RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: GABAS-01
Target: Glycated Human Serum Albumin (GHSA)
Type of nucleic acid: ssDNA
Sequence: 5'ATGCGGATCCCGCGCGCAGTGCAGGGAGCCGCTCCACGTACGTTGCGCGAAGCTTGCGC3'
Sequence length: 59
GC content: 0.6949152542372882
Affinity: Kd: 1.748 ± 0.227 nM
Pool type: 5′-ATGCGGATCCCGCGC-N30-GCGCGAAGCTTGCGC-3′
Pool random region: 30
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: Detection: " This result shows the potential application of GABAS-01 as an effective on-site detection probe of GHSA. In addition, these properties of GABAS-01 are expected to contribute to detection of GHSA in diagnostic fields. GHSA allows for a more accurate diagnosis and treatment; therefore, it can be used as a more accurate marker for diabetes mellitus."
Reference (2020, Biosensors (Basel) ): Kim, A.-R., Choi, Y., Kim, S.-H., Moon, H.-S., Ko, J.-H., & Yoon, M.-Y. (2020). Development of a Novel ssDNA Sequence for a Glycated Human Serum Albumin and Construction of a Simple Aptasensor System Based on Reduced Graphene Oxide (rGO). Biosensors, 10(10), 141. doi:10.3390/bios10100141
Aptamer: C7
Target: Rituximab, anti-CD20 lgG1 antibody
Type of nucleic acid: ssDNA
Sequence: 5’GGCCATTGTGGACTTCTTTGGGTAATTCAGGGGCTCGATT3’
Sequence length: 40
GC content: 0.5
Affinity: Kd: 8.8nM
Pool type: 5´-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3´
Pool random region: 40
Binding buffer/conditions: 20 mM Tris pH 7.6, 100 mM NaCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% v/v Tween 20
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research and Therapeutic: " These aptamers are suitable to act as pre-sensor for protein precipitation, which may be useful for studying the unfolding process of antibodies. This study demonstrates the potential of aptamer selection for specific stress-based protein variants, which has potential impact for quality control of biopharmaceuticals. The use of aptamers provides a unique opportunity to select for structurally modified proteins that are impossible to screen for when using in vivo generated antibodies. In a broader context, aptamers selected for unfavourable protein conformations might be used as pre-sensors for protein precipitation and misfolded proteins in biopharmaceuticals."
Additional information: the antibody, rituximab, was extensively heat treated and that heat treated formation was what the aptamer bound to
Reference (2020, PLoS One ): Kohlberger, M., Wildner, S., Regl, C., Huber, C. G., & Gadermaier, G. (2020). Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies. PloS one, 15(11), e0241560. https://doi.org/10.1371/journal.pone.0241560
Aptamer: C2
Target: Rituximab, anti-CD20 lgG1antibody
Type of nucleic acid: ssDNA
Sequence: 5´ATACCAGCTTATTCAATTTAGTATTCACGGCAGAGTCTGGCAGACTTGTCTTCTTGTGAGATAGTAAGTGCAATCT3´
Sequence length: 76
GC content: 0.3947368421052631
Affinity: Kd: 65.8 nM
Pool type: 5´-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3´
Pool random region: 40
Binding buffer/conditions: 20 mM Tris pH 7.6, 100 mM NaCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% v/v Tween 20
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research and Therapeutic: " These aptamers are suitable to act as pre-sensor for protein precipitation, which may be useful for studying the unfolding process of antibodies. This study demonstrates the potential of aptamer selection for specific stress-based protein variants, which has potential impact for quality control of biopharmaceuticals. The use of aptamers provides a unique opportunity to select for structurally modified proteins that are impossible to screen for when using in vivo generated antibodies. In a broader context, aptamers selected for unfavourable protein conformations might be used as pre-sensors for protein precipitation and misfolded proteins in biopharmaceuticals."
