Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 211
Aptamer sequence: AGGAAGGCTTTAGGTGGAAT
Target unique ID: P04585
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_207 PF1-D (16-25) 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: AGGAAGGCTTTAGGTGGAAT
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_207 Description PF1-D (16-25)
Aptamer chemistry DNA Length 20 nt
GC content 45.0% Molecular weight 6,501.01 Da
Molarity of 1 μg/μl solution 153.82 μM Number of G-quadruplexes 2
G-Score 18 Function Targeted therapy
Sequence AGGAAGGCTTTAGGTGGAAT
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 211
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_198 DNA AGGAAGGCTTTAGGTCTGAG 80.00%
Apta_196 DNA AGGAAGGCTTTAGGTCTGAGATCTC 76.00%
Apta_200 DNA AGGAAGGCTTTAGGT 75.00%
Apta_208 DNA AGGAAGGGGTGGAAT 75.00%
Apta_210 DNA AGGTTGGTTGGTTGGAAT 70.00%
Apta_206 DNA AGGAAGGGGTCTGAGATCTCGGAAT 68.00%
Apta_184 DNA AGGAAGGCTTTAGGTCTGAGATCTCGGAAT 66.67%
Apta_191 DNA AGGAAGGCTTTACCTCTGAGATCTCGGAAT 66.67%
Apta_192 DNA AGGAAGGCTTTAGCTCTGAGATCTCGGAAT 66.67%
Apta_215 DNA AGGAAGGCTTTAGGTCCGAGATCTCGGAAT 66.67%
Apta_203 DNA GGAAGGCTTTAGGTCTGAGATCTCGG 65.38%
Apta_193 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGAAT 64.52%
Apta_186 DNA AGGAACGCTTTAGGTCTGAGATCTCGGAAT 63.33%
Apta_194 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGGAAT 62.50%
Apta_195 DNA AGGAAGGCTTTAGGGGTCTGAGATCTCGGAAT 62.50%
Apta_185 DNA ACCAAGGCTTTAGGTCTGAGATCTCCCAAT 60.00%
Apta_189 DNA AGGAACCCTTTACCTCTGAGATCTCGGAAT 60.00%
Apta_190 DNA AGGAACCCTTTAGGTCTGAGATCTCGGAAT 60.00%
Apta_209 DNA AAGGCTTTAGGTCTG 60.00%
Apta_214 DNA AGGAAGGCTTTAGGTTTCCTAAAGCCTTCC 60.00%

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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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