RosettaCommons/UTexasAptamer huggingface dataset:
Aptamer: 8
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCTATGAACCAAGGGAGGGGCAGGGCGGGTAGGGTTAATAACGGATTCCGAGCGCCCAGCTCCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 104
GC content: 0.6153846153846154
Affinity: Kd: 1.1x10^-5 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 13
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCACGAAGAAACAGGGCGCTTCGAACGAACATGGGCAGGGTGGGAAGTTTTAAAGTGGTACCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 103
GC content: 0.5631067961165048
Affinity: Kd: 9.1x10^-6 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 14
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCCAGCGTAAGGTCGTGGGTGGTTGGGTGCCTAAGCGTATACTTACAGCGATTGATTTGGTCCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 104
GC content: 0.5673076923076923
Affinity: Kd: 1.2x10^-4 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 20
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCGGTGCGGGTAGGGATGAGGGCGGGTCGGGTTGAGTGTGAGCTTAGGGGTGGCGGATCTACCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 104
GC content: 0.6442307692307693
Affinity: Kd: 6.3x10^-6 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 22
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCCTAGAGTAACCTGTTGGGAGGGCGGGTAGGGCCCATTGAGAGGAGGACGTATTCGTCCGCCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 104
GC content: 0.6153846153846154
Affinity: Kd: 1.3x10^-5 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 26
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCCAATGGGGTCGGGCGGGCCGGGTGTCATGGTGGACGGAGATGGGACGTAGAGGGCGGTCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 102
GC content: 0.6666666666666666
Affinity: Kd: 1.6x10^-6 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 30
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCGCGGCAAATCAGCATACGAGTGTACAGGGACGGGACGGGTGGGTAAAAGGTGTCGCCTCAGCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 105
GC content: 0.6095238095238096
Affinity: Kd: 2.7x10^-6 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 32
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCCCAACTTGGGCGGAGGGCTAACGGTGGGGGGATATTATGAGGGGTGGAGGTATTAACCATTCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 105
GC content: 0.580952380952381
Affinity: Kd: 9.8x10^-6 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 33
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'TAGGGAATTCGTCGACGGATCCCCGGGGATTAGAATAGTGGAGGGCCGGTGGCAAATGGGTAAGTAGGTTGAAGGGCTAAATTCTGCAGGTCGACGCATGCGCCG3'
Sequence length: 105
GC content: 0.5619047619047619
Affinity: Kd: 2.2x10^-4 M
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: 26-3'
Target: Hematoporphyrin IX (HPIX)
Type of nucleic acid: ssDNA
Sequence: 5'ATGGTGGACGGAGATGGGACGTAG3'
Sequence length: 24
GC content: 0.5833333333333334
Affinity: Not reported
Pool type: 5'-TAGGGAATTCGTCGACGGATCC-N59-CTGCAGGTCGACGCATGCGCCG-3'
Pool random region: 59
Binding buffer/conditions: 100 mM Tris±acetate pH 8.0, 200 mM sodium acetate,50 mM potassium acetate, 25 mM magnesium acetate,5% dioxane
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: To determine which sequence is necessary to recognize hpix, these two ssdnas were synthesized for aptamer 26 and their binding affinity to hpix was analyzed.
Application as quoted in the referenced paper: Detection: " In the present study, we selected single-stranded DNAs (ssDNAs) which were capable of binding to hematoporphyrin IX (HPIX) with μM order of dissociation constants. Structural analysis of these aptamers indicated that guanine-rich (G-rich) sequences are necessary for recognition of HPIX. From the CD spectrum of the binding site of the aptamer, the structure of G-rich sequence is indicated to form the parallel guanine-quartet (G-quartet)."
Reference (2000, Bioorg Med Chem Lett ): Okazawa, A., Maeda, H., Fukusaki, E., Katakura, Y., & Kobayashi, A. (2000). In vitro selection of hematoporphyrin binding DNA aptamers. Bioorganic & medicinal chemistry letters, 10(23), 2653–2656. https://doi.org/10.1016/s0960-894x(00)00540-0
Aptamer: cAMP - b (parent)
Target: Second messenger adenosine 3',5'-cyclic monophosphate (cAMP; 1)
Type of nucleic acid: ssRNA
Sequence: 5'GGAAGAGAUGGCGACUAAAACGACUUGUCGCGUGCUGCCCGCCUGUUCGCUUCUGCACCCCGGCGGUAAGCUUGGCAC3'
Sequence length: 78
GC content: 0.6153846153846154
Affinity: No reported
Pool type: 5′-GGAAGAGAUGGCGAC-N50-CGGUAAGCUUGGCAC-3'
Pool random region: 50
Binding buffer/conditions: 20 mM Tris-HCl (pH 7.5 at 23 °C), 450 mM NaCl, 100 mM KCl, 10 mM MgCl2, 1 mM MnCl2, and 5 mM CaCl2
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: Detection: " Precise molecular recognition is a hallmark of many natural biological receptors and biocatalysts. A high degree of chemical discrimination is important because receptors and enzymes need to perform biochemical functions only with cognate ligands or substrates from a complex mixture of compounds whose constituents typically include closely related analogs."