Additional information: the antibody, rituximab, was extensively heat treated and that heat treated formation was what the aptamer bound to
Reference (2020, PLoS One ): Kohlberger, M., Wildner, S., Regl, C., Huber, C. G., & Gadermaier, G. (2020). Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies. PloS one, 15(11), e0241560. https://doi.org/10.1371/journal.pone.0241560
Aptamer: C10
Target: Rituximab, anti-CD20 lgG1 antibody
Type of nucleic acid: ssDNA
Sequence: 5’ACTTCGGCTAGTTAGGGGGTAGTTTAGATCGTCTCTACAT3’
Sequence length: 40
GC content: 0.45
Affinity: Kd: 17.6 nM
Pool type: 5´-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3´
Pool random region: 40
Binding buffer/conditions: 20 mM Tris pH 7.6, 100 mM NaCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% v/v Tween 20
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research and Therapeutic: " These aptamers are suitable to act as pre-sensor for protein precipitation, which may be useful for studying the unfolding process of antibodies. This study demonstrates the potential of aptamer selection for specific stress-based protein variants, which has potential impact for quality control of biopharmaceuticals. The use of aptamers provides a unique opportunity to select for structurally modified proteins that are impossible to screen for when using in vivo generated antibodies. In a broader context, aptamers selected for unfavourable protein conformations might be used as pre-sensors for protein precipitation and misfolded proteins in biopharmaceuticals."
Additional information: the antibody, rituximab, was extensively heat treated and that heat treated formation was what the aptamer bound to
Reference (2020, PLoS One ): Kohlberger, M., Wildner, S., Regl, C., Huber, C. G., & Gadermaier, G. (2020). Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies. PloS one, 15(11), e0241560. https://doi.org/10.1371/journal.pone.0241560
Aptamer: C57
Target: Rituximab, anti-CD20 lgG1 antibody
Type of nucleic acid: ssDNA
Sequence: 5´ATACCAGCTTATTCAATTGGCGTATGCAGTTTTGTAGGGTTATCAAGGCTTGACGATTAGATAGTAAGTGCAATCT3´
Sequence length: 76
GC content: 0.3815789473684211
Affinity: Kd: 82.4 nM
Pool type: 5´-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3´
Pool random region: 40
Binding buffer/conditions: 20 mM Tris pH 7.6, 100 mM NaCl, 2 mM MgCl2, 5 mM KCl, 1 mM CaCl2, 0.02% v/v Tween 20
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Research and Therapeutic: " These aptamers are suitable to act as pre-sensor for protein precipitation, which may be useful for studying the unfolding process of antibodies. This study demonstrates the potential of aptamer selection for specific stress-based protein variants, which has potential impact for quality control of biopharmaceuticals. The use of aptamers provides a unique opportunity to select for structurally modified proteins that are impossible to screen for when using in vivo generated antibodies. In a broader context, aptamers selected for unfavourable protein conformations might be used as pre-sensors for protein precipitation and misfolded proteins in biopharmaceuticals."
Additional information: the antibody, rituximab, was extensively heat treated and that heat treated formation was what the aptamer bound to
Reference (2020, PLoS One ): Kohlberger, M., Wildner, S., Regl, C., Huber, C. G., & Gadermaier, G. (2020). Rituximab-specific DNA aptamers are able to selectively recognize heat-treated antibodies. PloS one, 15(11), e0241560. https://doi.org/10.1371/journal.pone.0241560
Aptamer: XK-10
Target: Klebsiella Pneumoniae Carbapenemase 2 (KPC-2) specifically on KPC-2 Escherichia coli (E. coli)
Type of nucleic acid: ssDNA
Sequence: 5′GACAGGCAGGACACCGTAACGGCAGGACACCGTAACGGGTATGCAGCTATCCCGGGCGCTGTCTGAAGATCGTGTGCTGCTCTGCTACCTCCCTCCTCTTC3′
Sequence length: 101
GC content: 0.6039603960396039
Affinity: Kd: 0.81 ± 0.13 nM via SPR & 12.9 ± 1.03 nM via microarray chip 
Pool type: 5′-GACAGGCAGGACACCGTAAC-N40-CTGCTACCTCCCTCCTCTTC-3′ also 5′-GACAGGCAGGACACCGTAAC-3N-GTCC-5N-GGAC-2N-GCC-4N-GGC-3N-GTTACGGTGCTGCTACCTCCCTCCTCTTC-3′
Pool random region: 40
Binding buffer/conditions: 1 × PBSMCT: 137 mM NaCl, 2.7 mM KCl, 5 mM MgCl2 and 1 mM CaCl2, 0.05% Tween-20, pH 7.4
Divalent salt: MgCl/CaCl
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: " Aptamer XK-10 was specifically bound to KPC-2 that identified by fluorescence polarization, and was also used to detect KPC-2. In addition, two methods were used to verify the specificity of aptamer XK-10 to KPC-2 E. coli and further suggesting that XK-10 could specifically recognize KPC-2 protein on the surface of KPC-2 E. coli. The Precision-SELEX was more efficient than traditional bacteria screening and could also be extended to screen other bacteria that express other kind of enzymes. recision-SELEX could simplify screening process and provide an accurate and efficient method to select aptamers for bacteria."
