RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: M52
Target: Murine CD200R1
Type of nucleic acid: ssDNA
Sequence: 5'GACGATAGCGGTGACGGCACAGACGTTTATTACCATTATGCCTATGTAACGTATGCCGCTTCCGTCCGTCGCTC3'
Sequence length: 74
GC content: 0.527027027027027
Affinity: Kd: >1000 nM
Pool type: 5'-GACGATAGCGGTGACGGCACAGACG-N25-CGTATGCCGCTTCCGTCCGTCGCTC-3'
Pool random region: 25
Binding buffer/conditions: PBS (pH 7.4)
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapuetic: " CD200R1 expressed on the surface of myeloid and lymphoid cells delivers immune inhibitory signals to modulate inflammation when engaged with its ligand CD200. We report the development and characterization of DNA aptamers, which bind to murine CD200R1 and act as potent signalling molecules in the absence of exogenous CD200. As DNA aptamers exhibit inherent advantages over conventional protein-based therapeutics including low immunogenicity, ease of synthesis, low cost, and long shelf life, such CD200R1 agonistic aptamers may emerge as useful and safe nonsteroidal anti-inflammatory therapeutic agents."
Reference (2014, Mol Ther Nucleic Acids ): Prodeus, A., Cydzik, M., Abdul-Wahid, A., Huang, E., Khatri, I., Gorczynski, R., & Gariépy, J. (2014). Agonistic CD200R1 DNA Aptamers Are Potent Immunosuppressants That Prolong Allogeneic Skin Graft Survival. Molecular therapy. Nucleic acids, 3(8), e190. https://doi.org/10.1038/mtna.2014.41
Aptamer: CD4-#1-F
Target: CD4-expressing human cells
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCACCACCACCGTACAATTCGCTTTCTTTTTTCATTACCTACTCTGGCTGGACACGGTGGCTTAGT 3'
Sequence length: 81
GC content: 0.4938271604938271
Affinity: Not reported
Pool type: 5′-ATCCAGAGTGACGCAGCA-N45-TGGACACGGTGGCTTAGT 3′
Pool random region: 45
Binding buffer/conditions: Not reported
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not appilcable
Application as quoted in the referenced paper: Therapeutic: " To investigate the potential clinical application of aptamers to prevention of HIV infection, single-stranded DNA (ssDNA) aptamers specific for CD4 were developed using the systematic evolution of ligands by exponential enrichment approach and next generation sequencing. Functional studies showed that the aptamer polymers significantly blocked binding of viral gp120 to CD4-expressing cells by up to 70% inhibition. These findings provide a new approach to prevent HIV-1 transmission using oligonucleotide aptamers."
Reference (2014, Int J Biochem Cell Biol ): Zhao, N., Pei, S. N., Parekh, P., Salazar, E., & Zu, Y. (2014). Blocking interaction of viral gp120 and CD4-expressing T cells by single-stranded DNA aptamers. The international journal of biochemistry & cell biology, 51, 10–18. https://doi.org/10.1016/j.biocel.2014.03.008
Aptamer: A08
Target: Ochratoxin A (OTA)
Type of nucleic acid: ssDNA
Sequence: 5'AGCCTCGTCTGTTCTCCCGGCAGTGTGGGCGAATCTATGCGTACCGTTCGATATCGTGGGGAAGACAAGCAGACGT3'
Sequence length: 76
GC content: 0.5657894736842105
Affinity: Kd: 290 ± 150 nM
Pool type: 5'-AGCCTCGTCTGTTCTCCC-N40-GGGAAGACAAGCAGACGT-3'
Pool random region: 40
Binding buffer/conditions: 10 mM Na2HPO4, 2 mM KH2PO4, 2.7 mM KCl, 137 mM NaCl, pH 7.4
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Mw = 403.81 G/mol
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Nucleic acid aptamers are emerging as useful molecular recognition tools for food safety monitoring. This work describes the selection of novel DNA aptamers that bind to the important food contaminant ochratoxin A (OTA). This label-free detection platform is capable of rapid, selective, and sensitive OTA quantification with a limit of detection of 9 nM and linear quantification up to 100 nM."
