RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: LDH-Aad1-−3
Target: Lactate dehydrogenase-5 (LDH-5), Human
Type of nucleic acid: 5-uracil-modified-DNA
Sequence: 5'GTATAGTAGCCAGCCAGCCTTAGGCTGCTGGCTCGTGaGaCGGaTaTCaGGTCTCATAAACGGCGAGGTGTCAATTCC3'
Sequence length: 78
GC content: 0.5384615384615384
Affinity: Kd: 235 pM
Pool type: 5'-GTATAGTAGCCAGCCAGCCTTAGG-N30-CATAAACGGCGAGGTGTCAATTCC3'
Pool random region: 30
Binding buffer/conditions: Selection buffer (SB; 40 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), pH7.5, 125 mM NaCl, 5 mM KCl, 1 mM MgCl2, 0.01% Tween 20)
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Biosensor: " Human C-reactive protein (CRP) and lactate dehydrogenase are important markers in clinical laboratory testing-the former is used to detect in vivo inflammation, and the latter is used to detect cell necrosis and tissue destruction. We developed aptamers that bind to human CRP and human lactate dehydrogenase-5 (LDH-5). A potential application of these aptamers as sensor elements includes high-sensitivity target detection in point-of-care testing; These aptamers could be useful as biosensor elements with an electrochemical base of the target analyte."
Additional information: Used a modified DNA library containing the following base-appended base modifications: analog adenine derivative at the fifth position of uracil (Uad), analog guanine derivative at the fifth position of uracil (Ugu), and analog adenine derivative at the seventh position of adenine (Aad).*a indicates Aad
Reference (2020, Int J Mol Sci ): Minagawa, H., Kataoka, Y., Fujita, H., Kuwahara, M., Horii, K., Shiratori, I., & Waga, I. (2020). Modified DNA Aptamers for C-Reactive Protein and Lactate Dehydrogenase-5 with Sub-Nanomolar Affinities. International Journal of Molecular Sciences, 21(8), 2683. https://doi.org/10.3390/ijms21082682
Aptamer: TN2
Target: Triple-negative breast cancer (TNBC) cell line MDA-MB-231
Type of nucleic acid: ssRNA
Sequence: 5'UAGGGAAGAGAAGGACAUAUGAUAAGGCCGACGUAAUGUGUCGGUCGUUACGCGUCGUGCACGUUGACUAGUACAUGACCACUUGA3'
Sequence length: 86
GC content: 0.4883720930232558
Affinity: Kd: 59.12 ± 12.93 by streptavidin-biotin colorimetric assay and 73.02 ± 12 by flow cytometric assay
Pool type: 5'-TAGGGAAGAGAAGGACATATGAT-N40-TTGACTAGTACATGACCACTTGA-3'
Pool random region: 40
Binding buffer/conditions: 0.3 M NaAc buffer containing 2 mM EDTA (Invitrogen)
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " These aptamers inhibit TNBC cell capacity of growing in vitro as mammospheres, indicating they could also act as anti-tumor agents. Therefore, our newly identified aptamers are a valuable tool for selectively dealing with TNBC. Further, these aptamers interfere with the TNBC cells’ capacity of growing in vitro as mammospheres, a feature associated with the malignant phenotype, thus indicating they could be employed as important anti-tumor agents. In addition to therapeutic utility, TNBC aptamers may be useful as specific probes for molecular imaging, thus increasing a repertoire that is currently extremely scarce."
Reference (2020, iScience ): Camorani, S., Granata, I., Collina, F., Leonetti, F., Cantile, M., Botti, G., Fedele, M., Guarracino, M. R., & Cerchia, L. (2020). Novel Aptamers Selected on Living Cells for Specific Recognition of Triple-Negative Breast Cancer. IScience, 23(4), 100979. https://doi.org/10.1016/j.isci.2020.100974
Aptamer: TN3
Target: Triple-negative breast cancer (TNBC) cell line MDA-MB-232
Type of nucleic acid: ssRNA
Sequence: 5'UAGGGAAGAGAAGGACAUAUGAUCCGAUCUCACGCGCACCUUCUCUUCAGCGCGCGACUGGCAUUGACUAGUACAUGACCACUUGA3'
Sequence length: 86
GC content: 0.5116279069767442
Affinity: Kd: 21.91 ± 3.08 by streptavidin-biotin colorimetric assay and 28.93 ± 9.72 by flow cytometric assay
Pool type: 5'-TAGGGAAGAGAAGGACATATGAT-N40-TTGACTAGTACATGACCACTTGA-3'
Pool random region: 40
Binding buffer/conditions: 0.3 M NaAc buffer containing 2 mM EDTA (Invitrogen)
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " These aptamers inhibit TNBC cell capacity of growing in vitro as mammospheres, indicating they could also act as anti-tumor agents. Therefore, our newly identified aptamers are a valuable tool for selectively dealing with TNBC. Further, these aptamers interfere with the TNBC cells’ capacity of growing in vitro as mammospheres, a feature associated with the malignant phenotype, thus indicating they could be employed as important anti-tumor agents. In addition to therapeutic utility, TNBC aptamers may be useful as specific probes for molecular imaging, thus increasing a repertoire that is currently extremely scarce."
