Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 217
Aptamer sequence: AGGAAGGCAAAAGGAAAAAAAAAAAGGAAA
Target unique ID: P04585
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_213 PF1A Protein POL_HV1H2 > 750 nM 50 mM Tris-HCl, pH 8, 1mM DTT, 80 mM KCl, 6 mM MgCl2 for ten minutes 22554064
Structure information of aptamer
Aptamer Sequence: AGGAAGGCAAAAGGAAAAAAAAAAAGGAAA
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_213 Description PF1A
Aptamer chemistry DNA Length 30 nt
GC content 30.0% Molecular weight 9,678.15 Da
Molarity of 1 μg/μl solution 103.33 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence AGGAAGGCAAAAGGAAAAAAAAAAAGGAAA
Applications Inhibiting function against the WT HIV-1 RT
Target information
Type Detail Type Detail
Uniprot ID P04585 Protein name Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved into: Matrix protein p17 (MA); Capsid protein p24 (CA); Spacer peptide 1 (SP1) (p2); Nucleocapsid protein p7 (NC); Transframe peptide (TF); p6-pol (p6*); Protease (EC 3.4.23.16) (PR) (Retropepsin); Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2) (p66 RT); p51 RT; p15; Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]
Gene name(s) gag-pol Organism Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved into: Matrix protein p17 (MA); Capsid protein p24 (CA); Spacer peptide 1 (SP1) (p2); Nucleocapsid protein p7 (NC); Transframe peptide (TF); p6-pol (p6*); Protease (EC 3.4.23.16) (PR) (Retropepsin); Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2) (p66 RT); p51 RT; p15; Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]
Status reviewed in uniprot database Length 1435
Mass 162,042 Activity regulation The viral protease is inhibited by many synthetic protease inhibitors (PIs), such as amprenavir, atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and saquinavir
Involvement in disease N/A Catalytic activity Reaction=Specific for a P1 residue that is hydrophobic, and P1' variable
PDB ID(s)
1A30;1BV7;1BV9;1BVE;1BVG;1BWA;1BWB;1C0T;1C0U;1C1B;1C1C;1DMP;1DTQ;1DTT;1E6J;1EP4;1ESK;1EX4;1EXQ;1FB7;1FK9;1FKO;1FKP;1G6L;1HIV;1HVH;1HVR;1HWR;1HXB;1JKH;1JLA;1JLB;1JLC;1JLE;1JLF;1JLG;1JLQ;1KLM;1LV1;1LW0;1LW2;1LWC;1LWE;1LWF;1NCP;1O1W;1ODW;1ODY;1QBR;1QBS;1QBT;1QBU;1REV;1RT1;1RT2;1RT3;1RT4;1RT5;1RT6;1RT7;1RTD;1RTH;1RTI;1RTJ;1S1T;1S1U;1S1V;1S1W;1S1X;1T05;1TAM;1TKT;1TKX;1TKZ;1TL1;1TL3;1VRT;1VRU;2HND;2HNY;2HNZ;2KOD;2NPH;2OPP;2OPQ;2OPR;2OPS;2RF2;2RKI;2WHH;2WOM;2WON;2YNF;2YNG;2YNH;2YNI;3AO2;3C6T;3C6U;3DI6;3DLE;3DLG;3DM2;3DMJ;3DOK;3DOL;3DOX;3DRP;3DRR;3DRS;3DYA;3E01;3FFI;3I0R;3I0S;3KJV;3KK1;3KK2;3KK3;3KT2;3KT5;3LAK;3LAL;3LAM;3LAN;3LP0;3LP1;3LP2;3M8P;3M8Q;3MEC;3MED;3MEE;3MEG;3N3I;3NBP;3PHV;3QIN;3QIO;3QIP;3T19;3T1A;3TAM;4B3O;4B3P;4B3Q;4I7F;4KSE;4KV8;4NCG;4Q1W;4Q1X;4Q1Y;4Q5M;4QLH;4U1H;4U1I;4U1J;4U7Q;4U7V;5DGU;5DGW;5EU7;5HRN;5HRP;5HRR;5HRS;5IM7;5J2M;5J2N;5J2P;5J2Q;5K14;5KAO;5T82;5TC2;5VZ6;5XOS;5XOT;5YRS;6BJ2;6BJ3;6BSG;6BSH;6BSI;6BSJ;6DIF;6DIL;6DJ1;6DJ2;6DJ5;6DJ7;6DV0;6DV4;6E7J;6E9A;6EWA;6EX9;6GL1;6J1V;6J1W;6OR7;6OTZ;6P1I;6P1X;6P2G;6PYL;6SKK;6SKM;6SKN;6SLQ;6SLU;6SMU;6UIR;6UIS;6UIT;6UJX;6UJY;6UJZ;6UK0;6VPZ;6VQ2;6VQD;6VQE;6VQY;6VQZ;6WAZ;6WB1;6WPF;6WPH;6WPJ;
Function Mediates, with Gag polyprotein, the essential events in virion assembly, including binding the plasma membrane.
Activity data

No relevant experimental diagram

 Interaction ID 217
Target type Protein
Target unique ID P04585
Activity > 750 nM
Binding Conditions/Buffer

50 mM Tris-HCl, pH 8, 1mM DTT, 80 mM KCl, 6 mM MgCl2 for ten minutes
Assay

N/A
PubMed ID 22554064
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_184 DNA AGGAAGGCTTTAGGTCTGAGATCTCGGAAT 56.67%
Apta_212 RNA AGGAAGGCUUUAGGUCUGAGAUCUCGGAAU 56.67%
Apta_215 DNA AGGAAGGCTTTAGGTCCGAGATCTCGGAAT 56.67%
Apta_322 DNA GAAGTGAAAATGACAGAACACAACA 56.67%
Apta_322 DNA GAAGTGAAAATGACAGAACACAACA 56.67%
Apta_193 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGAAT 54.84%
Apta_186 DNA AGGAACGCTTTAGGTCTGAGATCTCGGAAT 53.33%
Apta_192 DNA AGGAAGGCTTTAGCTCTGAGATCTCGGAAT 53.33%
Apta_1058 RNA GUAAGGCAGCUUACAAACAUUAAGGCACAG 53.33%
Apta_194 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGGAAT 53.12%
Apta_195 DNA AGGAAGGCTTTAGGGGTCTGAGATCTCGGAAT 53.12%
Apta_190 DNA AGGAACCCTTTAGGTCTGAGATCTCGGAAT 50.00%
Apta_191 DNA AGGAAGGCTTTACCTCTGAGATCTCGGAAT 50.00%
Apta_206 DNA AGGAAGGGGTCTGAGATCTCGGAAT 50.00%
Apta_207 DNA AGGAAGGCTTTAGGTGGAAT 50.00%
Apta_326 DNA GCAACAGGGTATCCAAAGGATCAAA 50.00%
Apta_580 DNA ATGCGGGTATATGGTGCGAGAAAACAAGGGGCATACTGGA 50.00%
Apta_343 DNA AACAGAGGGACAAACGGGGGAAGATTTGACGTCGACGAC 48.72%
Apta_513 DNA TAGGGAAAACCAACCGCCCAGAACTGCAGCATAAC 48.57%
Apta_1139 DNA AATAGGGTAAAAAAAAAAAGTTGGTCCTATG 48.39%

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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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