Additional information: The forward primer, SELF, 5'-AGCCTCGTCTGTTCTCCC-3', and reverse primer, SELR, 5'-BIOTIN-ACGTCTGCTTGTCTTCCC-3', were also synthesized and prepared for the selection procedure.
Reference (2014, Toxins (Basel) ): McKeague, M., Velu, R., Hill, K., Bardóczy, V., Mészáros, T., & DeRosa, M. C. (2014). Selection and characterization of a novel DNA aptamer for label-free fluorescence biosensing of ochratoxin A. Toxins, 6(8), 2435–2452. https://doi.org/10.3390/toxins6082435
Aptamer: B08
Target: Ochratoxin A (OTA)
Type of nucleic acid: ssDNA
Sequence: 5'AGCCTCGTCTGTTCTCCCGGCGCATGATCATTCGGTGGGTAAGGTGGTGGTAACGTTGGGGAAGACAAGCAGACGT3'
Sequence length: 76
GC content: 0.5657894736842105
Affinity: Kd: 110 ± 50 nM
Pool type: 5'-AGCCTCGTCTGTTCTCCC-N40-GGGAAGACAAGCAGACGT-3'
Pool random region: 40
Binding buffer/conditions: 10 mM Na2HPO4, 2 mM KH2PO4, 2.7 mM KCl, 137 mM NaCl, pH 7.4
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Mw = 403.81 G/mol
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Nucleic acid aptamers are emerging as useful molecular recognition tools for food safety monitoring. This work describes the selection of novel DNA aptamers that bind to the important food contaminant ochratoxin A (OTA). This label-free detection platform is capable of rapid, selective, and sensitive OTA quantification with a limit of detection of 9 nM and linear quantification up to 100 nM."
Additional information: The forward primer, SELF, 5'-AGCCTCGTCTGTTCTCCC-3', and reverse primer, SELR, 5'-BIOTIN-ACGTCTGCTTGTCTTCCC-3', were also synthesized and prepared for the selection procedure.
Reference (2014, Toxins (Basel) ): McKeague, M., Velu, R., Hill, K., Bardóczy, V., Mészáros, T., & DeRosa, M. C. (2014). Selection and characterization of a novel DNA aptamer for label-free fluorescence biosensing of ochratoxin A. Toxins, 6(8), 2435–2452. https://doi.org/10.3390/toxins6082435
Aptamer: No. 6
Target: U-2 OS human osteosacroma cells
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCATGGTGGGGGTTTTGGCGTTATTTGTGCTTTTTTGGCGGGGTGGACACGGTGGCTTAGT3'
Sequence length: 76
GC content: 0.5394736842105263
Affinity: Not reported
Pool type: 5'-ATCCAGAGTGACGCAGCA-N40-TGGACACGGTGGCTTAGT-3'
Pool random region: 40
Binding buffer/conditions: Binding buffer (1 L Dulbecco's phosphate buffered saline (DPBS) containing 4.5 g of glucose, 1 g BSA (Sigma), 100 mg yeast tRNA (Invitrogen) and 5 ml of 1 M MgCl2)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Osteosarcoma is the most common primary malignant bone tumor in adolescents and young adults. In the present study, we have designed a novel aptamer using the cell-based Systematic Evolution of Ligands Exponential Enrichment (cell-SELEX) technique that specifically recognizes the U-2 OS human osteosarcoma cell line. The generation of aptamer libraries can be used not only for the specific diagnosis of osteosarcoma, but also to build a platform for developing probe-carrier-antitumor drugs complexes and targeted therapies for osteosarcoma."
Reference (2015, Int J Clin Exp Med ): Wang, H., Liang, J., Ma, Y., Sun, B., Li, X., Wei, Y., Fu, G., Li, M., & Xia, W. (2015). Identification of a novel molecular probe for recognition of human osteosarcoma cell using the cell-SELEX method. International journal of clinical and experimental medicine, 8(10), 18151–18157.
