Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 214
Aptamer sequence: AGGTTGGTTGGTTGGAAT
Target unique ID: P04585
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_210 PF1-18ntTlinkG 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: AGGTTGGTTGGTTGGAAT
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_210 Description PF1-18ntTlinkG
Aptamer chemistry DNA Length 18 nt
GC content 44.4% Molecular weight 5,880.60 Da
Molarity of 1 μg/μl solution 170.05 μM Number of G-quadruplexes 2
G-Score 21 Function Targeted therapy
Sequence AGGTTGGTTGGTTGGAAT
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 214
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_208 DNA AGGAAGGGGTGGAAT 72.22%
Apta_211 DNA GGTTGGTGTGGTTGG 72.22%
Apta_207 DNA AGGAAGGCTTTAGGTGGAAT 70.00%
Apta_202 DNA AAGGCTTTAGGTCTGAGATCTCGGAAT 66.67%
Apta_199 DNA TAGGTCTGAGATCTCGGAAT 65.00%
Apta_197 DNA GGCTTTAGGTCTGAGATCTCGGAAT 64.00%
Apta_206 DNA AGGAAGGGGTCTGAGATCTCGGAAT 64.00%
Apta_184 DNA AGGAAGGCTTTAGGTCTGAGATCTCGGAAT 60.00%
Apta_186 DNA AGGAACGCTTTAGGTCTGAGATCTCGGAAT 60.00%
Apta_190 DNA AGGAACCCTTTAGGTCTGAGATCTCGGAAT 60.00%
Apta_196 DNA AGGAAGGCTTTAGGTCTGAGATCTC 60.00%
Apta_193 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGAAT 58.06%
Apta_192 DNA AGGAAGGCTTTAGCTCTGAGATCTCGGAAT 56.67%
Apta_215 DNA AGGAAGGCTTTAGGTCCGAGATCTCGGAAT 56.67%
Apta_757 DNA GGTGGTGGTGGTTGTGGTGGTGG 56.52%
Apta_194 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGGAAT 56.25%
Apta_195 DNA AGGAAGGCTTTAGGGGTCTGAGATCTCGGAAT 56.25%
Apta_806 DNA GGTTGGATGTAAGGTTGGAGGGGGG 56.00%
Apta_200 DNA AGGAAGGCTTTAGGT 55.56%
Apta_1021 DNA CTGTTTGGTAGGCAG 55.56%

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