAACCUAC 390

CUAUUCGAGUUCCCACGAAUCCCCCAUCAAGAACCUAC 391

BN UGCCAAGCCGAGGCCCGGCCAGCAUCCCUCACGAGAGAGG 392

UGCCAAAGCCGAGGCCCGGCCAGCAUCCCUCACGAGAGAGG 393

UGCCAAGCCGAGGCCCGGCCAGCAUCCCUCACGAGAGAGC 394

UGCCAAGCCGAGGCCCGGCCAGCAUCCCUCACGAGAGAG 395

UGCCAAGCCGAGGCCCGGCCAGCAUCCCCCACGAGAGAGG 396

UGCCAAGCCGAGGCCCGGCCAGCAUCCCUCACGAGAGAGA 397

UGCCAAGCCGGGGCCCGGCCAGCAUCCCUCACGAGAGAGG 398

UGCCAAGCCGAGGCCCGGCCAGCAUCCCUCACGAGAGGG 399

BO GCCAAGCACGUAGCCCGUGCCCCCACCCGCCUGUGUGCUG 400

CCAAGCACGUAGCCCGUGCCCCCACCCGCCUGUGUGCUG 401

GCCAAGCACGUAGCCCGUGCCCCCACCCGCCUGUGUGCGG 402

GCCAAGCACGUAGCCCGUGCCCCCACCCACCUGUGUGCUG 403

GCCAAGCACGUAGCCCGUGCCCCCACCCGCCUGUGUGCUC 404

GCCAAGCACGUAGCCCGUGCCCCCACCCGCCUGUGUGCCG 405

GCCAAAGCACGUAGCCCGUGCCCCCACCCGCCUGUGUGCUG 406

GCCAAGCACGUAGCCCGUGCCCCCACCCGCCUGUGUGCUA 407

BP UGCCAAGCACGAAGCCCGUGCCCCCAUCCAGAGUGUGAGA 408

UGCCAAAGCACGAAGCCCGUGCCCCCAUCCAGAGUGUGAGA 409

UGCCAAGCACGAAGCCCGUGCCCCCAUCCAGAGUGUGGGA 410

UGCCAAGCACGAGGCCCGUGCCCCCAUCCAGAGUGUGAGA 411

UGCCAAGCACGAAGCCCGUGCCCCCAUUCAGAGUGUGAGA 412

UGCCAAGCACGAAGCCCGUGCCCCCAUCCAGAGUGCGAGA 413

UGCCAAGCACGAAGCCCGUGCCCCCAUCCAGAGCGUGAGA 414

UGCCAAGCACGAAGCCCGUGCCCCCAUCCAGAGUGUGAGG 415

UGCCAAGCACGAAGCCCGUGCCCCCAUCCAGGGUGUGAGA 416

BQ AGCCAGCUUU UGCAUACCACGUGCAAUUCACUCCACCCGUCA 417

AGCCAGCUUUGCCAUACCACGUGCAAUUCACUCCACCCGUCA 418

AGCCAGCCUUUGCAUACCACGUGCAAUUCACUCCACCCGUCA 419

AGCCAGCUUU UGCAUACCACGUGCAAUUCACUCCACCCGUCG 420

AGCCAGCUUU UGCACACCACGUGCAAUUCACUCCACCCGUCA 421

AGCCAAGCUUUGCAUACCACGUGCAAUUCACUCCACCCGUCA 422

BR CUUUGUAAACCCGGCAAACAAAAUCAACUUCCAUCAUCAA 423

CUUUGUAAACCCGGCAAACAAAAUCAACUUCCAUCACCAA 424

BS CCAU UGUAGCGACCACACAAUUCCCCAUCGGACAGCAUGG 425

CCAU UGUAGCGACCACACAAUUCCCCAUCGGACAGCAUG 426 CCAUUGUAGCGACCACACAAUUCCCCAUCGGACAGCGUGG 427

CCAUUGUAGCGACCACACAAUUCCCCAUCGGACAGCACGG 428

CCAUUGUAGCGACCACACAAUUCCCCAUCGGACAGCAUGC 429

CCAUUGUAGCGACCACACAAUCCCCCAUCGGACAGCAUGG 430

CCAUUGUAGCGACCACACAAUUCCCCAUCGGACAGCAUGU 431

BT CUCUCGCCGUUCCCAGGCACGACAAAAUCAACUUCCCGCU 432

CUCUCGCCGUUCCCAGGCGCGACAAAAUCAACUUCCCGCU 433