Aptamer: O31
Target: Monoclonal antibody against OA (OA-mAb-F(ab′)2)
Type of nucleic acid: ssDNA
Sequence: 5'GAGGCAGCACTTCACACGATCTGTATTCCGTGAATAACTTAGCTGGTAATGGCGTTCGTTCCGCTGCGTAATGACTGTAGTGATG3'
Sequence length: 85
GC content: 0.4823529411764706
Affinity: Ka: 1.47 nM
Pool type: 5′-GAGGCAGCACTTCACACGATCTG-N40-CTGCGTAATGACTGTAGTGATG-3'
Pool random region: 40
Binding buffer/conditions: binding buffer (20 mM Hepes, 150 mM NaCl, 2 mM KCl, 2 mM MgCl2, and 2 mM CaCl2, pH 7.4)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " Okadaic acid (OA) is produced by Dinophysis and Prorocentrum dinoflagellates and primarily accumulates in bivalves, and this toxin has harmful effects on consumers and operators. In this work, we first report the use of aptamers as novel non-toxic probes capable of binding to a monoclonal antibody against OA (OA-mAb). The above data provides strong evidence that internal-image functional aptamers could be applicable as novel probes in a non-toxic assay."
Reference (2015, Mar Drugs ): Lin, C., Liu, Z. S., Wang, D. X., Li, L., Hu, P., Gong, S., Li, Y. S., Cui, C., Wu, Z. C., Gao, Y., Zhou, Y., Ren, H. L., & Lu, S. Y. (2015). Generation of Internal-Image Functional Aptamers of Okadaic Acid via Magnetic-Bead SELEX. Marine drugs, 13(12), 7433–7445. https://doi.org/10.3390/md13127066
Aptamer: CLN3-T
Target: C-Met receptor
Type of nucleic acid: ssDNA
Sequence: 5'GAAAAGTTATCAGGCCTGGATGGTAGCTCGGTCGGGGTGGGTGGGTTGGCAAGTCTGATT3'
Sequence length: 60
GC content: 0.55
Affinity: Kd: 0.10 nM
Pool type: 5'-GGAGGGAAAAGTTATCAGGC-N40-TGATTAGTTTTGGAGTACTCGCTCC-3'
Pool random region: 40
Binding buffer/conditions: Dulbecco's PBS
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Trancated version of cln3 by the deletion of 25 bases in the primer region
Application as quoted in the referenced paper: Diagnostic and Therapeutic: " The human receptor tyrosine kinase c-Met plays an important role in the control of critical cellular processes. Since c-Met is frequently over expressed or deregulated in human malignancies, blocking its activation is of special interest for therapy. We report the generation of the RNA aptamer CLN64 containing 2'-fluoro pyrimidine modifications by systematic evolution of ligands by exponential enrichment (SELEX). CLN3 and CLN64 aptamers exhibit valuable tools to further understand the structural and functional basis for c-Met activation or inhibition by synthetic ligands and their interplay with HGF binding."
Additional information: Initially found selected in Boltz, A., Piater, B., Toleikis, L., Guenther, R., Kolmar, H., & Hock, B. (2011). Bi-specific aptamers mediating tumor cell lysis. The Journal of biological chemistry, 286(24), 21896–21905. https://doi.org/10.1074/jbc.M111.238261
Reference (2015, PLoS One ): Piater, B., Doerner, A., Guenther, R., Kolmar, H., & Hock, B. (2015). Aptamers Binding to c-Met Inhibiting Tumor Cell Migration. PloS one, 10(12), e0142412. https://doi.org/10.1371/journal.pone.0142412
Aptamer: CLN64
Target: C-Met receptor
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGAGGGAAAAGUUAUCAGGCCGCUAGUUACCAGGUGUAGCUGACCAAGCGGAUGUGUGUUGAUUAGUUUUGGAGUACUCGCUCC3'
Sequence length: 84
GC content: 0.5
Affinity: Kd: 1.03 ± 0.15 nM
Pool type: 5'-GGAGGGAAAAGTTATCAGGC-N40-TGATTAGTTTTGGAGTACTCGCTCC-3'
Pool random region: 40
Binding buffer/conditions: Dulbecco's PBS
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: " The human receptor tyrosine kinase c-Met plays an important role in the control of critical cellular processes. Since c-Met is frequently over expressed or deregulated in human malignancies, blocking its activation is of special interest for therapy. We report the generation of the RNA aptamer CLN64 containing 2'-fluoro pyrimidine modifications by systematic evolution of ligands by exponential enrichment (SELEX). CLN3 and CLN64 aptamers exhibit valuable tools to further understand the structural and functional basis for c-Met activation or inhibition by synthetic ligands and their interplay with HGF binding."
