RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: H63
Target: Mycobacterium tuberculosis HspX antigen
Type of nucleic acid: ssDNA
Sequence: 5′GTCTTGACTAGTTACGCCGGGAACAATATGTTCAAGGGCTCTTTAAAGTTTTAGTTCGTTTGTCATTCAGTTGGCGCCTC3′
Sequence length: 80
GC content: 0.4375
Affinity: Kd: 371 ±  0.02 nM
Pool type: 5′-GTCTTGACTAGTTACGCC-N44-TCATTCAGTTGGCGCCTC-3′
Pool random region: 44
Binding buffer/conditions: 10 mM Tris pH 7.5, 10 mM MgCl2, 50 mM KCl, 25 mM NaCl
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: Detection: " Herein, we report the selection and characterization of a panel of high affinity ssDNA aptamers against Mycobacterium tuberculosis (Mtb) HspX antigen by combining subtractive SELEX technology with biophysical characterization. An in silico secondary structure-guided approach of post-SELEX optimization through aptamer truncation and mutation studies led to the selection and evolution of aptamer H63 and its variant (H63 SL-2 M6), which demonstrated a high degree of accuracy as a diagnostic tool for TBM and has potential for translation into a rapid format test for TBM using CSF specimens."
Reference (2018, Tuberculosis (Edinb) ): Dhiman, A., Haldar, S., Mishra, S. K., Sharma, N., Bansal, A., Ahmad, Y., Kumar, A., Sharma, T. K., & Tyagi, J. S. (2018). Generation and application of DNA aptamers against HspX for accurate diagnosis of tuberculous meningitis. Tuberculosis (Edinburgh, Scotland), 112, 27–36. https://doi.org/10.1016/j.tube.2018.07.004
Aptamer: H63 SL-2 M6
Target: Mycobacterium tuberculosis HspX antigen
Type of nucleic acid: ssDNA
Sequence: 5′GTCTTGACTAGTTACGCCGGGAACAATATGTTCAAGGGCTTTTTTTTTTTTTAGTTCGTTTGTCATTCAGTTGGCGCCTC3′
Sequence length: 80
GC content: 0.4125
Affinity: Kd: 90 ± 2E-5 nM
Pool type: 5′-GTCTTGACTAGTTACGCC-N44-TCATTCAGTTGGCGCCTC-3′
Pool random region: 44
Binding buffer/conditions: 10 mM Tris pH 7.5, 10 mM MgCl2, 50 mM KCl, 25 mM NaCl
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Truncated (28-mer) and mutated derived from aptamer h63
Application as quoted in the referenced paper: Detection: "Herein, we report the selection and characterization of a panel of high affinity ssDNA aptamers against Mycobacterium tuberculosis (Mtb) HspX antigen by combining subtractive SELEX technology with biophysical characterization. An in silico secondary structure-guided approach of post-SELEX optimization through aptamer truncation and mutation studies led to the selection and evolution of aptamer H63 and its variant (H63 SL-2 M6), which demonstrated a high degree of accuracy as a diagnostic tool for TBM and has potential for translation into a rapid format test for TBM using CSF specimens."