Reference (2020, iScience ): Camorani, S., Granata, I., Collina, F., Leonetti, F., Cantile, M., Botti, G., Fedele, M., Guarracino, M. R., & Cerchia, L. (2020). Novel Aptamers Selected on Living Cells for Specific Recognition of Triple-Negative Breast Cancer. IScience, 23(4), 100979. https://doi.org/10.1016/j.isci.2020.100974
Aptamer: TN20
Target: Triple-negative breast cancer (TNBC) cell line MDA-MB-233
Type of nucleic acid: ssRNA
Sequence: 5'UAGGGAAGAGAAGGACAUAUGAUCGAUGCGCACCGAUCUCUCUUCUGCACGUCCUUCGGCACAUUGACUAGUACAUGACCACUUGA3'
Sequence length: 86
GC content: 0.4883720930232558
Affinity: Kd: 24.30 ± 4.99 by streptavidin-biotin colorimetric assay and 23.92 ± 3.59 by flow cytometric assay
Pool type: 5'-TAGGGAAGAGAAGGACATATGAT-N40-TTGACTAGTACATGACCACTTGA-3'
Pool random region: 40
Binding buffer/conditions: 0.3 M NaAc buffer containing 2 mM EDTA (Invitrogen)
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " These aptamers inhibit TNBC cell capacity of growing in vitro as mammospheres, indicating they could also act as anti-tumor agents. Therefore, our newly identified aptamers are a valuable tool for selectively dealing with TNBC. Further, these aptamers interfere with the TNBC cells’ capacity of growing in vitro as mammospheres, a feature associated with the malignant phenotype, thus indicating they could be employed as important anti-tumor agents. In addition to therapeutic utility, TNBC aptamers may be useful as specific probes for molecular imaging, thus increasing a repertoire that is currently extremely scarce."
Reference (2020, iScience ): Camorani, S., Granata, I., Collina, F., Leonetti, F., Cantile, M., Botti, G., Fedele, M., Guarracino, M. R., & Cerchia, L. (2020). Novel Aptamers Selected on Living Cells for Specific Recognition of Triple-Negative Breast Cancer. IScience, 23(4), 100979. https://doi.org/10.1016/j.isci.2020.100974
Aptamer: TN58
Target: Triple-negative breast cancer (TNBC) cell line MDA-MB-235
Type of nucleic acid: ssRNA
Sequence: 5'UAGGGAAGAGAAGGACAUAUGAUGCAACGUUGUGGUCCCGUUUGCACUUUGUUUACGCGCGCAUUGACUAGUACAUGACCACUUGA3'
Sequence length: 86
GC content: 0.4651162790697674
Affinity: Kd: 17.17 ± 2.87 by streptavidin-biotin colorimetric assay and 26.09 ± 3.20 by flow cytometric assay
Pool type: 5'-TAGGGAAGAGAAGGACATATGAT-N40-TTGACTAGTACATGACCACTTGA-3'
Pool random region: 40
Binding buffer/conditions: 0.3 M NaAc buffer containing 2 mM EDTA (Invitrogen)
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " These aptamers inhibit TNBC cell capacity of growing in vitro as mammospheres, indicating they could also act as anti-tumor agents. Therefore, our newly identified aptamers are a valuable tool for selectively dealing with TNBC. Further, these aptamers interfere with the TNBC cells’ capacity of growing in vitro as mammospheres, a feature associated with the malignant phenotype, thus indicating they could be employed as important anti-tumor agents. In addition to therapeutic utility, TNBC aptamers may be useful as specific probes for molecular imaging, thus increasing a repertoire that is currently extremely scarce."