Additional information: 2´-fluoro-CTP (fCTP), 2´-fluoro-UTP (fUTP)
Reference (2015, PLoS One ): Piater, B., Doerner, A., Guenther, R., Kolmar, H., & Hock, B. (2015). Aptamers Binding to c-Met Inhibiting Tumor Cell Migration. PloS one, 10(12), e0142412. https://doi.org/10.1371/journal.pone.0142412
Aptamer: CLN64-T
Target: C-Met receptor
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'GGAGGGAAAAGUUAUCAGGCCCGCUAGUUACCAGGUGUAGCUGACCAAGCGGAUGUGUGUUGAUU3'
Sequence length: 65
GC content: 0.5076923076923077
Affinity: Kd: 3.83 ± 2.40 nM
Pool type: 5'-GGAGGGAAAAGTTATCAGGC-N40-TGATTAGTTTTGGAGTACTCGCTCC-3'
Pool random region: 40
Binding buffer/conditions: Dulbecco's PBS
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated version of cln64 by the deletion of 20 bases from the primer region
Application as quoted in the referenced paper: Diagnostic and Therapeutic: " The human receptor tyrosine kinase c-Met plays an important role in the control of critical cellular processes. Since c-Met is frequently over expressed or deregulated in human malignancies, blocking its activation is of special interest for therapy. We report the generation of the RNA aptamer CLN64 containing 2'-fluoro pyrimidine modifications by systematic evolution of ligands by exponential enrichment (SELEX). CLN3 and CLN64 aptamers exhibit valuable tools to further understand the structural and functional basis for c-Met activation or inhibition by synthetic ligands and their interplay with HGF binding."
Additional information: 2´-fluoro-CTP (fCTP), 2´-fluoro-UTP (fUTP)
Reference (2015, PLoS One ): Piater, B., Doerner, A., Guenther, R., Kolmar, H., & Hock, B. (2015). Aptamers Binding to c-Met Inhibiting Tumor Cell Migration. PloS one, 10(12), e0142412. https://doi.org/10.1371/journal.pone.0142412
Aptamer: CSC-16
Target: Colorectal cancer stem cells (CR-CSC)
Type of nucleic acid: ssDNA
Sequence: 5'GGCAGGAAGACAAACAGCGGTCTGACTGGGTAGCAGTAGAAGGCGTCGGTCCCGGGGGTCTGTGGTGCTGT3'
Sequence length: 71
GC content: 0.6197183098591549
Affinity: Kd: 27.4 ± 4.9 nM
Pool type: 5'-GGCAGGAAGACAAACA-N40-GGTCTGTGGTGCTGT-3'
Pool random region: 40
Binding buffer/conditions: 1 L of Dulbecco's phosphate-buffered saline (DPBS, Invitrogen Co., USA), 100 mg transfer ribonucleic acid (Sigma Co., USA), 4.5 g of glucose, and 5 mL of 1 M MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Colorectal cancer (CRC) is the most frequently diagnosed cancer around the world, causing about 700,000 deaths every year. These results demonstrated that the integrated microfluidic system is able to rapidly screen aptamers with high affinity and selectivity within a shorter period of time. This technology is promising for screening of aptamer targeting agents for these cancer cells, which could be useful for early diagnosis of CR-CSC/CRC or even target therapeutics."
