RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: Cs5
Target: CDC133 (cell surface markers of Colorectal cancer (CRC))
Type of nucleic acid: ssDNA
Sequence: 5'TTACATCGAGTGGCTTATAAAGTAGGCGTAGGGCTAGGCGGAGAGATGTAA3'
Sequence length: 51
GC content: 0.4705882352941176
Affinity: Kd: 16.3 ± 6.8 nM
Pool type: 5'-ATACCAGCTTATTCAATT-N40-AGATAGTAAGTGCAATCT-3'
Pool random region: 40
Binding buffer/conditions: 0.1 mg mL-1 yeast tRNA (USA) and 1 mg mL1 BSA (Sigma) into the washing buffer (4.5 g L-1 glucose, 5 mM MgCl2, 0.05 g L-1 CaCl2, and Dulbecco's phosphate buffered saline (DPBS))
Divalent salt: MgCl/CaCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 120 kDa
Application as quoted in the referenced paper: Therapeutic and Diagnostic: " we explored the Cs5-mediated in vitro and in vivo treatment of colorectal cancer via chimera (CD133-aptCs5-Dox) composed of the aptamer and the anticancer drug doxorubicin (Dox). Therefore, our work provides a novel and promising tool for CD133 related cancer diagnosis and treatment."
Additional information: 5'FAM-modified sequences
Reference (2022, J Mater Chem B ): Li, W., Wang, Z., Gao, T., Sun, S., Xu, M., & Pei, R. (2022). Selection of CD133-targeted DNA aptamers for the efficient and specific therapy of colorectal cancer. Journal of materials chemistry. B, 10(12), 2057–2066. https://doi.org/10.1039/d1tb02729h
Aptamer: Apt.6
Target: Angiotensin converting enzyme 2 (hACE2), Human
Type of nucleic acid: ssDNA
Sequence: 5'ATAGTCCCTGGCGTGCTTGACAGCAACACGAACACTGAACGTTCTTAACAAGCCTGGCAGAGCAGGTACGGTGTCA3'
Sequence length: 76
GC content: 0.5263157894736842
Affinity: IC50= 29-43 nM
Pool type: 5'-TGACACCGTACCTGCTCT-N40-AAGCACGCCAGGGACTAT-3'
Pool random region: 40
Binding buffer/conditions: NaCl 140 mM, KCl2 mM, MgCl2 5 mM, CaCl2 2 mM, Tris pH 7.4 20 mM, Tween 20 0.05% [v/v])
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported 
Application as quoted in the referenced paper: Therapeutic: "Our approach brings a significant innovation to the therapeutic paradigm of the SARS-CoV-2 pandemic by protecting the target cell instead of focusing on the virus; this is particularly attractive in light of the increasing number of viral mutants that may potentially escape the currently developed immune-mediated neutralization strategies. by applying in vitro and in silico approaches, we demonstrated that these aptamers could generate a steric hindrance on ACE2, thus preventing the binding of the cleaved S1 subunit SARS-CoV-2 S to the cellular receptor regardless of the viral variant and inhibiting the infection of pseudoviral particles carrying the S protein from SARS-CoV-2."
Additional information: Constant region of Aptamer sequence does not match with the given pool sequnce.
Reference (2022, Pharmacol Res ): Villa, A., Brunialti, E., Dellavedova, J., Meda, C., Rebecchi, M., Conti, M., Donnici, L., De Francesco, R., Reggiani, A., Lionetti, V., & Ciana, P. (2022). DNA aptamers masking angiotensin converting enzyme 2 as an innovative way to treat SARS-CoV-2 pandemic. Pharmacological research, 175, 105982. https://doi.org/10.1016/j.phrs.2021.105982
Aptamer: Apt.14
Target: Angiotensin converting enzyme 2 (hACE2), Human
Type of nucleic acid: ssDNA
Sequence: 5'ATAGTCCCTGGCGTGCTTCCGCGAGAGTTCGACATTCCCGAAAGTACGACGAAAGTCCAGAGCAGGTACGGTGTCA3'
Sequence length: 76
GC content: 0.5526315789473685
Affinity: IC50= 94-186 nM
Pool type: 5'-TGACACCGTACCTGCTCT-N40-AAGCACGCCAGGGACTAT-3'
Pool random region: 40
Binding buffer/conditions: NaCl 140 mM, KCl2 mM, MgCl2 5 mM, CaCl2 2 mM, Tris pH 7.4 20 mM, Tween 20 0.05% [v/v])
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.4
Molecular weight of target: Not reported 
Application as quoted in the referenced paper: Therapeutic: "Our approach brings a significant innovation to the therapeutic paradigm of the SARS-CoV-2 pandemic by protecting the target cell instead of focusing on the virus; this is particularly attractive in light of the increasing number of viral mutants that may potentially escape the currently developed immune-mediated neutralization strategies. by applying in vitro and in silico approaches, we demonstrated that these aptamers could generate a steric hindrance on ACE2, thus preventing the binding of the cleaved S1 subunit SARS-CoV-2 S to the cellular receptor regardless of the viral variant and inhibiting the infection of pseudoviral particles carrying the S protein from SARS-CoV-2."