Reference (2020, iScience ): Camorani, S., Granata, I., Collina, F., Leonetti, F., Cantile, M., Botti, G., Fedele, M., Guarracino, M. R., & Cerchia, L. (2020). Novel Aptamers Selected on Living Cells for Specific Recognition of Triple-Negative Breast Cancer. IScience, 23(4), 100979. https://doi.org/10.1016/j.isci.2020.100974
Aptamer: TN145
Target: Triple-negative breast cancer (TNBC) cell line MDA-MB-236
Type of nucleic acid: ssRNA
Sequence: 5'UAGGGAAGAGAAGGACAUAUGAUCCUCAGCGCGCAACUUCCCUCCGUUCCCUGCCACGCGUCA3'
Sequence length: 63
GC content: 0.5714285714285714
Affinity: Kd: 26.88 ± 3.68 streptavidin-biotin colorimetric assay and 37.36 ± 3.50 by flow cytometric assay
Pool type: 5'-TAGGGAAGAGAAGGACATATGAT-N40-TTGACTAGTACATGACCACTTGA-3'
Pool random region: 40
Binding buffer/conditions: 0.3 M NaAc buffer containing 2 mM EDTA (Invitrogen)
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " These aptamers inhibit TNBC cell capacity of growing in vitro as mammospheres, indicating they could also act as anti-tumor agents. Therefore, our newly identified aptamers are a valuable tool for selectively dealing with TNBC. Further, these aptamers interfere with the TNBC cells’ capacity of growing in vitro as mammospheres, a feature associated with the malignant phenotype, thus indicating they could be employed as important anti-tumor agents. In addition to therapeutic utility, TNBC aptamers may be useful as specific probes for molecular imaging, thus increasing a repertoire that is currently extremely scarce."
Reference (2020, iScience ): Camorani, S., Granata, I., Collina, F., Leonetti, F., Cantile, M., Botti, G., Fedele, M., Guarracino, M. R., & Cerchia, L. (2020). Novel Aptamers Selected on Living Cells for Specific Recognition of Triple-Negative Breast Cancer. IScience, 23(4), 100979. https://doi.org/10.1016/j.isci.2020.100974
Aptamer: aptamer-X35
Target: Mas-related G-protein coupled receptor X2 (MRGPRX2)
Type of nucleic acid: ssDNA
Sequence: 5'ATGACCATGACCCTCCACACTGTAGGCACCACGGGTCCCTGGCAGTTAAAAGTACGTTTGTCAGACTGTGGCAGGGAAACA3'
Sequence length: 81
GC content: 0.5308641975308642
Affinity: Not reported
Pool type: 3′-ATGACCATGACCCTCCACAC-N40-TCAGACTGTGGCAGGGAAAC-5′
Pool random region: 40
Binding buffer/conditions: 200 μg/ml mock-liposomes lacking protein, 2 mg/ml bovine serum albumin, 150 mM NaCl, and 20 mM Tris-HCl (pH 7.4)
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: 46 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " Overall, our findings establish aptamer-X35 as a potential therapeutic candidate against perioperative anaphylaxis. We identified an aptamer against MRGPRX2 that inhibits histamine release from RBL-2H3 cells expressing MRGPRX2. This MRGPRX2 aptamer represents a potential drug candidate against non-IgE-dependent anaphylaxis. Inhibiting MRGPRX2 activation may represent a novel approach for controlling various allergic reactions."