Reference (2000, Biochemistry ): Koizumi, M., & Breaker, R. R. (2000). Molecular recognition of cAMP by an RNA aptamer. Biochemistry, 39(30), 8983–8992. https://doi.org/10.1021/bi000149n
Aptamer: cAMP - b
Target: Second messenger adenosine 3',5'-cyclic monophosphate (cAMP; 1)
Type of nucleic acid: ssRNA
Sequence: 5'GGAAGAGAUGGCGACUAAAACGACUUGUCGC3'
Sequence length: 31
GC content: 0.5161290322580645
Affinity: Kd: 10 uM
Pool type: 5′-GGAAGAGAUGGCGAC-N50-CGGUAAGCUUGGCAC-3'
Pool random region: 50
Binding buffer/conditions: 20 mM Tris-HCl (pH 7.5 at 23 °C), 450 mM NaCl, 100 mM KCl, 10 mM MgCl2, 1 mM MnCl2, and 5 mM CaCl2
Divalent salt: MgCl/CaCl
Buffer type: Tris Buffers
pH: 7.5
Molecular weight of target: Not reported
Post-SELEX modifications: Truncation
Application as quoted in the referenced paper: Detection: " Precise molecular recognition is a hallmark of many natural biological receptors and biocatalysts. A high degree of chemical discrimination is important because receptors and enzymes need to perform biochemical functions only with cognate ligands or substrates from a complex mixture of compounds whose constituents typically include closely related analogs."
Reference (2000, Biochemistry ): Koizumi, M., & Breaker, R. R. (2000). Molecular recognition of cAMP by an RNA aptamer. Biochemistry, 39(30), 8983–8992. https://doi.org/10.1021/bi000149n
Aptamer: B-2
Target: R5 helix peptide
Type of nucleic acid: ssRNA
Sequence: 5'GGGAAACUGGAUGGAAUGGGCUCGAUGAAAAUCGACCGUGCGCUGAAAAGCACGCGAGGUCCUGCUGUAAGUGUGCCA3'
Sequence length: 78
GC content: 0.5512820512820513
Affinity: Kd: 10 nM
Pool type: 5'-GGGAAACUGG AUGGAAUGGGCUCG -N30-CGAGGUCCUGCUGUAAGUGUGCCA-3'
Pool random region: 30
Binding buffer/conditions: 10 mM HEPES, pH7.5, lOOmMNaCI
Buffer type: Other Buffers
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Drug delivery and inhibition: "RNA-binding proteins play a key role in fundamental cellular processes such as translation mRNA processing and early development, and in viral processes on infection by RNA viruses. Understanding RNA-protein interactions is important to study how RNA-binding proteins recognize specifically the target RNA and for drug design to inhibit infection of RNA viruses."
Reference (2000, Nucleic Acids Symp Ser ): Fukusho, S., Furusawa, H., & Okahata, Y. (2000). In vitro selection and analysis of RNA aptamer recognize arginine-rich motif (ARM) model peptide on a QCM. Nucleic acids symposium series, (44), 187–188. https://doi.org/10.1093/nass/44.1.187
Aptamer: 06.50 aptamer
Target: Basic fibroblast growth factor (bFGF(155)), Human
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGGACGATGCGGTGACGTAAGAGTGTAATCGATGCAGCCTGGCAGACGACGAGCGGGA3'
Sequence length: 61
GC content: 0.6065573770491803
Affinity: Kd: 560 pM
Pool type: 5'-GGGAGGACGATGCGG-N61-CAGACGACGAGCGGGA-3'
Pool random region: 61
Binding buffer/conditions: Nitrocellulose filter binding buffer: 1×PBS/2 mM MgCl2/0.01% HSA/1.0 mM dithiothreitol (DTT)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 18 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Here, then, is strong evidence in support of the importance of target affinity for PhotoSELEX-evolved diagnostics. These results indicate the feasibility of PhotoSELEX-evolved diagnostics, but they also indicate the importance of identifying the very best photocross-linking aptamers for use in diagnostic systems."