Additional information: Constant region of Aptamer sequence does not match with the given pool sequnce.
Reference (2022, Pharmacol Res ): Villa, A., Brunialti, E., Dellavedova, J., Meda, C., Rebecchi, M., Conti, M., Donnici, L., De Francesco, R., Reggiani, A., Lionetti, V., & Ciana, P. (2022). DNA aptamers masking angiotensin converting enzyme 2 as an innovative way to treat SARS-CoV-2 pandemic. Pharmacological research, 175, 105982. https://doi.org/10.1016/j.phrs.2021.105982
Aptamer: Seq. ID no. 3
Target: Β-casomorphin-7 (BCM-7)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAAGAGAAGGACATATGATGAAAGAGCCGGACGGGGGGCTGGCAAGGGACGGGGGGGCTGTTGACTAGTACATGACCACTTGA3'
Sequence length: 87
GC content: 0.5632183908045977
Affinity: Kd: 28.93 ± 0.783 nM
Pool type: 5′-TAGGGAAGAGAAGGACATATGAT-N40-TTGACTAGTACATGACCACTTGA-3′
Pool random region: 40
Binding buffer/conditions: 5.0 mM Tris-HCl, 0.5 mM EDTA, and 1.0 M NaCl
Buffer type: Tris Buffers
Molecular weight of target: Not reported 
Application as quoted in the referenced paper: Biosensor: " The non-systematic evolution of ligands by the exponential enrichment (non-SELEX) method was used in the present study for the selection of β-casomorphin-7 (BCM-7)-specific aptamers. These aptamers were tested to evaluate their ability to detect BCM-7 peptide in the human urine sample. These aptamers have the potential in biosensor making for detecting BCM-7 peptide in urine samples of autistic patients."
Additional information: The main objective of the current work was to select aptamers by using the non-SELEX method (magnetic bead-based approach)
Reference (2022, J Dairy Sci ): Parashar, A., Bhushan, V., Mahanandia, N. C., Kumar, S., & Mohanty, A. K. (2022). Non-SELEX method for aptamer selection against β-casomorphin-7 peptide. Journal of dairy science, 105(7), 5545–5560. https://doi-org.ezproxy.lib.utexas.edu/10.3168/jds.2021-21569
Aptamer: RBD-1CM1
Target: Receptor-binding domain (RBD) of SARS-CoV-2 spike protein (S protein)
Type of nucleic acid: ssDNA
Sequence: 5'CAGCACCGACCTTGTGCTTTGGGAGTGCTGGTCTAAGGGCGTTAATAGACA 3'
Sequence length: 51
GC content: 0.5294117647058824
Affinity: Quartz Crystal Microbalance (QCM) Experiments
 -> KA: 8.3 uM
Pool type: Not reported
Binding buffer/conditions: 1X PBS (adjusted pH to 7.4 with the HCl solution)
Check "Other" section
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported 
Post-SELEX modifications: Two point mutation in parent sequence
Application as quoted in the referenced paper: Diagnostic and Detection: " Based on the experimental data of quartz crystal microbalance (QCM), the RBD-1CM1 aptamer could produce larger signals in mass change and exhibit an improved binding affinity to the S protein. Therefore, the RBD-1CM1 aptamer, which was selected from 1431 mutants, was the best potential candidate for the detection of SARS-CoV-2. The RBD-1CM1 aptamer can be an alternative biological element for the development of SARS-CoV-2 diagnostic testing."
Additional information: Parent paper: Song, Y.; Song, J.; Wei, X.; Huang, M.; Sun, M.; Zhu, L.; Lin, B.; Shen, H.; Zhu, Z.; Yang, C. Discovery of aptamers targeting the receptor-binding domain of the SARS-CoV-2 spike glycoprotein. Anal. Chem. 2020, 92, 9895–9900. [CrossRef] [PubMed]. 