Additional information: *pool is reported in the 3'-5' direction but the aptamer is reported in the 5'-3' and the primer regions match when they shouldn't
Reference (2020, Eur J Pharmacol ): Suzuki, Y., Liu, S., Ogasawara, T., Sawasaki, T., Takasaki, Y., Yorozuya, T., & Mogi, M. (2020). A novel MRGPRX2-targeting antagonistic DNA aptamer inhibits histamine release and prevents mast cell-mediated anaphylaxis. European Journal of Pharmacology, 878, 173104. https://doi.org/10.1016/j.ejphar.2020.173104
Aptamer: DDT_13
Target: 1,1,1-trichloro-2-(p-chlorophenyl)-2-(o-chlorophenyl) ethane (O,p'-DDT)
Type of nucleic acid: ssDNA
Sequence: 5'TCCAGCACTCCACGCATAACGAATTGTGCTCAATGCGCCCCTGCAGTGAATGTGGAATTTGTTATGCGTGCGACGGTGAA3'
Sequence length: 80
GC content: 0.5125
Affinity: Kd: 412.3 ± 124.6 nM
Pool type: 5'-TCCAGCACTCCACGCATAAC-N40-GTTATGCGTGCGACGGTGAA-3'
Pool random region: 40
Binding buffer/conditions: 1mM CaCl2, 2.5 mM KCl, 1.5 mM KH2PO4, 0.5 mM MgCl2·6H2O, 137 mM NaCl, 8mM Na2HPO4, pH 7.2
Divalent salt: MgCl/CaCl
Buffer type: PBS/phosphate buffers
pH: 7.2
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic: " The good bioactivities of DDT_13 were demonstrated for the analysis of spiked lake water and tap water samples. This study provides a novel o,p’-DDT-specific probe for its future applications. Both SGI assay (nano mole level) and AuNPs assay (micro mole level) showed that DDT_13 has the potential for detection of o,p’-DDT. With the further development of various signal amplification strategies, the DDT_13-based biosensor will contribute to detection of o,p’-DDT in real samples for humans and wildlife."
Reference (2020, Int J Mol Sci ): Zhang, W., Li, D., Zhang, J., Jiang, L., Li, Z., & Lin, J. S. (2020). Preparation and Characterization of Aptamers Against O,p'-DDT. International Journal of Molecular Sciences, 21(6), 2211. https://doi.org/10.3390/ijms21062211
Aptamer: Apt17
Target: SipA effector protein secreted by type three secretory system (T3SS)
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAAGAGAAGGACATATGATGCAATGGAACCGCTGAACGACCCTAGCATTATCAGTGTGGTTGACTAGTACATGACCACTTGA3′
Sequence length: 86
GC content: 0.4534883720930232
Affinity: Kd: 114.9 nM at 27 °C and 63.4 nM at 37 °C
Pool type: 5′-TAGGGAAGAGAAGGACATATGAT-N40-TTGACTAGT ACATGACCACTTGA-3′
Pool random region: 40
Binding buffer/conditions: Binding buffer (50 mM Tris-HCl, 100 mM NaCl, 5 mM KCl and 1 mM MgCl2, pH 7.4)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: ~50 kDa in sds-page
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Therapeutic and Diagnostic: " Salmonella Enteritidis is an important pathogen that can invade the intestinal cells of its host causing salmonellosis. SipA protein, an effector protein secreted by T3SS, maintains invasion of host cells more efficient. Thus, inhibitory aptamers against SipA protein were developed using magnetic bead-based Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. These results represent a corner stone for future studies that could aim to develop putative inhibitors against Salmonellosis."
Reference (2020, Int J Biol Macromol ): Shatila, F., Yalçın, H. T., Özyurt, C., Evran, S., Çakır, B., Yaşa, İ., & Nalbantsoy, A. (2020). Single-stranded DNA (ssDNA) Aptamer targeting SipA protein inhibits Salmonella Enteritidis invasion of intestinal epithelial cells. International Journal of Biological Macromolecules, 148, 518–524. https://doi.org/10.1016/j.ijbiomac.2020.01.132
Aptamer: RNV-L7
Target: Mammalian cell-expressed human recombinant low-density lipoprotein receptor (LDL-R) protein
Type of nucleic acid: ssDNA
Sequence: 5'GGACAGGACCACACCCAGCGCGGTCGGCGGGTGGGCGGGGGGAGAACGAGGTAGGGGTCAGGCTCCTGTGTGTCGCTTTGT3'
Sequence length: 81
GC content: 0.691358024691358
Affinity: Kd: 19.6 nM
Pool type: 5′-GGACAGGACCACACCCAGCG-N40-GGCTCCTGTGTGTCGCTTTGT-3′
Pool random region: 40
Binding buffer/conditions: PH 7.4 PBS containing 4.5 mM MgCl2, 0.005% Tween 20, and 100 μg/mL tRNA (Sigma, R8759)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Addition of an antimir-21 dnazyme component that will recognize and inhibit the expression of endogenous mir-21 target in the cytoplasm
Application as quoted in the referenced paper: Therapeutic: " Low-density lipoprotein receptor (LDL-R) is a cell surface receptor protein expressed in a variety of solid cancers, including lung, colon, breast, brain, and liver, and therefore it opens up opportunities to deliver lysosome-sensitive anti-cancer agents, especially synthetic nucleic acid-based therapeutic molecules. In this study, we focused on developing novel nucleic acid molecules specific to LDL-R. As currently there are no reports on LDL-R aptamer development, we think that RNV-L7 could be beneficial toward the development of targeted cancer therapeutics."
