Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 289
Aptamer sequence: GAUAAUACGACUCACUAUAGGGUUCACUGCAGACUUGACGAAGCUUGCAGAAAAGGGGGAAGAAGAGGGUGAUUCAGGCGAGAGAAUGGAUCCACAUCUACGAAUUC
Target unique ID: P0C6X7
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_280 ES15-1 Protein R1AB_SARS 1.2 nM 30 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1.5 mM MgCl2 , 2 mM dithiothreitol (DTT) and 1% (w/v) BSA 18082623
Structure information of aptamer
Aptamer Sequence: GAUAAUACGACUCACUAUAGGGUUCACUGCAGACUUGACGAAGCUUGCAGAAAAGGGGGAAGAAGAGGGUGAUUCAGGCGAGAGAAUGGAUCCACAUCUACGAAUUC
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_280 Description ES15-1
Aptamer chemistry RNA Length 107 nt
GC content 46.7% Molecular weight 34,958.69 Da
Molarity of 1 μg/μl solution 28.61 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence GAUAAUACGACUCACUAUAGGGUUCACUGCAGACUUGACGAAGCUUGCAGAAAAGGGGGAAGAAGAGGGUGAUUCAGGCGAGAGAAUGGAUCCACAUCUACGAAUUC
Applications Efficiently inhibit double-stranded DNA unwinding activity of the helicase by up to 85% with an IC50 value of 1.2 nM
Target information
Type Detail Type Detail
Uniprot ID P0C6X7 Protein name Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor nsp1 (Leader protein) (Non-structural protein 1) (nsp1); Non-structural protein 2 (nsp2) (p65 homolog); Papain-like protease nsp3 (PL-PRO) (EC 3.4.19.12) (EC 3.4.22.-) (Non-structural protein 3) (nsp3) (PL2-PRO); Non-structural protein 4 (nsp4); 3C-like proteinase nsp5 (3CL-PRO) (3CLp) (EC 3.4.22.69) (Main protease) (Mpro) (Non-structural protein 5) (nsp5) (SARS coronavirus main proteinase); Non-structural protein 6 (nsp6); Non-structural protein 7 (nsp7); Non-structural protein 8 (nsp8); Non-structural protein 9 (nsp9); Non-structural protein 10 (nsp10) (Growth factor-like peptide) (GFL); RNA-directed RNA polymerase nsp12 (Pol) (RdRp) (EC 2.7.7.48) (Non-structural protein 12) (nsp12); Helicase nsp13 (Hel) (EC 3.6.4.12) (EC 3.6.4.13) (Non-structural protein 13) (nsp13); Proofreading exoribonuclease nsp14 (ExoN) (EC 2.1.1.-) (EC 3.1.13.-) (Guanine-N7 methyltransferase) (Non-structural protein 14) (nsp14); Uridylate-specific endoribonuclease nsp15 (EC 4.6.1.-) (NendoU) (Non-structural protein 15) (nsp15); 2'-O-methyltransferase nsp16 (EC 2.1.1.57) (Non-structural protein 16) (nsp16)]
Gene name(s) rep 1a-1b Organism Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor nsp1 (Leader protein) (Non-structural protein 1) (nsp1); Non-structural protein 2 (nsp2) (p65 homolog); Papain-like protease nsp3 (PL-PRO) (EC 3.4.19.12) (EC 3.4.22.-) (Non-structural protein 3) (nsp3) (PL2-PRO); Non-structural protein 4 (nsp4); 3C-like proteinase nsp5 (3CL-PRO) (3CLp) (EC 3.4.22.69) (Main protease) (Mpro) (Non-structural protein 5) (nsp5) (SARS coronavirus main proteinase); Non-structural protein 6 (nsp6); Non-structural protein 7 (nsp7); Non-structural protein 8 (nsp8); Non-structural protein 9 (nsp9); Non-structural protein 10 (nsp10) (Growth factor-like peptide) (GFL); RNA-directed RNA polymerase nsp12 (Pol) (RdRp) (EC 2.7.7.48) (Non-structural protein 12) (nsp12); Helicase nsp13 (Hel) (EC 3.6.4.12) (EC 3.6.4.13) (Non-structural protein 13) (nsp13); Proofreading exoribonuclease nsp14 (ExoN) (EC 2.1.1.-) (EC 3.1.13.-) (Guanine-N7 methyltransferase) (Non-structural protein 14) (nsp14); Uridylate-specific endoribonuclease nsp15 (EC 4.6.1.-) (NendoU) (Non-structural protein 15) (nsp15); 2'-O-methyltransferase nsp16 (EC 2.1.1.57) (Non-structural protein 16) (nsp16)]
Status reviewed in uniprot database Length 7073
Mass 790,248 Activity regulation Inhibited by Remdesivir (GS-5734)
Involvement in disease N/A Catalytic activity Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1)
PDB ID(s)
1Q2W;1QZ8;1UJ1;1UK2;1UK3;1UK4;1UW7;1WOF;1YSY;1Z1I;1Z1J;2A5A;2A5I;2A5K;2ACF;2AHM;2ALV;2AMD;2AMQ;2BX3;2BX4;2C3S;2D2D;2DUC;2FAV;2FE8;2FYG;2G9T;2GA6;2GDT;2GRI;2GT7;2GT8;2GTB;2GX4;2GZ7;2GZ8;2GZ9;2H2Z;2H85;2HOB;2HSX;2IDY;2JZD;2JZE;2JZF;2K7X;2K87;2OP9;2OZK;2PWX;2Q6G;2QC2;2QCY;2QIQ;2RHB;2RNK;2V6N;2VJ1;2XYQ;2XYR;2XYV;2Z3C;2Z3D;2Z3E;2Z94;2Z9G;2Z9J;2Z9K;2Z9L;3D62;3E9S;3EBN;3R24;4TWW;4TWY;4WY3;4ZUH;5B6O;5C5N;5C5O;5C8S;5C8T;5C8U;5E6J;5F22;5N19;5N5O;5NFY;6JYT;6LNQ;6NUR;6NUS;6W79;6WCO;7LCP;7LCQ;
Function Multifunctional protein involved in the transcription and replication of viral RNAs.
Activity data
Interaction ID 289
Target type Protein
Target unique ID P0C6X7
Activity 1.2 nM
Binding Conditions/Buffer