This paper proposed in-silico approach, an aptamer (RBD-1C) reported by Song et al. was used as the parent
sequence for the production of one-point and two-point mutated sequences.
The parent sequence: 5'CAGCACCGACCTTGTGCTTTGGGATGCTGGTCCAAGG GCGTTAATGGACA -3'
RBD-1C1M was specifically chosen because of its ZDOCK and ZRANK values (used to evaluate intermolecular interactions). It has the lowest ZRANK value of -98..551 and a ZDOCK value of 51.5. 

The binding/selection buffer was clearly mentioned; The closest binding buffer was
Reference (2022, Int J Mol Sci ): Lin, Y. C., Chen, W. Y., Hwu, E. T., & Hu, W. P. (2022). In-Silico Selection of Aptamer Targeting SARS-CoV-2 Spike Protein. International journal of molecular sciences, 23(10), 5810. https://doi-org.ezproxy.lib.utexas.edu/10.3390/ijms23105810
Aptamer: OS-7.9 aptamer
Target: Osteosarcoma MG-63 cell line, Human
Type of nucleic acid: ssDNA
Sequence: 5'ATCCAGAGTGACGCAGCAGGGCACATTGTTCACACACAGATCACATTACGGAAAACACAACTACACGAAATGTCGTTGGTGGCCC3'
Sequence length: 85
GC content: 0.4941176470588235
Affinity: Kd: 12.8 ± 0.9 nM
Pool type: 5'-ATCCAGAGTGACGCAGCA-N50-AATGTCGTTGGTGGCCC-3'
Pool random region: 50
Binding buffer/conditions: Phosphate-Buffered Saline (PBS) 1 × with 4.5 mg/mL glucose [Acros] and 5 mM MgCl2 [VWR], 1 mg/mL bovine serum albumin (BSA) [NZYTech].
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: Not reported 
Application as quoted in the referenced paper: Diagnostic and Therapeutic: " OS-7.9 could recognize a common protein expressed in these cancer cells, possibly becoming a potential molecular probe for early diagnosis and targeted therapies for metastatic disease. ese outcomes sug_x0002_gest that the OS-7.9 aptamer may be considered a potenial probe for further use in cancer research, namely for develop_x0002_ing early diagnosis assays and therapies for metastatic dis_x0002_ease, as well as for searching common membrane proteins existing in these diferent types of cancers."
Reference (2022, Invest New Drugs ): Tsogtbaatar, K., Sousa, D. A., Ferreira, D., Tevlek, A., Aydın, H. M., Çelik, E., & Rodrigues, L. (2022). In vitro selection of DNA aptamers against human osteosarcoma. Investigational new drugs, 40(1), 172–181. https://doi-org.ezproxy.lib.utexas.edu/10.1007/s10637-021-01161-y
Aptamer: CA15-2
Target: HIV-1 Capsid (CA) lattice tubes
Type of nucleic acid: ssRNA
Sequence: 5'GGAAGAAGAGAAUCAUACACAAGAUCGACGUACCUCAGGGUGGUGUAUGACUGAGGUGAAGACUGUGAACCAUGGCAUGCGGGCAUAAGGUAGGUAAGUCCAUA3'
Sequence length: 104
GC content: 0.4807692307692308
Affinity: Kd: 350 ± 50 nM (using MST at a CA protein concentration of 0.1 - 1000 nM); Kd: 502 ± 57 nM (using nitrocellulose filter binding assays at a CA protein concentration of 10-7500 nM)
Pool type: 5'-GCCAGGAAGAAGAGAATCATACACAAGA-N56-GGGCATAAGGTAGGTAAGTCCATA-3'
Pool random region: 56
Binding buffer/conditions: 50 mM Tris–HCl [pH 7.5], 100 mM KCl, 50 mM NaCl, 1 mM MgCl2)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Research and Therapeutic: " This paper found that aptamer CA15-2 was able to inhibit viral replication when expressed in producer cells, but not when expressed in target cells, opening the door to further examination of the mechanisms underlying viral inhibition by aptamer CA15-2. Importantly, aptamers that recognize accessible sites specific to CA lattice or other CA assembly forms provide an opportunity to investigate impact of these interactions on diverse steps of HIV-1 replication, to further examine CA interactions with host factors, and to identify potentially novel interaction surfaces present on CA assembly forms, all of which could increase our understanding of viral biology and inform development of therapeutics."
