Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 415
Aptamer sequence: GCAATGGTACGGTACTTCCGGATGCGGAAACTGGCTAATTGGTGAGGCTGGGGCGGTCGTGCAGCAAAAGTGCACGCTACTTTGCTAA
Target unique ID: P59595
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_409 1 Protein NCAP_SARS 4.93 nM 50 mM Tris/Cl, pH 8.0, 150 mM NaCl, 1.5 mM MgCl2, 2 mM dithiothreitol (DTT) and 1% (w/v) BSA 21920814
Structure information of aptamer
Aptamer Sequence: GCAATGGTACGGTACTTCCGGATGCGGAAACTGGCTAATTGGTGAGGCTGGGGCGGTCGTGCAGCAAAAGTGCACGCTACTTTGCTAA
The optimal secondary structure in dot-bracket notation: .(((((((.((((..(((((....)))))))))))).))))....(((.(((..((.((((((.......)))))))).))).)))..
The centroid secondary structure in dot-bracket notation: .(((.(((.((((..(((((....))))))))))))..)))....(((......((.((((((.......)))))))).....)))..
The MFE structure
The Centroid structure
The mountain plot representation
Aptamer information
Type Detail Type Detail
Aptamer ID Apta_409 Description 1
Aptamer chemistry DNA Length 88 nt
GC content 54.5% Molecular weight 27,367.49 Da
Molarity of 1 μg/μl solution 36.54 μM Number of G-quadruplexes 2
G-Score 20 Function Aptasensor
Sequence GCAATGGTACGGTACTTCCGGATGCGGAAACTGGCTAATTGGTGAGGCTGGGGCGGTCGTGCAGCAAAAGTGCACGCTACTTTGCTAA
Applications Selected ssDNA aptamer may be a good alternative detection probe for the rapid and sensitive detection of SARS
Target information
Type Detail Type Detail
Uniprot ID P59595 Protein name Nucleoprotein (Nucleocapsid protein) (NC) (Protein N)
Gene name(s) N 9a Organism Nucleoprotein (Nucleocapsid protein) (NC) (Protein N)
Status reviewed in uniprot database Length 422
Mass 46,025 Activity regulation N/A
Involvement in disease N/A Catalytic activity N/A
PDB ID(s)
1SSK;1X7Q;2CJR;2GIB;2JW8;2OFZ;2OG3;3I6L;6IEX;7LG0;
Function Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M.
Activity data
Interaction ID 415
Target type Protein
Target unique ID P59595
Activity 4.93 nM
Binding Conditions/Buffer

50 mM Tris/Cl, pH 8.0, 150 mM NaCl, 1.5 mM MgCl2, 2 mM dithiothreitol (DTT) and 1% (w/v) BSA
Assay

Affinity measurement of N protein-selected ssDNA aptamers interaction by ELISA. The N protein was incubated with increasing concentrations of 5′-biotinylated aptamer 1 and 11. After addition of streptavidin-HRP, the amount of N protein-aptamer complex was calculated andgraphed as a function of aptamer concentration. The graph was fit to the Michaelis–Menten equation and the Kd was calculated (4.93± 0.30 nM (aptamer 1) and 9.02±1.89 nM (aptamer 11))
PubMed ID 21920814
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_151 DNA GCAATGGTACGGTACTTCCGCGGTCCGGGGTGGGTGGGTGGTGGGGGGTGCGGGGGGGCGGCCGCAAAAGTGCACGCTACTTTGCTAA 78.41%
Apta_408 DNA GCAATGGTACGGTACTTCCGTCATCAGCTTGTGATGTGGATGCGAACTGCAAAAGTGCACGCTACTTTGCTAA 73.86%
Apta_994 DNA GCAATGGTACGGTACTTCCGGACAGTGCTGAAAACTGTGACCCCCCAAAAGTGCACGCTACTTTGCTAA 70.45%
Apta_995 DNA GCAATGGTACGGTACTTCCCCACCCCACGCTGCTCCCAAAAGTGCACGCTACTTTGCTAA 63.64%
Apta_1107 DNA GCGCGATGGACTGTACCTTCGGCGTAACTGATATTCCTGATGATTCTGGCGAGACGTAGCACAAACCCGGTGTATA 56.82%
Apta_81 RNA GCAAUGGUACGGUACUUCCAAGUGCGGGGGGGAGGUGGUGGUUCCAAAAGUGCACGCUACUUUGCUAA 55.68%
Apta_110 DNA AGCAGCACAGAGGTCAGATGGTTAGGAAGGTGAATAGGTACGACTGCAGGTCTATCGCAGCCTATGCGTGCTACCGTGAA 53.41%
Apta_110 DNA AGCAGCACAGAGGTCAGATGGTTAGGAAGGTGAATAGGTACGACTGCAGGTCTATCGCAGCCTATGCGTGCTACCGTGAA 53.41%
Apta_175 DNA AGCAGCACAGAGGTCAGATGAGGACTGTCGATAAGTATAATGGCAAGTAGCTCGATACATCCTATGCGTGCTACCGTGAA 53.41%
Apta_178 DNA AGCAGCACAGAGGTCAGATGCGGTATGCTGGGTCATCTAACTGGGGATATTCTGATATTGCCTATGCGTGCTACCGTGAA 53.41%
Apta_589 DNA GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG 53.41%
Apta_1006 DNA ATAGGAGTCGACCGACCAGAACTTGTCTTAGGAGGTTTACGGTGGGAATAGTGCGTCTACATCTAGACTC 53.41%
Apta_589 DNA GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG 53.41%
Apta_1128 DNA GCCGAGATTGCACTTACTATCTCAATAGGGTAAAAAAAAAAAGTTGGTCCTATGGGTGGGTTGTTCAGTAATTGAATAAGCTGGTATGCGC 52.75%
Apta_76 DNA CAGCGCTAGGGCTTTTAGCGTAATGGGTAGGGTGGTGCGGTGCAGATATCGGAATTGGTG 52.27%
Apta_80 RNA GCAAUGGUACGGUACUUCCUUUGGAAGAUAGCUGGAGAACUAACCAAAAGUGCACGCUACUUUGCUAA 52.27%
Apta_104 DNA AGCAGCACAGAGGTCAGATGCAAACCACAGCCTGAGTGGTTAGCGTATGTCATTTACGGACCTATGCGTGCTACCGTGAA 52.27%
Apta_104 DNA AGCAGCACAGAGGTCAGATGCAAACCACAGCCTGAGTGGTTAGCGTATGTCATTTACGGACCTATGCGTGCTACCGTGAA 52.27%
Apta_233 DNA AGCAGCACAGAGGTCAGATGTGAAACATAGCATATTTACTTATGTCGCCTTGCCGGTTCCTATGCGTGCTACCGTGAA 52.27%
Apta_587 DNA GGAATGGATCCACATCCATGGATGGGCAATGCGGGGTGGAGAATGGTTGCCGCACTTCGGCTTCACTGCAGACTTGACGAAGCTT 52.27%

ABOUT

AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

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