30 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1.5 mM MgCl2 , 2 mM dithiothreitol (DTT) and 1% (w/v) BSA
Assay

Inhibition of the helicase activity of the SCV helicase in the presence of various concentrations of the ES15 RNA
PubMed ID 18082623
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_157 RNA GGGUUCACUGCAGACUUGACGAAGCUUACAAACAAGAGCAAAAAGGGAGUUGACGUAGACUGUGCGGAAUGGAUCCACAUCUACGAAUUC 65.42%
Apta_816 RNA GGGUUCACUGCAGACUUGACGAAGCUUGAGAGAUGCCCCCUGAUGUGCAUUCUUGUUGUGUUGCGGCAAUGGAUCCACAUCUACGAAUUC 59.81%
Apta_705 RNA CCGUAAUACGACUCACUAUAGGGGAGCUCGGUACCGAAUUCAAGGUACUCUGUGCUUGUCGAUGUGUAUUGAUGGCACUUUCGAGUCAACGAGUUGACAGAACAAGUAGUCAAGCUUUGCAGAGAGGAUCCUU 54.14%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 53.27%
Apta_566 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCCUGCGAUGCAGAAAGGUGCUGACGACACAUCGAAACGGUAGCGAGAGCUC 53.27%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 53.27%
Apta_874 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACAGAAGGACGUCGAAACGGUAGCGAGAGCUC 52.99%
Apta_168 RNA AAUUAACCCUCACUAAAGGGAACUGUUGUGAGUCUCAUGUCGAAGAGCGGUUAAGGGAGAUUUAGGCAGCAGCUUGGACAGUGUAUCGGCUGAGUUGAGCGUCUAGUCUUGUCU 52.63%
Apta_171 RNA GGGAGCUCAGAAUAAACGCUCAACCAGUCUUGUGGCUUUGAAAGAGAGGAGUGUUCGACAUGAGGCCCGGAUCCGGC 52.34%
Apta_382 RNA GGCGUGACCUGAUGAGUCACGCAGACGCUAGCGAAUUGGUUCCUCGAAAGGGGAAAGCGUUAUUAAGAAACCAAAAUGUGUUACGAAACGUUCCC 52.34%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 52.34%
Apta_549 RNA GGAGCUCAGCCUUCACUGCAUGAUAAACCGAUGCUGGGCGAUUCUCCUGAAGUAGGGGAAGAGUUGUCAUGUAUGGGGGCACCACGGUCGGAUCCUG 51.40%
Apta_562 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUUAGGGCCAAGUGUGGUGAAAGACACACUCGAAACGGUAGCGAGAGCUC 51.40%
Apta_563 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGAAAGCCAAAGCCGUAGCGCAGAUGAUCUCGCCAUCAGUACCGAAACGGUAGCGAGAGCUC 51.40%
Apta_719 RNA GGAAUGGAUCCACAUCUACGAAGGCUUUGAAGGUGAGACCGUGCAAAUGAGGAUGGUGUGGAUGAUUAGGGUUGUCGGUUUUCACUGCAGACUUGACGAAGCUU 51.40%
Apta_137 RNA GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC 50.47%
Apta_428 RNA GAAGCUUACAAGAAGGACAGCACGAAUAAAACCUGCGUAAAUCCGCCCCAUUUGUGUAAGGGUAGUGGGUCGAAUUCCGCUCA 50.47%
Apta_433 RNA GGGAGACAAGAAUAAACGCUCAACGUUCAGUAUAACAGUCCGAGUCUAACACACAAUGGGACACUGAAUUCGACAGGAGGCUCACAACAGGC 50.47%
Apta_598 RNA GGGAAUUCCGCGUGUGCGCCGCGGAAGACGUUGGAAGGAUAGAUACCUACAACGGGGAAUAUAGAGGCCAGCACAUAGUGAGGCCCUCCUCCC 50.47%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 50.47%

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AptaDB is an online database we developed to integrate comprehensive information about aptamer.
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