Additional information: We describe aptamer CA15-2, which selectively binds CA lattice, but not CA monomer or CA hexamer, suggesting that it targets an interface present and accessible only on CA lattice. The 56N reverse primer with a 5'-amino group attached to a C-6 alkyl chain (5' amino modifier C6) was purchased from Integrated DNA Technologies
The Kd values reported may underrepresent the true bind strength of CA15-2.
Reference (2022, Nucleic Acids Res ): Gruenke, P. R., Aneja, R., Welbourn, S., Ukah, O. B., Sarafianos, S. G., Burke, D. H., & Lange, M. J. (2022). Selection and identification of an RNA aptamer that specifically binds the HIV-1 capsid lattice and inhibits viral replication. Nucleic acids research, 50(3), 1701–1717. https://doi-org.ezproxy.lib.utexas.edu/10.1093/nar/gkab1293
Aptamer: C7
Target: SARS-CoV-2 Spike glycoprotein
Type of nucleic acid: ssDNA
Sequence: 5'CACGACGACAGAGACCACAGCACGTGGCCCACGTTAATCCGTTATAAGTCAAGCTCGATTGTTCGTCTCTGGCTGCTGG3'
Sequence length: 79
GC content: 0.5443037974683544
Affinity: Kd: 89.41 ± 18 nM
Pool type: 5'-CACGACGACAGAGACCACAG-N40-TGTTCGTCTCTGGCTGCTGG-3'
Pool random region: 40
Binding buffer/conditions: 50 mM Tris-HCl pH 7.0, 110 mM NaCl, 1 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Biosensor: "Two selected non-competing DNA aptamers, C7 and C9 were successfully used as sensitive and specific biological recognition elements for the development of electrochemical and fluorescent aptasensors for the SARS-CoV-2 Spike glycoprotein with detection limits of 0.07 fM and 41.87 nM, respectively. As proof-of-concept applications, selected paired aptamers were implemented in a electrochemical aptasensor and a simple sandwich-type fluorescent aptasensor capable of detecting and quantifying S protein in diluted human saliva of multiple donors suggesting a novel tool for the rapid and opportune diagnosis of COVID-19"
Additional information: In this work, the paper used a combination of Ideal-Filter Capillary Electrophoresis SELEX (IFCE-SELEX).
Reference (2022, Anal Biochem ): Martínez-Roque, M. A., Franco-Urquijo, P. A., García-Velásquez, V. M., Choukeife, M., Mayer, G., Molina-Ramírez, S. R., Figueroa-Miranda, G., Mayer, D., & Alvarez-Salas, L. M. (2022). DNA aptamer selection for SARS-CoV-2 spike glycoprotein detection. Analytical biochemistry, 645, 114633. https://doi.org/10.1016/j.ab.2022.114633
Aptamer: C9
Target: SARS-CoV-2 Spike glycoprotein
Type of nucleic acid: ssDNA
Sequence: 5'CACGACGACAGAGACCACAGGGGGGCGTCAAGCGGGGTCACATCGGAGTAGGGAATCTTGTGTTCGTCTCTGGCTGCTGG3'
Sequence length: 80
GC content: 0.6125
Affinity: Kd: 231.9 ± 15 nM
Pool type: 5'-CACGACGACAGAGACCACAG-N40-TGTTCGTCTCTGGCTGCTGG-3'
Pool random region: 40
Binding buffer/conditions: 50 mM Tris-HCl pH 7.0, 110 mM NaCl, 1 mM MgCl2
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 7
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Biosensor: "Two selected non-competing DNA aptamers, C7 and C9 were successfully used as sensitive and specific biological recognition elements for the development of electrochemical and fluorescent aptasensors for the SARS-CoV-2 Spike glycoprotein with detection limits of 0.07 fM and 41.87 nM, respectively. As proof-of-concept applications, selected paired aptamers were implemented in a electrochemical aptasensor and a simple sandwich-type fluorescent aptasensor capable of detecting and quantifying S protein in diluted human saliva of multiple donors suggesting a novel tool for the rapid and opportune diagnosis of COVID-20"
Additional information: In this work, the paper used a combination of Ideal-Filter Capillary Electrophoresis SELEX (IFCE-SELEX).