Additional information: Forward primer, 5′-TTTTTTTTTTTTTTTTTTTT/iSp9/ACAAAGCGACACACAGGAGCC-3′; reverse primer, 5′-GGACAGGACCACACCCAGCG-3′.
Reference (2020, Mol Ther Nucleic Acids ): Wang, T., Rahimizadeh, K., & Veedu, R. N. (2020). Development of a Novel DNA Oligonucleotide Targeting Low-Density Lipoprotein Receptor. Molecular Therapy - Nucleic Acids, 19, 190–198. https://doi.org/10.1016/j.omtn.2019.11.004
Aptamer: caDNApt-1
Target: Cyclic adenosine monophosphate (cAMP)
Type of nucleic acid: ssDNA
Sequence: 5'ATACCAGCTTATTCAATTATTCAATTCGAGGCGGGTGGGTGGGTTGAATGATAGTAAGTGCAATCT3'
Sequence length: 66
GC content: 0.4090909090909091
Affinity: Kd: 1 mM
Pool type: 5'-ATACCAGCTTATTCAATT-N40-GATAGTAAGTGCAATCT-3'
Pool random region: 40
Binding buffer/conditions: Tris⋅Cl (20 mm, pH 7.5), NaCl (100 mm), KCl (5 mm), MgCl2 (1 mm) and CaCl2 (1 mm; selection buffer, SB)
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Biosensor and Detection: " Using non-denaturing gel electrophoresis and fluorescence spectroscopy, we characterize the structural changes caDNApt-1 undergoes upon binding to cAMP and reveal its potential as a cAMP sensor. This aptamer thus adopts a scaffold structure that optimally binds to nucleotides having a cyclic phosphodiester bond, rather than a phosphate chain at the 5 position of the ribose sugar, and undergoes conformational changes upon binding to cAMP, leaving it well-placed for sensor development. cAMP induces a conformational change upon binding. This is potentially important for future design of cAMP reporters."
Reference (2020, Chembiochem ): Sharma, S., Zajac, M., & Krishnan, Y. (2019). A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition. ChemBioChem, 21(1–2), 157–162. https://doi.org/10.1002/cbic.201900259
Aptamer: CD63-1
Target: CD63 protein
Type of nucleic acid: ssDNA
Sequence: 5’TAACACGACAGACGTTCGGAGGTCGAACCCTGACAGCGTGGG3'
Sequence length: 42
GC content: 0.5952380952380952
Affinity: Kd: 38.71 ± 6.22 nM via ELISA assay
Pool type: 5′-TAGGGAAGAGAAGGACATATGAT-N43-TTGACTAGTACATGACCACTTGA-3′
Pool random region: 43
Binding buffer/conditions: PH 7.4 PBS containing 2.0 mM MgCl2, 0.02% Tween 20, and 100 µg/mL Salmon Sperm DNA (ThermoFisher, 15632011)
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: Therapeutic and Diagnostic: " The developed aptamers could be useful towards efficient isolation of native state exosomes from clinical samples and various theranostic applications for CD63-positive cancers. Current CD63 aptamer related exosome applications focus mainly on high-sensitive exosome detection (via establishing aptamer biosensors) for diagnostic purposes."