Additional information: utilized two pools, however XK-10 sequence was most present in both end round libraries | utilized Precision-SELEX. . Primers for PCR amplification consisted of TAMRA-modified forward primer (TAMRA-FP) and biotinylated-modified reverse primer (Biotin-RP). TAMRA-FP: 5′-TAMRA-GACAGGCAGGACACCGTAAC-3′, Biotin-RP: 5′-Biotin-GAAGAGGAGGGAGGTAGCAG-3′.
Reference (2021, Talanta ): Yu, F., Chen, J., Wang, Z., Yang, H., Li, H., Jia, W., Xue, S., Xie, H., & Xu, D. (2021). Screening aptamers for serine β-lactamase-expressing bacteria with Precision-SELEX. Talanta, 224, 121750. https://doi.org/10.1016/j.talanta.2020.121750
Aptamer: OC2
Target: Osteocalcin (OC) - osteoporosis biomarker
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGGCGATGAGAACGGGAGCCTGATGATACACACGAGCGATCGCTCATAAAAGCCGTGCCCGAGATAGTAAGTGCAATCT3′
Sequence length: 96
GC content: 0.4791666666666667
Affinity: Kd: 55.5 nM via fluorescence-based assay
Pool type: 5′-ATACCAGCTTATTCAATT-N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 2 mM MgCl2, 50 mM Tris (pH 7.5) and 150 mM NaCl in distilled water
Divalent salt: MgCl
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: " The high-affinity aptamers for each analyte were used to fabricate the graphene oxide-based fluorescence assay for the sensitive detection of BC or OC. The assay is highly sensitive which can detect OC and BC in the picogram range. This assay can selectively detect the target molecules against other non-specific proteins. This simple fluorescence assay is potentially applicable for the rapid detection of BC and OC biomarkers osteoporosis and bone resorption cases. Finally, we estimate the amount of BC and OC in known serum samples. As this is very simple and fast, we believe that these sensors might be applied for the analysis of clinical samples."
Reference (2021, Talanta ): Chinnappan, R., Zaghloul, N. S., AlZabn, R., Malkawi, A., Abdel Rahman, A., Abu-Salah, K. M., & Zourob, M. (2021). Aptamer selection and aptasensor construction for bone density biomarkers. Talanta, 224, 121818. https://doi.org/10.1016/j.talanta.2020.121818
Aptamer: BC1
Target: Beta-crosslap (BC) - osteoporosis biomarker
Type of nucleic acid: ssDNA
Sequence: 5’ATGACGGGGGTCTAGGCAAGTAATAACGGGGGCAAGCTTTTCTATCTCGTTCTAGGGTA3’
Sequence length: 59
GC content: 0.4915254237288136
Affinity: Kd: 69.34 nM via fluorescence-based assay
Pool type: 5′-ATACCAGCTTATTCAATT-N60-AGATAGTAAGTGCAATCT-3′
Pool random region: 60
Binding buffer/conditions: 2 mM MgCl2, 50 mM Tris (pH 7.5) and 150 mM NaCl in distilled water
Divalent salt: MgCl
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: " The high-affinity aptamers for each analyte were used to fabricate the graphene oxide-based fluorescence assay for the sensitive detection of BC or OC. The assay is highly sensitive which can detect OC and BC in the picogram range. This assay can selectively detect the target molecules against other non-specific proteins. This simple fluorescence assay is potentially applicable for the rapid detection of BC and OC biomarkers osteoporosis and bone resorption cases. Finally, we estimate the amount of BC and OC in known serum samples. As this is very simple and fast, we believe that these sensors might be applied for the analysis of clinical samples."