Reference (2022, Anal Biochem ): Martínez-Roque, M. A., Franco-Urquijo, P. A., García-Velásquez, V. M., Choukeife, M., Mayer, G., Molina-Ramírez, S. R., Figueroa-Miranda, G., Mayer, D., & Alvarez-Salas, L. M. (2022). DNA aptamer selection for SARS-CoV-2 spike glycoprotein detection. Analytical biochemistry, 645, 114633. https://doi.org/10.1016/j.ab.2022.114633
Aptamer: 24-2 (Spinach)
Target: The fluorophore in Green fluorescent protein (GFP) (Ser65-Tyr66-Gly67)
Type of nucleic acid: ssRNA
Sequence: 5'GACGCAACUGAAUGAAAUGGUGAAGGACGGGUCCAGGUGUGGCUGCUUCGGCAGUGCAGCUUGUUGAGUAGAGUGUGAGCUCCGUAACUAGUCGCGUC3'
Sequence length: 98
GC content: 0.5510204081632653
Affinity: KD: 537 nM
Pool type: 5ʼ-ATACGCTCTAGAATTCAATT-N70-AGATAGCTCGAGCAATGC-3ʼ
Pool random region: 70
Binding buffer/conditions: 40 mM HEPES pH 7.4 (or 40 mM Bicine pH 8.0), 125 mM KCl, 5 mM MgCl2, and 5% DMSO
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported 
Post-SELEX modifications: Truncation and mutagenesis of 24-2 (Spinach)
Application as quoted in the referenced paper: Research and Biosensor: " An RNA-fluorophore complex resembling enhanced GFP (EGFP), termed Spinach, emits a green fluorescence comparable in brightness to fluorescent proteins. Spinach is markedly resistant to photobleaching, and Spinach fusion RNAs can be imaged in living cells. These RNA mimics of GFP provide an approach for genetic encoding of fluorescent RNAs. RNAs can be tagged with Spinach, providing a simple strategy for introducing a compact fluorescent tag for live cell imaging of RNAs, while avoiding the problems associated with current methods for tagging RNAs. Spinach is different from GFP in that it exhibits considerable resistance to photobleaching, and fluorescence is observed shortly after Spinach transcription in cells, which contrasts with the delay in acquisition of fluorescence by nascent GFP due to the requirement for fluorophore maturation"
Additional information: Purified single stranded DNA library was then used in a PCR reaction to gently amplify the library and to create double stranded DNA templates for RNA in vitro synthesis.
Reference (2011,Science ): Paige, J. S., Wu, K. Y., & Jaffrey, S. R. (2011). RNA mimics of green fluorescent protein. Science (New York, N.Y.), 333(6042), 642–646. https://doi.org/10.1126/science.1207339
Aptamer: 13-2
Target: The fluorophore in Green fluorescent protein (GFP) (Ser65-Tyr66-Gly67)
Type of nucleic acid: ssRNA
Sequence: 5'UCUAGAAUUCAAUUUGCGUAUUGAGACAGGGCCGCGCUAUUUCUGGAGGGGCGGUACAUGAAAGUGGUGGUUGGGUGCGGUCGGAGAUAGCUCGAGCAAUGC3'
Sequence length: 102
GC content: 0.5294117647058824
Affinity: KD: 464 nM
Pool type: 5ʼ-AUACGCUCUAGAAUUCAAUU-N70-AGAUAGCUCGAGCAAUGC-3ʼ
Pool random region: 70
Binding buffer/conditions: 40 mM HEPES pH 7.4 (or 40 mM Bicine pH 8.0), 125 mM KCl, 5 mM MgCl2, and 5% DMSO
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported 
Application as quoted in the referenced paper: Research and Biosensor: " An RNA-fluorophore complex resembling enhanced GFP (EGFP), termed Spinach, emits a green fluorescence comparable in brightness to fluorescent proteins. Spinach is markedly resistant to photobleaching, and Spinach fusion RNAs can be imaged in living cells. These RNA mimics of GFP provide an approach for genetic encoding of fluorescent RNAs. RNAs can be tagged with Spinach, providing a simple strategy for introducing a compact fluorescent tag for live cell imaging of RNAs, while avoiding the problems associated with current methods for tagging RNAs. Spinach is different from GFP in that it exhibits considerable resistance to photobleaching, and fluorescence is observed shortly after Spinach transcription in cells, which contrasts with the delay in acquisition of fluorescence by nascent GFP due to the requirement for fluorophore maturation"
Additional information: Purified single stranded DNA library was then used in a PCR reaction to gently amplify the library and to create double stranded DNA templates for RNA in vitro synthesis.