Reference (2018, Tuberculosis (Edinb) ): Dhiman, A., Haldar, S., Mishra, S. K., Sharma, N., Bansal, A., Ahmad, Y., Kumar, A., Sharma, T. K., & Tyagi, J. S. (2018). Generation and application of DNA aptamers against HspX for accurate diagnosis of tuberculous meningitis. Tuberculosis (Edinburgh, Scotland), 112, 27–36. https://doi.org/10.1016/j.tube.2018.07.004
Aptamer: PSA-1
Target: Prostate-specific antigen (PSA)
Type of nucleic acid: ssDNA
Sequence: 5'GGACGGTTGCGCTATATTTAACCAAAAGTCTGGATTAACA3'
Sequence length: 40
GC content: 0.4
Affinity: Kd: 177 ± 65 nM
Pool type: 5'-AGGGTTGATAGGTTAAGAGC-N40-CGATGTCAACTAGCTGTTGGG-3'
Pool random region: 40
Binding buffer/conditions: PBS 1 × 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: " The selected aptamer was employed to design an aptamer-based sensor with a sandwich format to detect hPSA. The sensor supports the measurement in serum samples with a minimal dilution and a limit of detection of 0.66 ng/mL, which allows the evaluation of PSA levels with clinical significance in the diagnosis of prostate cancer. The new aptamers we identify are employed as signaling receptors in a sandwich electrochemical aptasensor for the detection of PSA. The evaluation of the clinical performance of the aptasensor in serum at different PSA levels suggests it may be a promising approach to improve the cancer specificity of PSA analysis. The proposed aptasensor could provide an alternative approach for the detection of PSA, with potential to improve clinical outcomes of PSA tests and to reduce the number of unnecessary biopsies for the diagnosis of prostate cancer."
Reference (2019, Biosens Bioelectron ): Díaz-Fernández, A., Miranda-Castro, R., de-Los-Santos-Álvarez, N., Rodríguez, E. F., & Lobo-Castañón, M. J. (2019). Focusing aptamer selection on the glycan structure of prostate-specific antigen: Toward more specific detection of prostate cancer. Biosensors & bioelectronics, 128, 83–90. https://doi.org/10.1016/j.bios.2018.12.040
Aptamer: Ylac8
Target: Lactoferrin
Type of nucleic acid: ssDNA
Sequence: 5'GCAGGACACCGTAACACGGGCTTTTGCTTTATCGTACCCTTTATGCTAGATTGTCCTGC3'
Sequence length: 59
GC content: 0.4915254237288136
Affinity: Kd: 1.0 ± 0.12 nM
Pool type: 5'-GACAGGCAGGACACCGTAAC-N40-CTGCTACCTCCCTCCTCTTC-3'
Pool random region: 40
Binding buffer/conditions:  1 ×PBS (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4·12H2O, 2 mM KH2PO4)
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: " We report a novel method for efficiently screening aptamers from a complex ssDNA library based on silver decahedral nanoparticles (AgNP) and fluorescence activated cell sorting (FACS). In this method, target protein (lactoferrin) and negative proteins (α-lactalbumin, β-lactoglobulin, bovine serum albumin, casein) were respectively immobilized on polystyrene microspheres (PS) to form PSLac, PSα-Lac, PSβ-Lac, PSBSA and PSCas. Six aptamers (Ylac1, Ylac4, Ylac5, Ylac6, Ylac8 and Ylac9) were obtained after five-round of selection. These aptamers showed good specificity towards lactoferrin in the presence of negative proteins. In a word, AgNP-FACS SELEX (AgFACS-SELEX) is a rapid, sensitive and highly efficient method for screening aptamers."
Reference (2019, Talanta ): Yu, F., Li, H., Sun, W., Zhao, Y., Xu, D., & He, F. (2019). Selection of aptamers against Lactoferrin based on silver enhanced and fluorescence-activated cell sorting. Talanta, 193, 110–117. https://doi.org/10.1016/j.talanta.2018.09.063
Aptamer: XQ-P3
Target: PD-L1 (MDA-MB-231 PD-L1 OE cells), Human
Type of nucleic acid: ssDNA
Sequence: 5'ACCGACCGTGCTGGACTCATCTCGCTTTTTTCACGGTCCACACTACTATGAGCGAGCCTGGCG3'
Sequence length: 63
GC content: 0.5714285714285714
Affinity: Kd: 15 ± 1.74 nM
Pool type: 5′-ACCGACCGTGCTGGACTCA-N25-ACTATGAGCGAGCCTGGCG-3′
Pool random region: 25
Binding buffer/conditions: D-PBS supplemented with 4.5 g/L of glucose, 5 mM of MgCl2, 0.1 mg/mL of yeast tRNA, and 1 mg/mL of BSA
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: " In summary, these findings suggest that the selected PD-L1 aptamer might have potential implication in immune modulation and targeted therapy against TNBC. The aptamer-paclitaxel conjugate also exhibited improved cellular uptake and cytotoxicity in PD-L1 over-expressed TNBC cells. This strategy could be a novel method used to select active aptamers against various membrane proteins for both therapeutic and diagnostic applications."