Reference (2021, Talanta ): Chinnappan, R., Zaghloul, N. S., AlZabn, R., Malkawi, A., Abdel Rahman, A., Abu-Salah, K. M., & Zourob, M. (2021). Aptamer selection and aptasensor construction for bone density biomarkers. Talanta, 224, 121818. https://doi.org/10.1016/j.talanta.2020.121818
Aptamer: T-2
Target: Thyroglobulin (Tg)
Type of nucleic acid: ssDNA
Sequence: 5′CCTAACCGATATCACACTCACCGCGTGAGCGGGGAGGCGATGCCCAGGCTAACTTGACTCAGTTGGTCGTCATTGGAGTATC3'
Sequence length: 82
GC content: 0.5609756097560976
Affinity: Kd: 3.18 μM via sequence homology using Clustal X software & 4.51 nM via TFI assay
Pool type: 5′-CCTAACCGATATCACACTCAC-N40-GTTGGTCGTCATTGGAGTATC-3′
Pool random region: 40
Binding buffer/conditions: Four kinds of incubation solutions (separately adding 1 mM MgCl2, 2.7 mM KCl, and 40 mM NaCl) were used: a) 25 mM trizma base, 192 mM glycine, 5 mM K2HPO4 (TGK, pH 8.3); b) 25 mM Tris–HCl (pH 7.4); c) 50 mM H3BO3/Na2B4O7 solution (BBS, pH 8.7); d) 8.1 mM Na2HPO4, 1.1 mM KH2PO4 (PBS, pH 7.4)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8.3
Molecular weight of target: ~660 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " CE-based detection validated the application feasibility of aptamer for Tg detection. However, the detection limit was still higher than those of the two traditional methods of RIA (10−13 M) and IMA (10−15 M), so more sensitive aptasensors were required to be further developed for convenient diagnose and postoperative monitoring of differentiated thyroid cancer. The recognition and detection of Tg are significant for the diagnose and postoperative monitoring of thyroid cancer."
Additional information: utilized CE-SELEX
Reference (2021, Talanta ): Zhu, C., Li, L., Fang, S., Zhao, Y., Zhao, L., Yang, G., & Qu, F. (2021). Selection and characterization of an ssDNA aptamer against thyroglobulin. Talanta, 223(Pt 1), 121690. https://doi.org/10.1016/j.talanta.2020.121690
Aptamer: ARH1t6
Target: RNase H2 from Clostridium difficile (C. difficile) (CDH2)
Type of nucleic acid: ssDNA
Sequence: 5'TTACGTCAAGGTGTCACTCCGCCAGGTGTGCGACGGTCGT3'
Sequence length: 40
GC content: 0.6
Affinity: Kd: 1.8 ± 0.5 nM & inhibition constant (IC50) of 7.1 ± 0.6 nM
Pool type: 5'-TTACGTCAAGGTGTCACTCC-N40-GAAGCATCTCTTTGGCGTG-3'
Pool random region: 40
Binding buffer/conditions: HEPES buffer: 50 mM HEPES, 150 mM NaCl, 6 mM KCl, 2.5 mM MgCl2, 2.5 mM CaCl2, 0.01% v/v Tween-20, pH 7.4
Divalent salt: MgCl/CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated begining at the 3' end to 40 nucleotides total
Application as quoted in the referenced paper: Diagnostic and Drug Development: " Test to detect C. This work demonstrates that a ubiquitous protein like RNase H2 can still be used as the target for the development of highly specific aptamers and the combination of the protein and the aptamer can achieve the recognition specificity needed for a diagnostic test and drug development"
Reference (2021, ACS Appl Mater Interfaces ): Li, J., Gu, J., Zhang, H., Liu, R., Zhang, W., Mohammed-Elsabagh, M., Xia, J., Morrison, D., Zakaria, S., Chang, D., Arrabi, A., & Li, Y. (2021). A Highly Specific DNA Aptamer for RNase H2 from Clostridium difficile. ACS applied materials & interfaces, 13(8), 9464–9471. https://doi.org/10.1021/acsami.0c20277