Additional information: utilized Competitive SELEX
Reference (2020, Molecules ): Song, Z., Mao, J., Barrero, R. A., Wang, P., Zhang, F., & Wang, T. (2020). Development of a CD63 Aptamer for Efficient Cancer Immunochemistry and Immunoaffinity-Based Exosome Isolation. Molecules (Basel, Switzerland), 25(23), 5585. https://doi.org/10.3390/molecules25235585
Aptamer: CD63-1
Target: CD63 positive cells, including breast cancer MDA-MB-231 cells and CD63-overexpressed HEK293T cells
Type of nucleic acid: ssDNA
Sequence: 5’TAACACGACAGACGTTCGGAGGTCGAACCCTGACAGCGTGGG3'
Sequence length: 42
GC content: 0.5952380952380952
Affinity: Kd: 96.92 nM and 113.20 nM for MDA-MB-231 and HEK293T/CD63 cells respectively via flow cytometry
Pool type: 5′-TAGGGAAGAGAAGGACATATGAT-N43-TTGACTAGTACATGACCACTTGA-3′
Pool random region: 43
Binding buffer/conditions: PH 7.4 PBS containing 2.0 mM MgCl2, 0.02% Tween 20, and 100 µg/mL Salmon Sperm DNA (ThermoFisher, 15632011)
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: Therapeutic and Diagnostic: " The developed aptamers could be useful towards efficient isolation of native state exosomes from clinical samples and various theranostic applications for CD63-positive cancers. Current CD63 aptamer related exosome applications focus mainly on high-sensitive exosome detection (via establishing aptamer biosensors) for diagnostic purposes."
Additional information: utilized Competitive SELEX
Reference (2020, Molecules ): Song, Z., Mao, J., Barrero, R. A., Wang, P., Zhang, F., & Wang, T. (2020). Development of a CD63 Aptamer for Efficient Cancer Immunochemistry and Immunoaffinity-Based Exosome Isolation. Molecules (Basel, Switzerland), 25(23), 5585. https://doi.org/10.3390/molecules25235585
Aptamer: CD63-2
Target: CD63 protein
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAAGAGAAGGACATATGATTAACCACCCCACCTCGCTCCCGTGACACTAATGCTAATTCCAATTGACTAGTACATGACCACTTGA3′
Sequence length: 89
GC content: 0.449438202247191
Affinity: Kd: 78.43 ± 12.53 nM via ELISA assay
Pool type: 5′-TAGGGAAGAGAAGGACATATGAT-N43-TTGACTAGTACATGACCACTTGA-3′
Pool random region: 43
Binding buffer/conditions: PH 7.4 PBS containing 2.0 mM MgCl2, 0.02% Tween 20, and 100 µg/mL Salmon Sperm DNA (ThermoFisher, 15632011)
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: Therapeutic and Diagnostic: " The developed aptamers could be useful towards efficient isolation of native state exosomes from clinical samples and various theranostic applications for CD63-positive cancers. Current CD63 aptamer related exosome applications focus mainly on high-sensitive exosome detection (via establishing aptamer biosensors) for diagnostic purposes."
Additional information: utilized Competitive SELEX
Reference (2020, Molecules ): Song, Z., Mao, J., Barrero, R. A., Wang, P., Zhang, F., & Wang, T. (2020). Development of a CD63 Aptamer for Efficient Cancer Immunochemistry and Immunoaffinity-Based Exosome Isolation. Molecules (Basel, Switzerland), 25(23), 5585. https://doi.org/10.3390/molecules25235585
Aptamer: E22P–AbD43
Target: Toxic beta-amyloid 42 dimer (Aβ42)
Type of nucleic acid: ssRNA
Sequence: 5'GGGACGAAGACCAACUGAACUUUGUGGUGGCGGCUACUCGUGUUCUUUUGACUUUGUCCGUGCUGCCACCUUACUUC3'
Sequence length: 77
GC content: 0.5194805194805194
Affinity: Kd: 20 ± 6.0 nM
Pool type: 5'-GGACGAAGACCAACUGAACUGAACUUU-N55-UUGUCCGUGCUGCCACCUUACUUC-3'
Pool random region: 55
Binding buffer/conditions: 50 mM sodium phosphate, and 100 mM NaCl, pH 7.4
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 50-100 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Therapeutic: " Cumulative evidence shows that metastable oligomers of Aβ42 can induce neuronal death and cognitive dysfunction, which is in contrast to end-stage mature fibrils whose contribution to Alzheimer's disease (AD) pathology is lower; The development of oligomer-specific inhibitors is imperative for making meaningful progress toward developing AD therapies without adverse effects"
Reference (2020, J Biol Chem ): Murakami, K., Obata, Y., Sekikawa, A., Ueda, H., Izuo, N., Awano, T., Takabe, K., Shimizu, T., & Irie, K. (2020). An RNA aptamer with potent affinity for a toxic dimer of amyloid β42 has potential utility for histochemical studies of Alzheimer's disease. The Journal of biological chemistry, 295(15), 4870–4880. https://doi.org/10.1074/jbc.RA119.010955)