Additional information: Binding buffer obtained from a different paper - Wu, X., Zhao, Z., Bai, H., Fu, T., Yang, C., Hu, X., Liu, Q., Champanhac, C., Teng, I. T., Ye, M., & Tan, W. (2015). DNA Aptamer Selected against Pancreatic Ductal Adenocarcinoma for in vivo Imaging and Clinical Tissue Recognition. Theranostics, 5(9), 985–994. https://doi.org/10.7150/thno.11938
Reference (2020, Med Sci Monit ): Wu, X., Li, F., Li, Y., Yu, Y., Liang, C., Zhang, B., Zhao, C., Lu, A., & Zhang, G. (2020). A PD-L1 Aptamer Selected by Loss-Gain Cell-SELEX Conjugated with Paclitaxel for Treating Triple-Negative Breast Cancer. Medical science monitor : international medical journal of experimental and clinical research, 26, e925583. https://doi.org/10.12659/MSM.925583
Aptamer: C4
Target: Rituximab, anti-CD20 lgG1 antibody
Type of nucleic acid: ssDNA
Sequence: 5´ATACCAGCTTATTCAATTGGACTTGTTTGCTCGAACGATGGTTTGTGCTTTTGTGTTAGATAGTAAGTGCAATCT3´
Sequence length: 75
GC content: 0.3733333333333333
Affinity: Kd: 86.7 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: C5
Target: Rituximab, anti-CD20 lgG1 antibody
Type of nucleic acid: ssDNA
Sequence: 5´ATACCAGCTTATTCAATTCGCTCCGTTTACTCGGTCTGCTATTGGCTTGCCTTTGTTTAGATAGTAAGTGCAATCT3´
Sequence length: 76
GC content: 0.4078947368421052
Affinity: Kd: 56.5 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: Cm-4
Target: Hepatitis B surface antigen (HBsAg)
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTAAGCGGGGTTGAGATATATTAACTAGACAACTTGTTAAAACTCGCGACTACAGATAGTAAGTGCAATCT3′
Sequence length: 87
GC content: 0.3563218390804598
Affinity: Kd: 148.41 ± 1.5 nM via flow cytometry analysis
Pool type: 5′-ATACCAGCTTATTCAATT-N52-AGATAGTAAGTGCAATCT-3′
Pool random region: 52
Binding buffer/conditions: DPBS, and 4.5 g of glucose, 100 mg tRNA, 1 g BSA and 5 ml of 1 M MgCl2; pH 7
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic and Drug Delivery: " Modified cell-SELEX as an efficient method can shorten the selection procedure and increase the success rate while the benefits of cell-based SELEX will be retained. Selected aptamers could be applied in purification columns, diagnostic kits, and drug delivery system against HBV-related liver cancer."