Aptamer: LI-H3-APT-3
Target: Salivary peptide histatin-3 (synthetic H3 peptides)
Type of nucleic acid: ssDNA
Sequence: 5′ACCGGGTGAGGGGGGTCCAGTGTTAGTAGCGATGGAGGGGTGAC3′
Sequence length: 44
GC content: 0.6363636363636364
Affinity: Kd: 1.97 ± 0.48 μM via ELASA
Pool type: 5′-GGTGACTGCTACTGTGTTGG-N44-CCACACATCCAAGCAGAACC-3′
Pool random region: 44
Binding buffer/conditions: 50 mM Tris, 137 mM NaCl, 5 mM MgCl2, pH 7.4
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated on both sides to remove the primer binding sites
Application as quoted in the referenced paper: Biosensor: " These novel aptamers have the potential to lead to the further development of refined sensing assays and platforms for the detection and quantification of histatin 3 in human saliva and other biological media. Overall, the measurement of H3 levels in saliva could provide special insight into human health conditions, including stress, HIV-infection, and associated oral candidiasis. H3 detection could also be an essential aspect of therapeutic drug monitoring if H3 can be established as an alternative therapeutic agent. Additionally, this SELEX approach is broadly applicable to identify the aptamers for other small molecules or molecules that are not suitable for the immobilization on solid surfaces. The aptamers report the binding event by conformational change and, thus, should find extensive application for use in sensing platforms that rely on such principles. These aptamers have the potential to facilitate the development of low cost and sensitive assays or biosensors for the H3 target."
Reference (2021, J Biotechnol ): Ojha, Y. R., Giovannucci, D. R., & Cameron, B. D. (2021). Selection and characterization of structure-switching DNA aptamers for the salivary peptide histatin 3. Journal of biotechnology, 327, 9–17. https://doi.org/10.1016/j.jbiotec.2020.12.018
Aptamer: AP32
Target: Sonic hedgehog ligand (SHh)
Type of nucleic acid: ssDNA
Sequence: 5'GCTTCCAATAACCTGCAAAATAACCTGGAAGC3'
Sequence length: 32
GC content: 0.4375
Affinity: Kd: 25.7 ± 4.1 nM via Bio-layer interferometry (BLI)
Pool type: 5'-AGTCCTGCACTACGCT-N40-AGATCGCAGCTGAGTC-3'
Pool random region: 40
Binding buffer/conditions: 8 mM Na2HPO4, 136 mM NaCl, 2 mM KH2PO4, 5 mM MgCl2, 0.01% salmon sperm DNA
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated from ap72
Application as quoted in the referenced paper: Diagnostic: " This novel aptasensor-based SHh assay may offer a reliable means in predicting early metastasis and poor prognosis in hepatocellular carcinoma. An AP32-aptasensor assay was developed to analyze SHh content in cell or tissue lysates and serum samples in a minimal volume. The assay enables a rapid, sensitive and reliable detection of SHh in a variety of sample types, has an acceptable positive rate and superior specificity in distinguishing HCC from paracancerous liver tissue, and may offer a novel bioassay for prediction of early metastasis (such as portal vein invasion), poor prognosis for HCC patients. The assay may be extended for any other tumors with significant involvement of hedgehog signaling activity, such as glioblastoma, basal cell carcinoma for further clinical validation."