Reference (2015, Sci Rep ): Hung, L. Y., Wang, C. H., Che, Y. J., Fu, C. Y., Chang, H. Y., Wang, K., & Lee, G. B. (2015). Screening of aptamers specific to colorectal cancer cells and stem cells by utilizing On-chip Cell-SELEX. Scientific reports, 5, 10326. https://doi.org/10.1038/srep10326
Aptamer: CSC-19
Target: Colorectal cancer stem cells (CR-CSC)
Type of nucleic acid: ssDNA
Sequence: 5'GGCAGGAAGACAAACACCCGGGACCGACGCCTTCTACTGCTACCCAGTCAGACCGCGGTCTGTGGTGCTGT3'
Sequence length: 71
GC content: 0.6197183098591549
Affinity: Kd: 157.2 ± 44.4 nM
Pool type: 5'-GGCAGGAAGACAAACA-N40-GGTCTGTGGTGCTGT-3'
Pool random region: 40
Binding buffer/conditions: 1 L of Dulbecco's phosphate-buffered saline (DPBS, Invitrogen Co., USA), 100 mg transfer ribonucleic acid (Sigma Co., USA), 4.5 g of glucose, and 5 mL of 1 M MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Colorectal cancer (CRC) is the most frequently diagnosed cancer around the world, causing about 700,000 deaths every year. These results demonstrated that the integrated microfluidic system is able to rapidly screen aptamers with high affinity and selectivity within a shorter period of time. This technology is promising for screening of aptamer targeting agents for these cancer cells, which could be useful for early diagnosis of CR-CSC/CRC or even target therapeutics."
Reference (2015, Sci Rep ): Hung, L. Y., Wang, C. H., Che, Y. J., Fu, C. Y., Chang, H. Y., Wang, K., & Lee, G. B. (2015). Screening of aptamers specific to colorectal cancer cells and stem cells by utilizing On-chip Cell-SELEX. Scientific reports, 5, 10326. https://doi.org/10.1038/srep10326
Aptamer: CSC-34
Target: Colorectal cancer stem cells (CR-CSC)
Type of nucleic acid: ssDNA
Sequence: 5'GGCAGGAAGACAAACACACAGCCGCACACACAGAACTCCAGGATCTTACCGCCTCAGGTCTGTGGTGCTGT3'
Sequence length: 71
GC content: 0.5633802816901409
Affinity: Kd: 48.6 ± 6.8 nM
Pool type: 5'-GGCAGGAAGACAAACA-N40-GGTCTGTGGTGCTGT-3'
Pool random region: 40
Binding buffer/conditions: 1 L of Dulbecco's phosphate-buffered saline (DPBS, Invitrogen Co., USA), 100 mg transfer ribonucleic acid (Sigma Co., USA), 4.5 g of glucose, and 5 mL of 1 M MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Colorectal cancer (CRC) is the most frequently diagnosed cancer around the world, causing about 700,000 deaths every year. These results demonstrated that the integrated microfluidic system is able to rapidly screen aptamers with high affinity and selectivity within a shorter period of time. This technology is promising for screening of aptamer targeting agents for these cancer cells, which could be useful for early diagnosis of CR-CSC/CRC or even target therapeutics."
Reference (2015, Sci Rep ): Hung, L. Y., Wang, C. H., Che, Y. J., Fu, C. Y., Chang, H. Y., Wang, K., & Lee, G. B. (2015). Screening of aptamers specific to colorectal cancer cells and stem cells by utilizing On-chip Cell-SELEX. Scientific reports, 5, 10326. https://doi.org/10.1038/srep10326
Aptamer: HCT-15
Target: Colon carcinoma cell lines (HCT-8), Human
Type of nucleic acid: ssDNA
Sequence: 5'GGCAGGAAGACAAACACGCAACAACATACGAAGCCACACAAAAAAAAACACAACCAGGTCTGTGGTGCTGT3'
Sequence length: 71
GC content: 0.4647887323943662
Affinity: Kd: 13.2 ± 3.8 nM
Pool type: 5'-GGCAGGAAGACAAACA-N40-GGTCTGTGGTGCTGT-3'
Pool random region: 40
Binding buffer/conditions: 1 L of Dulbecco's phosphate-buffered saline (DPBS, Invitrogen Co., USA), 100 mg transfer ribonucleic acid (Sigma Co., USA), 4.5 g of glucose, and 5 mL of 1 M MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Colorectal cancer (CRC) is the most frequently diagnosed cancer around the world, causing about 700,000 deaths every year. These results demonstrated that the integrated microfluidic system is able to rapidly screen aptamers with high affinity and selectivity within a shorter period of time. This technology is promising for screening of aptamer targeting agents for these cancer cells, which could be useful for early diagnosis of CR-CSC/CRC or even target therapeutics."