Additional information: utilized human embryonic kidney 293T (HEK293T) to overexpress HBsAg | utilized modified cell-SELEX
Reference (2021, Mol Biol Rep ): Mirian, M., Kouhpayeh, S., Shariati, L., Boshtam, M., Rahimmanesh, I., Darzi, L., Taghizadeh, R., Jahanian-Najafabadi, A., & Khanahmad, H. (2021). Generation of HBsAg DNA aptamer using modified cell-based SELEX strategy. Molecular biology reports, 48(1), 139–146. https://doi.org/10.1007/s11033-020-05995-2
Aptamer: PL1
Target: Programmed death-ligand 1 (PD-L1)-expressing cells
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTGTAGAGTATAAAAAGAGTGATGATCTTTTGTAGGTTTTTTAGATAGTAAGTGCAATCT3′
Sequence length: 76
GC content: 0.2894736842105263
Affinity: Kd: 95.73 ± 14.27 nM via flow cytometry analysis & 16.3 nM via SPR
Pool type: 5′-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3′
Pool random region: 40
Binding buffer/conditions: Yeast tRNA (0.1 mg mL−1, Sigma) and BSA (1 mg mL−1, Sigma) into 4.5 g L−1 glucose and 5 mM MgCl2 in Dulbecco's PBS without calcium and magnesium
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: " The results of the in vitro and in vivo assays demonstrate that this aptamer PL1 can block the interaction of PD-1/PD-L1, and inhibit the tumor growth of the CT26 colon carcinoma. The similar tumor inhibition efficacy and binding capacity of the aptamer PL1 as an antibody indicate that the aptamer PL1 can serve as an alternative therapeutic agent for cancer immunotherapy since the use of antibodies is often restricted by high cost, large size and poor tumor penetration."
Additional information: utilized Cell-SELEX
Reference (2021, J Mater Chem B ): Gao, T., Mao, Z., Li, W., & Pei, R. (2021). Anti-PD-L1 DNA aptamer antagonizes the interaction of PD-1/PD-L1 with antitumor effect. Journal of materials chemistry. B, 9(3), 746–756. https://doi.org/10.1039/d0tb01668c
Aptamer: GVI-1
Target: Grass carp reovirus (GCRV)-infected CIK cells
Type of nucleic acid: ssDNA
Sequence: 5'GACGCTTACTCAGGTGTGACTCGGGGTGTAGCTCGTTATGATTCGGACAAGACTTACCTTGCGCCTCTGGGATCGAAGGACGCAGATGAAGTCTC3'
Sequence length: 95
GC content: 0.5368421052631579
Affinity: Kd: 220.86 nM via flow cytometry
Pool type: 5'-GACGCTTACTCAGGTGTGACTCG-50N-CGAAGGACGCAGATGAAGTCTC-3'
Pool random region: 50
Binding buffer/conditions: 10% FBS (Life Technologies), 1.0 g/L bovine serum albumin (Solarbio, Beijing, China), 5 g/L glucose, 0.1 mg/ml yeast tRNA (Invitrogen, Carlsbad, CA, USA) and 5 mM MgCl2) and phosphatebuffered saline (PBS; 10 mM Na2HPO4.12 H2O, 2 mM KH2PO4,137 mM NaCl)
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: " detection assay for the rapid and sensitive diagnosis of grass carp reovirus (GCRV) infection in its early stage. These aptamers have great potentials in development of rapid diagnosis technology and antiviral agents against GCRV infection in aquaculture."
Additional information: Forward primer was labelled with 6-carboxyfluorescein (FAM) (5'-FAMGACGCTTACTCAGGTGTGACTCG-3'). Reverse primer was labelled with biotin (5'-Biotin-GAGACTTCATCTGCGTCCTTCG-3').
Reference (2021, J Fish Dis ): Yu, Q., Liu, M., Wu, S., Xiao, H., Qin, X., & Li, P. (2021). Generation and characterization of aptamers against grass carp reovirus infection for the development of rapid detection assay. Journal of fish diseases, 44(1), 33–44. https://doi.org/10.1111/jfd.13265
Aptamer: GVI-7
Target: Grass carp reovirus (GCRV)-infected CIK cells
Type of nucleic acid: ssDNA
Sequence: 5'GACGCTTACTCAGGTGTGACTCGTGAACCCACCTCAGGGCATCTTACATTTCTTCTAAGTTGTTACCATGTTTCGAAGGACGCAGATGAAGTCTC3'
Sequence length: 95
GC content: 0.4736842105263157
Affinity: Kd: 176.63 nM via flow cytometry
Pool type: 5'-GACGCTTACTCAGGTGTGACTCG-50N-CGAAGGACGCAGATGAAGTCTC-3'
Pool random region: 50
Binding buffer/conditions: 10% FBS (Life Technologies), 1.0 g/L bovine serum albumin (Solarbio, Beijing, China), 5 g/L glucose, 0.1 mg/ml yeast tRNA (Invitrogen, Carlsbad, CA, USA) and 5 mM MgCl2) and phosphatebuffered saline (PBS; 10 mM Na2HPO4.12 H2O, 2 mM KH2PO4,137 mM NaCl)
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: " detection assay for the rapid and sensitive diagnosis of grass carp reovirus (GCRV) infection in its early stage. These aptamers have great potentials in development of rapid diagnosis technology and antiviral agents against GCRV infection in aquaculture."