Reference (2021, Biosens Bioelectron ): Li, H. Y., Yin, F. F., Li, X. Y., Jia, W. N., Ding, J., Zhang, L., Wang, Z. H., Hu, Q. Q., Zuo, J. L., Jia, H. L., Wang, L. H., Fan, C. H., Gu, H. Z., & Wu, J. (2021). Novel aptasensor-based assay of sonic hedgehog ligand for detection of portal vein invasion of hepatocellular carcinoma. Biosensors & bioelectronics, 174, 112738. https://doi.org/10.1016/j.bios.2020.112738
Aptamer: AP72
Target: Sonic hedgehog ligand (SHh)
Type of nucleic acid: ssDNA
Sequence: 5'AGTCCTGCACTACGCTTCCAATAACCTGCAAAATAACCTGGAAGCACGTCATCATGAGATCGCAGCTGAGTC3'
Sequence length: 72
GC content: 0.4861111111111111
Affinity: Kd: 27.5 ± 3.0 nM via Bio-layer interferometry (BLI)
Pool type: 5'-AGTCCTGCACTACGCT-N40-AGATCGCAGCTGAGTC-3'
Pool random region: 40
Binding buffer/conditions: 8 mM Na2HPO4, 136 mM NaCl, 2 mM KH2PO4, 5 mM MgCl2, 0.01% salmon sperm DNA
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " This novel aptasensor-based SHh assay may offer a reliable means in predicting early metastasis and poor prognosis in hepatocellular carcinoma. An AP32-aptasensor assay was developed to analyze SHh content in cell or tissue lysates and serum samples in a minimal volume. The assay enables a rapid, sensitive and reliable detection of SHh in a variety of sample types, has an acceptable positive rate and superior specificity in distinguishing HCC from paracancerous liver tissue, and may offer a novel bioassay for prediction of early metastasis (such as portal vein invasion), poor prognosis for HCC patients. The assay may be extended for any other tumors with significant involvement of hedgehog signaling activity, such as glioblastoma, basal cell carcinoma for further clinical validation."
Reference (2021, Biosens Bioelectron ): Li, H. Y., Yin, F. F., Li, X. Y., Jia, W. N., Ding, J., Zhang, L., Wang, Z. H., Hu, Q. Q., Zuo, J. L., Jia, H. L., Wang, L. H., Fan, C. H., Gu, H. Z., & Wu, J. (2021). Novel aptasensor-based assay of sonic hedgehog ligand for detection of portal vein invasion of hepatocellular carcinoma. Biosensors & bioelectronics, 174, 112738. https://doi.org/10.1016/j.bios.2020.112738
Aptamer: IR-A43F
Target: Recombinant insulin receptor extracellular domain (His-Tagged)
Type of nucleic acid: 5-uracil-modified-DNA
Sequence: 5’TATGAGTGACCGTCCGCCTGUAUCCGCAGUAUCGGCAUUCAGCGACCCGGGCCACGACNAACAGCCACACCACCAGCCAAA3’
Sequence length: 80
GC content: 0.6
Affinity: Kd: 2.85 nM via filter binding assay
Pool type: 5′-TATGAGTGACCGTCCGCCTG-N40-CAGCCACACCACCAGCCAAA-3
Pool random region: 40
Binding buffer/conditions: 40 mM HEPES (pH 7.5), 102 mM NaCl, 5 mM KCl, 5 mM MgCl2, and 0.05% Tween-20
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Therapeutic: " Allosteric Modulator - Our study implies that aptamers are promising reagents for the development of allosteric modulators that discriminate a specific conformation of a target receptor. Studies of allosteric modulators are not only important to reveal mechanisms of receptor activation, but also to discover new drug candidates. IR-A43 acts as a ‘wedge' to stabilize the insulin-induced active conformation of the receptor to enhance insulin binding to the insulin receptor. Our model is a plausible explanation for the mutual positive cooperativity that occurs when insulin and IR-A43 bind to the insulin receptor. To confirm this model, further studies of the structure of the insulin receptor and IR-A43 complex are required."
Additional information: Modified nucleobase 5-[N-(1-naphthylmethyl)carboxamide]-2′-deoxyuridine (Nap-dU) was used in this sequence
Reference (2021, Nucleic Acids Res ): Yunn, N. O., Park, M., Park, S., Lee, J., Noh, J., Shin, E., & Ryu, S. H. (2021). A hotspot for enhancing insulin receptor activation revealed by a conformation-specific allosteric aptamer. Nucleic acids research, 49(2), 700–712. https://doi.org/10.1093/nar/gkaa1247