Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 173
Aptamer sequence: GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUUCGACAUGAGACUCACAACAGUUCCCUUUAGUGAGGGUUAAUU
Target unique ID: P04578
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_169 B40 Protein ENV_HV1H2 21 nM HBS buffer: 10 mM HEPES, pH 7.4, 150 mM NaCl, 1 mM CaCl2, 1 mM MgCl2, 2.7 mM KCl 15923374
Structure information of aptamer
Aptamer Sequence: GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUUCGACAUGAGACUCACAACAGUUCCCUUUAGUGAGGGUUAAUU
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_169 Description B40
Aptamer chemistry RNA Length 117 nt
GC content 48.7% Molecular weight 37,726.05 Da
Molarity of 1 μg/μl solution 26.51 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUUCGACAUGAGACUCACAACAGUUCCCUUUAGUGAGGGUUAAUU
Applications Bind specifically to the surface glycoprotein (gp120) of the R5 strain
Target information
Type Detail Type Detail
Uniprot ID P04578 Protein name Envelope glycoprotein gp160 (Env polyprotein) [Cleaved into: Surface protein gp120 (SU) (Glycoprotein 120) (gp120); Transmembrane protein gp41 (TM) (Glycoprotein 41) (gp41)]
Gene name(s) env Organism Envelope glycoprotein gp160 (Env polyprotein) [Cleaved into: Surface protein gp120 (SU) (Glycoprotein 120) (gp120); Transmembrane protein gp41 (TM) (Glycoprotein 41) (gp41)]
Status reviewed in uniprot database Length 856
Mass 97,213 Activity regulation N/A
Involvement in disease N/A Catalytic activity N/A
PDB ID(s)
1AIK;1DF4;1DF5;1DLB;1FAV;1G9M;1GC1;1GZL;1K33;1K34;1MZI;1RZJ;2CMR;2ME1;2MG1;2MG2;2MG3;2NY7;2PV6;2XRA;3D0V;3DNL;3DNN;3DNO;3DRO;3IDX;3IDY;3J70;3MNZ;3TYG;3VIE;4JPJ;4JPK;4YDV;4ZTO;5BN0;5C0R;5C0S;5CIL;5CIN;5CMU;5CMZ;5CN0;5DD0;5GHW;5H0N;5HFL;5HM1;5IVX;5KA5;5KA6;5NVP;5NWU;5NWW;5TKJ;5TKK;5WDF;5X08;5YB2;5YB3;5YB4;5YC0;5Z0W;5ZCX;6B9K;6BXP;6BXQ;6DE7;6DLN;6J5E;6JQK;6KTS;6MQC;6MQE;6MQM;6MQR;6MQS;6N16;6NCP;6NPR;6O3G;6O3J;6O3L;6O42;6P60;6P7H;6P8D;6PDR;6PDS;6PDU;6PEC;6PEF;6PSA;6RYF;6SNC;6SND;6SNE;6UBI;6UCE;6UCF;6UJU;6UJV;6WWC;7AEJ;7EKB;7EKK;7LOH;7LOI;
Function Oligomerizes in the host endoplasmic reticulum into predominantly trimers.
Activity data
Interaction ID 173
Target type Protein
Target unique ID P04578
Activity 21 nM
Binding Conditions/Buffer

HBS buffer: 10 mM HEPES, pH 7.4, 150 mM NaCl, 1 mM CaCl2, 1 mM MgCl2, 2.7 mM KCl
Assay

The titration yielded an equilibrium dissociation constant (Kd) of 21 ± 2 nM and 31 ± 2 nM for the aptamer B40 and B40t77 respectively
PubMed ID 15923374
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_170 RNA GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCC 65.81%
Apta_137 RNA GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC 55.56%
Apta_432 RNA GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC 53.85%
Apta_433 RNA GGGAGACAAGAAUAAACGCUCAACGUUCAGUAUAACAGUCCGAGUCUAACACACAAUGGGACACUGAAUUCGACAGGAGGCUCACAACAGGC 52.99%
Apta_893 RNA ACCGAGUCCAGAAGCUUGUAGUACUUAUGUCCCAUCGAACGCAGUGUAUCUUGCACCGACUCUCUGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC 52.14%
Apta_705 RNA CCGUAAUACGACUCACUAUAGGGGAGCUCGGUACCGAAUUCAAGGUACUCUGUGCUUGUCGAUGUGUAUUGAUGGCACUUUCGAGUCAACGAGUUGACAGAACAAGUAGUCAAGCUUUGCAGAGAGGAUCCUU 51.88%
Apta_171 RNA GGGAGCUCAGAAUAAACGCUCAACCAGUCUUGUGGCUUUGAAAGAGAGGAGUGUUCGACAUGAGGCCCGGAUCCGGC 51.28%
Apta_224 RNA GGGGCCACCAACGACAUUGAACCACGUAGGCUCGUUUCUGAGCCGAUCUCGAUGUUGAUAUAAAUAGUGCCCAUGGAUC 51.28%
Apta_272 RNA GGGAGACAAGAAUAAACGCUCAACACAGAACGCGGUCCCCACACAGGACAGGAGCCAGCCCCGGUUCGACAGGAGGCUCACAACAGGC 51.28%
Apta_854 RNA GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC 51.28%
Apta_43 RNA GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC 50.43%
Apta_225 RNA GGGGCCACCAACGACAUUUAUCGAAUUGAUAACCUUACGCGAGAGCGUAGUUCGUUGAUAUAAAUAGUGCCCAUGGAUC 50.43%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 50.43%
Apta_723 RNA GGGAGCUCAGAAUAAACGCUCAAAUCCGUGGACAGGGCGUAAGCGCCUUCGACAUGAGACACGGAUCCUGCGACGAAUUCAGC 50.43%
Apta_1124 RNA GGGCGAAUUCGGGUUGGAUAGUAGGCGCAUAUGGCAUCUUCGUGGUUGUGUAUUGCCCUUUAGUGAGGGUUAAUU 50.43%
Apta_1223 RNA GGAGGCGCCAACUGAAUGAAAGGUUACGCUUCAACGCCGUGCAGCUGCUUCGGCAGGCUUGUGAGUACAUGGCCCAUUGAUCCGUAACUAGUCGCGUCAC 50.43%
Apta_337 RNA GGGAGGAUAUUUUCUCAGACCGUAAGUACCGAAUGUGCUUUUGGCCGAUUUUUGGCCCCUGCAGUUGCAGCAUCGUGAACUAGGAUCCGGG 49.57%
Apta_410 RNA GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG 49.57%
Apta_494 RNA GGGAGAUACCAGCUUAUUCAAUUCUGGCAAUGGGCUAUCCCAAGUGCUAGGCUUCAGGGAGCGAGGACCAGACGACGUACCUAACCCUAAGGUGAGAUAGUAAGUGCAAUCU 49.57%
Apta_562 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUUAGGGCCAAGUGUGGUGAAAGACACACUCGAAACGGUAGCGAGAGCUC 49.57%

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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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