Additional information: Forward primer was labelled with 6-carboxyfluorescein (FAM) (5'-FAMGACGCTTACTCAGGTGTGACTCG-3'). Reverse primer was labelled with biotin (5'-Biotin-GAGACTTCATCTGCGTCCTTCG-3').
Reference (2021, J Fish Dis ): Yu, Q., Liu, M., Wu, S., Xiao, H., Qin, X., & Li, P. (2021). Generation and characterization of aptamers against grass carp reovirus infection for the development of rapid detection assay. Journal of fish diseases, 44(1), 33–44. https://doi.org/10.1111/jfd.13265
Aptamer: CX9
Target: Acute promyelocytic leukemia (APL) NB4 cell line
Type of nucleic acid: ssDNA
Sequence: 5′ATACCAGCTTATTCAATTCCATATGTGAGTTTCTTTTTTTGTTTCTCTTGGGCGGGCGAGATAGTAAGTGCAATCT3′
Sequence length: 76
GC content: 0.3815789473684211
Affinity: Kd: 16.2 ± 3.22 nM via flow analysis
Pool type: 5′‐ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT‐3′
Pool random region: 40
Binding buffer/conditions: 4.5 g/L glucoses, 5 mM MgCl2, 0.1 mg/ml yeast tRNA (Invitrogen), and 1 mg/ml bovine serum albumin (BSA) (Amresco) into PBS
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: " Aptamers hold great potential for cancer imaging, diagnosis, and therapy. The study indicates that aptamer CX9 exhibits high affinity and specificity with NB4 cells and lay a foundation for the rapid diagnostic method to detect APL with fluorescence‐labeled aptamer. Future studies are still needed to validate the target molecule and function of CX9 to NB4 cell."
Additional information: utilized Cell-SELEX
Reference (2021, J Clin Lab Anal ): Zhang, X. H., Wang, W., & Chen, X. (2021). Selection and identification of an ssDNA aptamer to NB4 cell. Journal of clinical laboratory analysis, 35(4), e23718. https://doi.org/10.1002/jcla.23718
Aptamer: Apt2
Target: MDA-MB-231 cells, Human
Type of nucleic acid: ssDNA
Sequence: 5′GCCTGTTGTGAGCCTCCTAACATGTTGTTGCCGGGACGCCTCCTTCACCAAAGTTGGTGTCCCCACCTACCATGCTTATTCTTGTCTCCC3′
Sequence length: 90
GC content: 0.5444444444444444
Affinity: Kd: 17.7 ± 2.7 nM
Pool type: 5′-GCCTGTTGTGAGCCTCCTAAC-N49-CATGCTTATTCTTGTCTCCC-3′
Pool random region: 49
Binding buffer/conditions: Phosphate-buffered saline (PBS) 1X pH 7.4, with 1 mM of CaCl2·2H2O [Panreac] and 0.5 mM of MgCl2·6H2O [VWR]
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 and Drug Delivery: " Soft-shelled turtle iridovirus (STIV) causes devastating virus disease in farmed soft-shelled turtles (Trionyx sinensis). In this study, single-stranded DNA (ssDNA) aptamers were generated against STIV-infected Fathead minnow (FHM) cells via Cell-SELEX (Cell based-Systematic Evolution of Ligands by Exponential enrichment technology). It is the first time that aptamers against STIV-infected cells have been selected and characterized. The aptamers have great potential in development of rapid diagnostic assays and targeted antiviral drugs against STIV in aquaculture."