CUCUCGCCGUUCCCGGGCACGACAAAAUCAACUUCCCGCU 434

CUCUCGCCGUUCCCAGGCACGACAAAAUCAACUUCCCGCA 435

BU AAGCCAAGCCGCGGCCCGGCCUUCCCAUGUGCUACUAGAG 436

AAAGCCAAGCCGCGGCCCGGCCUUCCCAUGUGCUACUAGAG 437

AAGCCAAAGCCGCGGCCCGGCCUUCCCAUGUGCUACUAGAG 438

GAGCCAAGCCGCGGCCCGGCCUUCCCAUGUGCUACUAGAG 439

AGCCAAGCCGCGGCCCGGCCUUCCCAUGUGCUACUAGAG 440

AAGCCAAGCCGUGGCCCGGCCUUCCCAUGUGCUACUAGAG 441

UGCCAAGCCGCGGCCCGGCCUUCCCAUGUGCUACUAGAG 442

AAGCCAAGCCGAGGCCCGGCCUUCCCAUGUGCUACUAGAG 443

BV CCAAAUGCCAAAGCCGUAGCCCGGCCAGUAGCCCACACGUC 444

CCAAAAUGCCAAAGCCGUAGCCCGGCCAGUAGCCCACACGUC 445

CCAAAUGCCAAGCCCGUAGCCCGGCCAGUAGCCCACACGUC 446

BW CCAUUACGCGACGUAAUUCCCCCAUCGUUUCCUCGUUAAG 447

CCAUUACGCGACGUAAUUCCCCCAUCGUCUCCUCGUUAAG 448

CCAUUACGCGACGUAAUUCCCCCAUCGCUUCCUCGUUAAG 449

CCAUUACGCGGCGUAAUUCCCCCAUCGUUUCCUCGUUAAG 450

CCAUUACGCGACGUAAUUCCCCCAUCGUUUCCUCGUUAGG 451

CCAUUACGCGACGUAAUUCCCCCAUCGUUUCCUCGCUAAG 452

CCAUUACGCGACGUAAUUCCCCCAUCGUUUCCUCGUUAUG 453

CCAUUACGCGACGUAAUUCCCCCAUCGUUUCCUCGUUAAA 454

BX CCAUCUAGAUCUCCGUAGAUUCCCCGGCUCUUUCUCGC 455

CCAUCUAGAUCUCCGUAGAUUCCCCAGCUCUUUCUCGC 456

CCAUCUAGAUCUCCGUAGAUCCCCCGGCUCUUUCUCGC 457

CCAUCUAGAUCUCCGUAGAUUCCCCCGCUCUUUCUCGC 458

CCAUCUAGAUCUCCGUAGAUUCCCCGGCUCUUCCUCGC 459

CCAUCUAGAUCUCCGUGAUUCCCCCGGCUCUUUCUCGC 460

CCAUCUAGAUCUCCGUAGUUCCCCCGGCUCUUUCUCGC 461

CCAUCUAGAUCCCCGUAGAUUCCCCGGCUCUUUCUCGC 462

CCAUCUAGAUCUCCGUAGAUUCCCCGGCUCCUUCUCGC 463

CCAUCUAUAUCUCCGUAGAUUCCCCGGCUCUUUCUCGC 464

BY ACUGUCUGCAUACACGGUAUGCCCAACGCCAUCCAAACCG 465 ACUGUCUGCAUACACGGUAUGCCCAACGCCAUCCAAACCGC 466

ACUGUCUGCAUACAUGGUAUGCCCAACGCCAUCCAAACCG 467

ACUGUCUGCAUACACGGUAUGCCCAACGCCAUCCAAAACCG 468

BZ ACCUGCGGCUAUUGCCAGCGCCAUAAGACCCUCCACAGUA 469

ACCUGCGGCUAUUGCCAGCGCCAUAAGACCCUCCACAGCA 470

CCUGCGGCUAUUGCCAGCGCCAUAAGACCCUCCACAGUA 471

ACCUGCGGCUAUUGCCAGCGCCAUAAGACCUUCCACAGUA 472

ACCUGCGGCUAUUGCCAGCGCCAUAAGACCCUCCGCAGUA 473

Table 5: Nucleolin Binding of Aptamer Families A-F

Table 6: Nucleolin Aptamer Truncates

Fv2 GGGACCACGCGCCAACGUGUCAGCUACACGCCGUGUUCCCCGGCAUAACC CAGAGGUCGAU (SEQ ID NO: 484)