Reference (2015, Sci Rep ): Hung, L. Y., Wang, C. H., Che, Y. J., Fu, C. Y., Chang, H. Y., Wang, K., & Lee, G. B. (2015). Screening of aptamers specific to colorectal cancer cells and stem cells by utilizing On-chip Cell-SELEX. Scientific reports, 5, 10326. https://doi.org/10.1038/srep10326
Aptamer: HCT-34
Target: Colon carcinoma cell lines (HCT-8), Human
Type of nucleic acid: ssDNA
Sequence: 5'GGCAGGAAGACAAACACCAAAAAAACACCAAAAACAAAACCACGGTCTGTGGTGCTGT3'
Sequence length: 58
GC content: 0.4482758620689655
Affinity: Kd: 12.3 ± 4.5 nM
Pool type: 5'-GGCAGGAAGACAAACA-N40-GGTCTGTGGTGCTGT-3'
Pool random region: 40
Binding buffer/conditions: 1 L of Dulbecco's phosphate-buffered saline (DPBS, Invitrogen Co., USA), 100 mg transfer ribonucleic acid (Sigma Co., USA), 4.5 g of glucose, and 5 mL of 1 M MgCl2
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Colorectal cancer (CRC) is the most frequently diagnosed cancer around the world, causing about 700,000 deaths every year. These results demonstrated that the integrated microfluidic system is able to rapidly screen aptamers with high affinity and selectivity within a shorter period of time. This technology is promising for screening of aptamer targeting agents for these cancer cells, which could be useful for early diagnosis of CR-CSC/CRC or even target therapeutics."
Reference (2015, Sci Rep ): Hung, L. Y., Wang, C. H., Che, Y. J., Fu, C. Y., Chang, H. Y., Wang, K., & Lee, G. B. (2015). Screening of aptamers specific to colorectal cancer cells and stem cells by utilizing On-chip Cell-SELEX. Scientific reports, 5, 10326. https://doi.org/10.1038/srep10326
Aptamer: TSA14
Target: RHER2/neu protein via TUBO cell line
Type of nucleic acid: ssRNA
Sequence: 5'ACCGAGUCCAGAAGCUUGUAGUACUGCUGGAGCAUUUAUGGAUGAACCUUGGACGGAAGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC3'
Sequence length: 100
GC content: 0.46
Affinity: Kd: 133.9 ± 12.78 nM
Pool type: 5'-ACCGAGTCCAGAAGCTTGTAGTACT-N35-GCCTAGATGGAGTTGAATTCTCCCTATAGTGAGTCGTATTAC-3'
Pool random region: 35
Binding buffer/conditions: 20 mM HEPES-NaOH, pH 7.4, 150 mM NaCl, 1.5 mM CaCl2, 0.5 mM MgCl2, 10% yeast tRNA (Sigma)
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: 185kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Development of molecules that specifically recognize cancer cells is one of the major areas in cancer research. Human epidermal growth factor receptor 2 (HER2) is specifically expressed on the surface of breast cancer cells. HER2 is associated with an aggressive phenotype and poor prognosis. In this study we aimed to isolate RNA aptamers that specifically bind to HER2 overexpressing TUBO cell line. We believe the selected aptamers could be useful ligands for targeted breast cancer therapy."
Additional information: TUBO is a cloned cell line established from a mammary carcinoma of the Her2-neu transgenic mice also on the Balb/c background. TUBO is considered to be a nonmetastatic cell line
Reference (2015, Iran J Basic Med Sci ): Moosavian, S. A., Jaafari, M. R., Taghdisi, S. M., Mosaffa, F., Badiee, A., & Abnous, K. (2015). Development of RNA aptamers as molecular probes for HER2(+) breast cancer study using cell-SELEX. Iranian journal of basic medical sciences, 18(6), 576–586.