Reference (2021, Sci Rep ): Ferreira, D., Barbosa, J., Sousa, D. A., Silva, C., Melo, L., Avci-Adali, M., Wendel, H. P., & Rodrigues, L. R. (2021). Selection of aptamers against triple negative breast cancer cells using high throughput sequencing. Scientific reports, 11(1), 8614. https://doi.org/10.1038/s41598-021-87998-y
Aptamer: LDH7r-1
Target: Lactate dehydrogenase (LDH), Human
Type of nucleic acid: ssDNA
Sequence: 5′ATAGGAGTCACGACGACCAGAATTTCGGGATGATGGTTTTATGGCCGCTTCGTATGTGCGTCTACCTCTTGACTAAT3'
Sequence length: 77
GC content: 0.4675324675324675
Affinity: Kd: 21.3 ± 3.9 nM
Pool type: 5′-ATAGGAGTCACGACGACCAGAA-N30-TATGTGCGTCTACCTCTTGACTAAT-3'
Pool random region: 30
Binding buffer/conditions: 50 mM Tris-HCl, 5 mM KCl, 100 mM NaCl, 1 mM MgCl2, pH 7.4
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " This study provides new ideas for rapid detection of LDH protein content and enzyme activity, thus contributing to the development of rapid medical detection and also provided new ideas for the rapid detection of other serum markers. This aptamer sequence has the potential use for LDH content and enzyme activity detections, which could further combine with the microfluidic chip and surface-enhanced Raman spectroscopy to construct a high-efficiency and low-cost method for rapid disease diagnosis."
Reference (2021, Anal Bioanal Chem ): Guo, L., Song, Y., Yuan, Y. et al. Identification of nucleic acid aptamers against lactate dehydrogenase via SELEX and high-throughput sequencing. Anal Bioanal Chem 413, 4427–4439 (2021). https://doi.org/10.1007/s00216-021-03397-2
Aptamer: Apt-2.5
Target: Major urinary protein 13 (MUP13) (rat urine biomarker)
Type of nucleic acid: ssDNA
Sequence: 5'ATACCAGCTTATTCAATTGTCCACAAAATCCTTATTTTCCTTCATAGGTTACAATTGTACAATCGTAATCAGTTAG3'
Sequence length: 76
GC content: 0.3157894736842105
Affinity: Kd: 19 ± 2 nM
Pool type: 5‘-ATACCAGCTTATTCAATT–N40 –ACAATCGTAATCAGTTAG-3‘
Pool random region: 40
Binding buffer/conditions: 100 mM NaCl, 20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 5 mM KCl, 1 mM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.6
Molecular weight of target: 18 kDa
Application as quoted in the referenced paper: Biomarker: " The assay showed that the aptamer could detect recombinant MUP13 spiked in filtered urine and the natural MUP13 in unfiltered urine, as a first step into translation to real world application. These are the first known assays to detect and quantify a MUP biomarker of rats."
Additional information: pool information: 76 bp- consisted of 76 bp oligonucleotides with a central random region flanked by two constant regions that acted as the primer binding sites. pool information was found in another paper doi: 10.1371/journal.pone.0134403

The Kd was obtained from Bead-based binding assay. The sequence of 1.4 and 2.5 aptamer is identical however, their secondary structure differ.
Reference (2022, Talanta ): Lucarelli, V., Colbert, D., Li, S., Cumming, M., Linklater, W., Mitchell, J., Travas-Sejdic, J., & Kralicek, A. (2022). Selection and characterization of DNA aptamers for the rat major urinary protein 13 (MUP13) as selective biorecognition elements for sensitive detection of rat pests. Talanta, 240, 123073. https://doi.org/10.1016/j.talanta.2021.123073