Fv3 GGGAGAGAGGAAGAGGGAUGGGACCACGCGCCAACGUGUCAGCUACACG

CCGUGUUCCCCGG (SEQ ID NO: 485)

Table 7: Ev3 Truncates

Table 8: Additional Nucleolin Aptamers

Ev3minl0 GGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCUGCUGUGCCA CCCACCG (SEQ ID NO: 505)

Ev3minll GAGAGGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCUGCUG

UGCCACCCACCG (SEQ ID NO: 506)

Ev3minl2 GGGAGAGAGGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCU

GCUGUGCCACCCAC (SEQ ID NO: 507)

Ev3minl3 GGGAGAGAGGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCU

GCUGUGCCACCCCG (SEQ ID NO: 508)

Ev3minl4 GGGAGAGAGGAAGAGGGAUGGGCACGGUCCGCGCUAACUGUACCUG

CUGGCCACCCACCG (SEQ ID NO: 509)

Ev3minl5 GGGAGAGAGGAAGAGGGAUGGGCACGGUCCGCGCUAACUGUACCGC

UGUGCCACCCACCG (SEQ ID NO: 510)

Ev3minl6 GGGAGAGAGGAAGAGGGAUGGGCACGGUCCAGCGCACUGUACCUGC

UGUGCCACCCACCG (SEQ ID NO: 511)

Ev3minl7 GGGAGAGAGGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCU

GCUGUGCCACCCACCG (SEQ ID NO: 512)

Ev3minl8 GGGAGAGGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCUGC

UGUGCCACCCACCG (SEQ ID NO: 513)

Ev3minl9 GGGAGAGGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCUGC

UGUGCCACCCACCG (SEQ ID NO: 514)

Ev3min20 GAGGAAGAGGGAUGGGCACGGUCCAGCGCUAACUGUACCUGCUGUG

CCACCCACCG (SEQ ID NO: 515)

Example 2 - Sensitizing Cancer Cells with Nucleolin Aptamers

We next tested the ability of the nucleolin aptamer truncates Bvl, Ev3, Ev4, Dv2, and

Fv3 to sensitize cancer cells that overexpress nucleolin on the cell surface to ionizing radiation (IR). We also included the Ev2 aptamer as a non-binding aptamer control. As shown in FIG. 6A,

Ev3 appears to be a potent radiosensitizer, significantly decreasing post-IR survival in HCT116 p53-null cells. Further radiation sensitization studies showed that Ev3 decreased post-IR survival by approximately 5-fold in HCT116 p53-null cells compared to the aptamer control Ev5, which was used as a control due to its ability to bind nucleolin protein yet lack of radiosensitizing properties (FIG. 6B). Given that a large number of tumors lack functional p53, which is associated with resistance to therapy, it is encouraging that the specific nucleolin aptamer Ev3 can efficiently sensitize p53-null cells to IR.

To determine whether the Ev3 aptamer' s ability to sensitize cancer cells to ionizing radiation was specific to the nucleolin protein, we tested the aptamer on hTERT-immortalized HFF cells (FIG. 7). hTERT-immortalized HFF cells that do not express nucleolin on cell surface were treated with 5ug of indicated aptamers and exposed to 2Gy IR 48h later. Cells were cultivated for lOd and survival was assessed by MTT assay. As seen in FIG. 7, Ev3 does not sensitize HFF (human foreskin fibroblasts) that do not express nucleolin on cell surface to radiation.

To determine the Ev3 and Ev5 aptamers could bind nucleolin expressed on a cell surface in a concentration-dependent manner, we performed a flow cytometry analysis with HCT116 p537- cells. Flow cytometry analysis of MFI (mean fluorescence intensity) of DL650-labeled Ev3 and Ev5 after incubation of HCT116 p537- cells with indicated aptamer concentrations. As shown in FIG. 8 and Table 9, Ev3 and Ev5 bind to nucleolin expressed on the cell surface in a concentration dependent manner.

Table 9: Ev3 and Ev5 Binding Data

To determine whether the EV3 aptamer could be truncated without affecting its radiosensitization function, we tested some Ev3 aptamer truncates (FIG. 10). HCT 116 p53 -/- colon cancer cells were treated with 5ug of indicated full-length aptamers or Ev3 truncates and exposed to 2Gy IR 48h later. Cells were cultivated for lOd and survival was assessed by MTT assay. FIG. 10 shows truncation of Ev3 resulted in reduced activity as radiosensitizer.

