Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 218
Aptamer sequence: AGGAAGGCTTTAGGTTTCCTAAAGCCTTCC
Target unique ID: P04585
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_214 PF1Flip Protein POL_HV1H2 667 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: AGGAAGGCTTTAGGTTTCCTAAAGCCTTCC
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_214 Description PF1Flip
Aptamer chemistry DNA Length 30 nt
GC content 46.7% Molecular weight 9,436.88 Da
Molarity of 1 μg/μl solution 105.97 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence AGGAAGGCTTTAGGTTTCCTAAAGCCTTCC
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 218
Target type Protein
Target unique ID P04585
Activity 667 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_196 DNA AGGAAGGCTTTAGGTCTGAGATCTC 70.00%
Apta_198 DNA AGGAAGGCTTTAGGTCTGAG 63.33%
Apta_203 DNA GGAAGGCTTTAGGTCTGAGATCTCGG 63.33%
Apta_204 DNA CCAAGGCTTTAGGTCTGAGATCTCCC 63.33%
Apta_215 DNA AGGAAGGCTTTAGGTCCGAGATCTCGGAAT 63.33%
Apta_195 DNA AGGAAGGCTTTAGGGGTCTGAGATCTCGGAAT 62.50%
Apta_193 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGAAT 61.29%
Apta_184 DNA AGGAAGGCTTTAGGTCTGAGATCTCGGAAT 60.00%
Apta_205 DNA TTAAGGCTTTAGGTCTGAGATCTCTT 60.00%
Apta_207 DNA AGGAAGGCTTTAGGTGGAAT 60.00%
Apta_359 DNA GGGAACGCGTTATTGGGTAACTTCCC 60.00%
Apta_194 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGGAAT 59.38%
Apta_185 DNA ACCAAGGCTTTAGGTCTGAGATCTCCCAAT 56.67%
Apta_186 DNA AGGAACGCTTTAGGTCTGAGATCTCGGAAT 56.67%
Apta_192 DNA AGGAAGGCTTTAGCTCTGAGATCTCGGAAT 56.67%
Apta_1258 DNA GGCGAAGGAGTCATGTAGGTGTGGTCGAGACCGCTGTGCT 55.00%
Apta_393 DNA AGGAGGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCT 54.05%
Apta_733 DNA TAGGCAGTGGTTTGACGTCCGCATGTTGGGAATAGCCACGCCT 53.49%
Apta_190 DNA AGGAACCCTTTAGGTCTGAGATCTCGGAAT 53.33%
Apta_191 DNA AGGAAGGCTTTACCTCTGAGATCTCGGAAT 53.33%

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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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