Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 495
Aptamer sequence: GGGAGACAAGAATAAACGCTCAAGGGCGTGGTGGGTGGGGTACTAATAATGTGCGTTTGTTCGACAGGAGGCTCACAACAGGC
Target unique ID: Q81258
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_490 r10/43 Protein POLG_HCVNZ 1.3 nM HEPES-buffered saline containing 1 mM CaCl2, 2.7 mM MgCl2, and 0.005% surfactant P-20 (HBS-CKM) 16940097
Structure information of aptamer
Aptamer Sequence: GGGAGACAAGAATAAACGCTCAAGGGCGTGGTGGGTGGGGTACTAATAATGTGCGTTTGTTCGACAGGAGGCTCACAACAGGC
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_490 Description r10/43
Aptamer chemistry DNA Length 83 nt
GC content 53.0% Molecular weight 25,933.61 Da
Molarity of 1 μg/μl solution 38.56 μM Number of G-quadruplexes 3
G-Score 52 Function Targeted therapy
Sequence GGGAGACAAGAATAAACGCTCAAGGGCGTGGTGGGTGGGGTACTAATAATGTGCGTTTGTTCGACAGGAGGCTCACAACAGGC
Applications Inhibition of HCV
Target information
Type Detail Type Detail
Uniprot ID Q81258 Protein name Genome polyprotein [Cleaved into: Core protein precursor (Capsid protein C) (p23); Mature core protein (p21); Envelope glycoprotein E1 (gp32) (gp35); Envelope glycoprotein E2 (NS1) (gp68) (gp70); Viroporin p7; Protease NS2 (p23) (EC 3.4.22.-) (Non-structural protein 2) (NS2); Serine protease/helicase NS3 (EC 3.4.21.98) (EC 3.6.1.15) (EC 3.6.4.13) (Hepacivirin) (NS3 helicase) (NS3 protease) (NS3P) (Viroporin p70); Non-structural protein 4A (NS4A) (p8); Non-structural protein 4B (NS4B) (p27); Non-structural protein 5A (NS5A) (p56/58); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5B) (p68)]
Gene name(s) N/A Organism Genome polyprotein [Cleaved into: Core protein precursor (Capsid protein C) (p23); Mature core protein (p21); Envelope glycoprotein E1 (gp32) (gp35); Envelope glycoprotein E2 (NS1) (gp68) (gp70); Viroporin p7; Protease NS2 (p23) (EC 3.4.22.-) (Non-structural protein 2) (NS2); Serine protease/helicase NS3 (EC 3.4.21.98) (EC 3.6.1.15) (EC 3.6.4.13) (Hepacivirin) (NS3 helicase) (NS3 protease) (NS3P) (Viroporin p70); Non-structural protein 4A (NS4A) (p8); Non-structural protein 4B (NS4B) (p27); Non-structural protein 5A (NS5A) (p56/58); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5B) (p68)]
Status reviewed in uniprot database Length 3021
Mass 329,578 Activity regulation Inhibited by the antiviral drug hexamethylene amiloride (By similarity)
Involvement in disease N/A Catalytic activity Reaction=Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1
PDB ID(s)
6P6S;
Function Packages viral RNA to form a viral nucleocapsid, and promotes virion budding.
Activity data
Interaction ID 495
Target type Protein
Target unique ID Q81258
Activity 1.3 nM
Binding Conditions/Buffer

HEPES-buffered saline containing 1 mM CaCl2, 2.7 mM MgCl2, and 0.005% surfactant P-20 (HBS-CKM)
Assay

The percentage of aptamer bound is plotted against the concentration of polymerase. Estimated values for KD are also shown. Results are expressed as the means of three replicates, and error bars represent the standard errors of the means
PubMed ID 16940097
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_501 DNA GGGAGACAAGAATAAACGCTCAATTTAACGTATTTATTCAAGCTCGTATTCGACAGGAGGCTCACAACAGGC 72.29%
Apta_502 DNA GGGAGACAAGAATAAACGCTCAAATGGACTTTTGAATGTGGCAACAAATTCGACAGGAGGCTCACAACAGGC 72.29%
Apta_790 DNA GGGAGACAAGAATAAACGCTCAAGAAGTGAAAATGACAGAACACAACATTCGACAGGAGGCTCACAACAGGC 71.08%
Apta_137 RNA GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC 62.79%
Apta_272 RNA GGGAGACAAGAAUAAACGCUCAACACAGAACGCGGUCCCCACACAGGACAGGAGCCAGCCCCGGUUCGACAGGAGGCUCACAACAGGC 62.50%
Apta_422 DNA GGGAGCTCAGAATAAACGCTCAATTCGGGAATGATTATCAAATTTATGCCCTCTGATTTCGACATGAGGCCCGGATC 61.45%
Apta_432 RNA GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC 61.11%
Apta_433 RNA GGGAGACAAGAAUAAACGCUCAACGUUCAGUAUAACAGUCCGAGUCUAACACACAAUGGGACACUGAAUUCGACAGGAGGCUCACAACAGGC 60.87%
Apta_454 DNA AGCTCCAGAAGATAAATTACAGGTGAGGGCGGGCGGGTGGTTGTAATATGATCGAATGGTATATGTGTGTTTGCAACTAGGATACTATGACCCCG 55.79%
Apta_171 RNA GGGAGCUCAGAAUAAACGCUCAACCAGUCUUGUGGCUUUGAAAGAGAGGAGUGUUCGACAUGAGGCCCGGAUCCGGC 55.42%
Apta_854 RNA GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC 55.17%
Apta_708 DNA CGTACGGAATTCGCTAGCGGGCGGGGGTGCTGGGGGAATGGAGTGCTGCGTGCTGCGGGGATCCGAGCTCCACGTG 54.22%
Apta_1115 DNA CGTACGGAATTCGCTAGCGGTGACGGACGTGGGGTGCACGAAGGGAGGGGATCCGAGCTCCACGTG 54.22%
Apta_1116 DNA CGTACGGAATTCGCTAGCCGGGGTGGGAACCAGTCTTGCGCGGGTGACGGATCCGAGCTCCACGTG 54.22%
Apta_459 DNA AGCTCCAGAAGATAAATTACAGGGGCGGGGGGGCGGGGGAGGCGGAAGGCCTGCTAAAGTCGTTGTGAGCGAACCAACTAGGATACTATGACCCC 52.63%
Apta_140 DNA GGCAGGAAGACAAACACGATGGGGGGGTATGATTTGATGTGGTTGTTGCATGATCGTGGTCTGTGGTGCTGT 51.81%
Apta_226 DNA GGGAGATCACTTACGGCACCGTATAGTCGTACATGAACGAGTGTGAGTGTTAAGCCTTTGGCGACAGGGCTCGGAACC 51.81%
Apta_403 DNA GTCTTGACTAGTTACGCCCCCAAGAACCCGCTTGCCGTGGTGACGTTGATCATGTCGTTTGGTCATTCAGTTGGCGCCTC 51.81%
Apta_1082 DNA GGCTGGTCCGCTGGGAACAAGGGCGGGAGGGAGGGTGTGGGTGCGACAAGCGGACCAGCC 51.81%
Apta_1090 DNA ATCCAGAGTGACGCAGCAGGGCTTGGGTTGGGAATAAGGATGTGGGAGGCGGCGAACATGGACACGGTGGCTTAGT 51.81%

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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