The Ev3 nucleolin aptamer has the potential for clinical application as a cancer- specific radio- and chemosensitizer and could improve the current regimens of cancer therapy. Further, the aptamer can be radiolabeled for use as a DNA damaging agent that will preferentially target tumors and simultaneously blunt the ability of the tumor cell to repair the radiation damage, thus enhancing the sensitivity of the tumor to the radioisotope.

Example 3 - Predicted Secondary Structures for Nucleolin Aptamers

Predicted secondary structures for nucleolin aptamers were generated using the mfold Web Server RNA Folding Form. Predicted structures for representative aptamers from families B, C, D, E, and F are shown in FIGS. 11A-11B, 12A-12B, 13A-13C, 14A-14D, and 15A-15B. Predicted structures for Ev3 truncates (Ev3.min2-25) are shown in FIGS. 16-37.

Claims

CLAIMS We claim:

1. An aptamer comprising

a polynucleotide having at least 80% sequence identity to any one of SEQ ID NOS: 1-490, 494-515

wherein the polynucleotide comprises an unmodified form or comprises a modified form comprising at least one nucleotide base modification.

2. The aptamer of claim 1, wherein the aptamer comprises a polynucleotide having at least 90% sequence identity to 5 ' -GGG AGAGAGGAAGAGGGAUGGG (SEQ ID NO: 491)- A Variable Region-CAUAACCCAGAGGUCGAUAGUACUGGAUCCCCCC (SEQ ID NO: 492)-3\ wherein the variable region comprises any one of SEQ ID NOS: 13-473 or a portion thereof.

3. The aptamer of claim 1, wherein the aptamer comprises a polynucleotide having at least 90% sequence identity to SEQ ID NO: 480 (Ev3 Aptamer).

4. The aptamer of any one of the preceding claims, wherein the dissociation constant (K_D) of the aptamer for a nucleolin protein is less than 100 nanomolar (nM).

5. The aptamer of any one of the preceding claims, wherein the polynucleotide comprises an RNA polynucleotide.

6. The aptamer of any one of the preceding claims, wherein the polynucleotide comprises a modified form comprising at least one nucleotide base modification selected from the group consisting of a 2'fluoro modification, a 2'O-methyl modification, a 5'

modification, and a 3 'modification.

7. The aptamer of any one of the preceding claims, wherein the polynucleotide comprises a 5' linker and/or a 3' linker.

8. The aptamer of any one of the preceding claims, wherein the polynucleotide further comprises an agent.

9. The aptamer of claim 8, wherein the agent is a stability agent selected from the group consisting of polyethylene glycol (PEG), cholesterol, albumin, and Elastin-like polypeptide.

10. The aptamer of claim 8, wherein the agent is a reporter moiety.

11. The aptamer of claim 10, wherein said reporter moiety is selected from the group consisting of a fluorophore moiety, an optical moiety, a magnetic moiety, a radiolabel moiety, an X-ray moiety, an ultrasound imaging moiety, a photoacoustic imaging moiety, a nanoparticle-based moiety, and a combination of two or more of the reporter moieties.

12. The aptamer of any one of claims 8-11, wherein the polynucleotide and the agent are linked by a covalent bond.

13. The aptamer of any one of claims 8-11, wherein the polynucleotide and the agent are linked by a tae system.

14. The aptamer of claim 13, wherein the tag system is selected from the group consisting of biotin/avidin, biotin/streptavidin, and biotin/NeutrAvidin.

15. A dimer, trimer, or tetramer comprising any one of the aptamers of claims 1-14.

16. A pharmaceutical composition comprising a pharmaceutical carrier and any one of the compositions of claims 1-15.

17. A method for treating cancer in a subject comprising administering to the subject a

therapeutically effective amount of any one of the compositions of claims 1-16.

18. The method of claim 17, further comprising administering a chemotherapeutic agent or radiation therapy to the subject.

19. The method of claim 18, wherein the composition is administered prior to the

administration of the chemotherapeutic agent or the radiation therapy.

20. Use of the composition of any one of claims 1-16 in the manufacture of a medicament for treating cancer in a subject.

21. The method or use of any one of claims 17-19, wherein the cancer is colon cancer.

22. The method or use of any one of claims 17-20, wherein the subject is a mammal.

23. The method or use of claim 22, wherein the mammal is a human.

24. A method of labeling or inhibiting nucleolin comprising contacting nucleolin with any one of the compositions of claims 1-16.

25. The method of claim 24, wherein the nucleolin is contacted by adding the composition to cells comprising nucleolin in vitro.

26. The method of claim 24, wherein the nucleolin is contacted by administering the

composition to a subject.