Reference (2000, J Biotechnol ): Golden, M. C., Collins, B. D., Willis, M. C., & Koch, T. H. (2000). Diagnostic potential of PhotoSELEX-evolved ssDNA aptamers. Journal of biotechnology, 81(2-3), 167–178. https://doi.org/10.1016/s0168-1656(00)00290-x
Aptamer: 06.15 aptamer
Target: Basic fibroblast growth factor (bFGF(155)), Human
Type of nucleic acid: ssDNA
Sequence: 5'GGGAGGACGATGCGGGCGAAGGCACACCGAGTTCATAGTATCCCACAGACGACGAGCGGGA3'
Sequence length: 61
GC content: 0.6229508196721312
Affinity: Kd: 16 pM
Pool type: 5'-GGGAGGACGATGCGG-N61-CAGACGACGAGCGGGA-3'
Pool random region: 61
Binding buffer/conditions: Nitrocellulose filter binding buffer: 1×PBS/2 mM MgCl2/0.01% HSA/1.0 mM dithiothreitol (DTT)
Divalent salt: MgCl
Buffer type: PBS/phosphate buffers
pH: 7.4
Molecular weight of target: 18 kDa
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Here, then, is strong evidence in support of the importance of target affinity for PhotoSELEX-evolved diagnostics. These results indicate the feasibility of PhotoSELEX-evolved diagnostics, but they also indicate the importance of identifying the very best photocross-linking aptamers for use in diagnostic systems."
Reference (2000, J Biotechnol ): Golden, M. C., Collins, B. D., Willis, M. C., & Koch, T. H. (2000). Diagnostic potential of PhotoSELEX-evolved ssDNA aptamers. Journal of biotechnology, 81(2-3), 167–178. https://doi.org/10.1016/s0168-1656(00)00290-x
Aptamer: Chi No 1
Target: Poly-beta-1,4-N-acetylglucosamine (Chitin) (poly-β-1,6-N-acetyl-D-glucosamine)
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAATTCGTCGACGGATCCCCCAGCAGCACTGGTAGTGAGGCAGTTCACCGGTGGGGCGGTGAGTTTGGCTGCTATTTATCTCCAGGTCGACGCATGCGCCG3′
Sequence length: 105
GC content: 0.6
Affinity: Binding Efficiency : <1%
Pool type: 5′-TAGGGAATTCGTCGACGGATCC-N59-CTCCAGGTCGACGC-ATGCGCCG-3′
Pool random region: 59
Binding buffer/conditions: 100 mM NaCl, 100 mM KCl, 5 mM MgCl2, 50 mM Tris–acetate (pH 8.0)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Oligosaccharide antigens play essential biological roles in cellular adhesion, molecular recognition, and so on. However, little is known about the interaction concerning oligosaccharide from the viewpoints of its molecular basis. The present study demonstrated that the in vitro selection method is applicable to obtain the DNA aptamer that selectively recognizes polysaccharide, which physiologically has an important meaning."
Additional information: G-cluster motifs that were sandwiched with palindrome sequences.
Reference (2000, Bioorg Med Chem Lett ): Fukusaki, E., Kato, T., Maeda, H., Kawazoe, N., Ito, Y., Okazawa, A., Kajiyama, S., & Kobayashi, A. (2000). DNA aptamers that bind to chitin. Bioorganic & medicinal chemistry letters, 10(5), 423–425. https://doi.org/10.1016/s0960-894x(00)00013-5
Aptamer: Chi No 23
Target: Poly-beta-1,4-N-acetylglucosamine (Chitin) (poly-β-1,6-N-acetyl-D-glucosamine)
Type of nucleic acid: ssDNA
Sequence: 5′TAGGGAATTCGTCGACGGATCCTGCGCATGTGAAAGGTTGCCTAACTGGACAGGGTTTAGGAGCGACTAGACACAGCTCCAGGTCGACGCATGCGCCG3′
Sequence length: 98
GC content: 0.5714285714285714
Affinity: Binding Efficiency : 18%
Pool type: 5′-TAGGGAATTCGTCGACGGATCC-N59-CTCCAGGTCGACGC-ATGCGCCG-3′
Pool random region: 59
Binding buffer/conditions: 100 mM NaCl, 100 mM KCl, 5 mM MgCl2, 50 mM Tris–acetate (pH 8.0)
Divalent salt: MgCl
Buffer type: Tris Buffers
pH: 8
Molecular weight of target: Not reported
Post-SELEX modifications: Not applicable
Application as quoted in the referenced paper: Diagnostic: " Oligosaccharide antigens play essential biological roles in cellular adhesion, molecular recognition, and so on. However, little is known about the interaction concerning oligosaccharide from the viewpoints of its molecular basis. The present study demonstrated that the in vitro selection method is applicable to obtain the DNA aptamer that selectively recognizes polysaccharide, which physiologically has an important meaning."
Additional information: G-cluster motifs that were sandwiched with palindrome sequences.
Reference (2000, Bioorg Med Chem Lett ): Fukusaki, E., Kato, T., Maeda, H., Kawazoe, N., Ito, Y., Okazawa, A., Kajiyama, S., & Kobayashi, A. (2000). DNA aptamers that bind to chitin. Bioorganic & medicinal chemistry letters, 10(5), 423–425. https://doi.org/10.1016/s0960-894x(00)00013-5