Reference (2011,Science ): Paige, J. S., Wu, K. Y., & Jaffrey, S. R. (2011). RNA mimics of green fluorescent protein. Science (New York, N.Y.), 333(6042), 642–646. https://doi.org/10.1126/science.1207339
Aptamer: 29-1
Target: RNA Mimic of Green Fluorescent Protein (Fluorophores, coupled with fluorescence-activated cell sorting (FACS); Escherichia coli
Type of nucleic acid: ssRNA
Sequence: 5'GAGACGCAACUGAAUGAAAUGGUGAAGGAGACGGUCGGGUCCAGGCACAAAAAUGUUGCCUGUUGAGUAGAGUGUGGGCUCCGUAACUAGUCGCGUCAC3'
Sequence length: 99
GC content: 0.5252525252525253
Affinity: Not reported
Pool type: 5'GAGACGCAACTGAATGAA-N26-CTGCTTCGGCAG-N26-TCCGTAACTAGTCGCGTCAC-3'
Pool random region: 26
Binding buffer/conditions: 40 mM HEPES pH 7.4, 100 mM KCl, 1 mM MgCl2, and 0.1% DMSO.
Divalent salt: MgCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported 
Application as quoted in the referenced paper: Detection: " Genetically encoded fluorescent ribonucleic acids (RNAs) have diverse applications, including imaging RNA trafficking and as a component of RNA-based sensors that exhibit fluorescence upon binding small molecules in live cells. tRNA-independent tagging for mammalian cell imaging, in vivo imaging; Reduced magnesium dependence contributes to a nearly 100% increase in brightness in E. coli and allows robust imaging of tagged RNA in mammalian cells without the need for additional magnesium in media. Additionally, unlike Spinach2, Broccoli does not require the use of a tRNA scaffold to promote its folding in vivo. Thus, selection of aptamers in living cells results in variants that exhibit properties allowing them to function well in cells without the need for extensive in vitro mutagenesis."
Additional information: Modification of the Terminal Stem-Loop of Broccoli. Purified single stranded DNA library was then used in a PCR reaction to gently amplify the library and to create double stranded DNA templates for RNA in vitro synthesis.
The middle fixed region in pool indicates a fixed region which is predicted to form a stable tetraloop and which was previously shown to facilitate  the formation of structured aptamers during SELEX.
Reference (2014,J Am Chem Soc): Filonov, G. S., Moon, J. D., Svensen, N., & Jaffrey, S. R. (2014). Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. Journal of the American Chemical Society, 136(46), 16299–16308. https://doi.org/10.1021/ja508478x
Aptamer: Aptamer 9.3
Target: Coagulation Factor IXa (FIXa)
Type of nucleic acid: 2'-fluoro-RNA
Sequence: 5'-GGGAUGGGGACUAUACCGCGUAAUGCUGCCUCCCCAUUCCGGAACGCU3'
Sequence length: 48
GC content: 0.6041666666666666
Affinity: Kd: 0.65 ± 0.2 nM
Pool type: 5′-GGGAGAGAGGAAGAGGGAUGGG-N40-CAUAACCCAGAGGUCGAU-3′
Pool random region: 40
Binding buffer/conditions: 20 mM HEPES, pH 7.4, 150 mM NaCl, 2 mM CaCl2, and 0.01% BSA
Divalent salt: CaCl
Buffer type: Other Buffers
pH: 7.4
Molecular weight of target: Not reported
Application as quoted in the referenced paper: Therapeutic: " Here we show that protein-binding oligonucleotides (aptamers) against coagulation factor IXa are potent anticoagulants. We also show that oligonucleotides complementary to these aptamers can act as antidotes capable of efficiently reversing the activity of these new anticoagulants in plasma from healthy volunteers and from patients who cannot tolerate heparin5. This generalizable strategy for rationally designing a drug–antidote pair thus opens up the way for developing safer regulatable therapeutics."
Additional information: Starting library contained 2'-fluoropyrimidines (2′F cytidine triphosphate and uridine triphosphate)
Reference (2002,Nature): Rusconi, C. P., Scardino, E., Layzer, J., Pitoc, G. A., Ortel, T. L., Monroe, D., & Sullenger, B. A. (2002). RNA aptamers as reversible antagonists of coagulation factor IXa. Nature, 419(6902), 90–94. https://doi.org/10.1038/nature00963