Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 185
Aptamer sequence: CCGTGTAAGGTTTCAGTGGCTTATCCGAAGTAACCCGAGA
Target unique ID: P04585
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_181 | WT12 | Protein | POL_HV1H2 | 652 pM | 10 mM HEPES pH 7.5, 150 mM NaCl, 80 mM KCl, and 5 mM MgCl2 | 33095511 |
Structure information of aptamer
| Aptamer Sequence: | CCGTGTAAGGTTTCAGTGGCTTATCCGAAGTAACCCGAGA |
| 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_181 | Description | WT12 |
| Aptamer chemistry | DNA | Length | 40 nt |
| GC content | 50.0% | Molecular weight | 12,575.88 Da |
| Molarity of 1 μg/μl solution | 79.52 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | CCGTGTAAGGTTTCAGTGGCTTATCCGAAGTAACCCGAGA | ||
| 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
 |
Interaction ID | 185 |
| Target type | Protein | |
| Target unique ID | P04585 | |
| Activity | 652 pM | |
| Binding Conditions/Buffer | 10 mM HEPES pH 7.5, 150 mM NaCl, 80 mM KCl, and 5 mM MgCl2 |
|
| Assay | IC50 values were calculated by fitting the data for the aptamers’ titration to a sigmoidal dose-response curve giving the values at 127.9 ± 10.33, 162.2 ± 10.02, 90.03 ± 6.49, 110.6 ± 9.89, and 84.81 ± 8.54 nM for WT3, WT7 WT12, WT48, and WT62, respectively (Figure 3 and Table 1). Whereas NVP gave the IC50 value at 688.6 ± 6.48 nM. All of the data indicated that the selected DNA aptamers inhibited the WT HIV-1 RT function in the nanomolar range |
|
| PubMed ID | 33095511 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_643 | DNA | ACCGATCCATCGAGTTTCTGAGAAAGGCCCGGAGAAACCGCGAGA | |
| Apta_391 | DNA | ACCGTGGAGGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCACGGT | |
| Apta_571 | DNA | ACCTGCGATAGGTAGTTTGTTTCTGTTGCCCTAGCGTCCGTCGTAACAAGTCA | |
| Apta_1272 | DNA | TCCGTGTATAGGTCGGGTCTCTTGCCAACTGATTCGTTGAAAAGTATAGCCCCGCAGGG | |
| Apta_964 | DNA | CACGAGAGGGGTGAGGTGTCGTATTAGAGGGAAGCTCCAA | |
| Apta_510 | DNA | TGTAATTTGTCTGCAGCGGTTCTTGATCGCTGACACCATATTATGAAGA | |
| Apta_149 | DNA | CCGTAGGTTCGGGGTCGGAGTGGTCCGGAAGATGGCGTGG | |
| Apta_160 | DNA | CGGTGCAGTGGATACATGCCAGCCGTAGCCATCGTGGATA | |
| Apta_193 | DNA | AGGAAGGCTTTAGGGTCTGAGATCTCGGAAT | |
| Apta_194 | DNA | AGGAAGGCTTTAGGGTCTGAGATCTCGGGAAT | |
| Apta_195 | DNA | AGGAAGGCTTTAGGGGTCTGAGATCTCGGAAT | |
| Apta_203 | DNA | GGAAGGCTTTAGGTCTGAGATCTCGG | |
| Apta_214 | DNA | AGGAAGGCTTTAGGTTTCCTAAAGCCTTCC | |
| Apta_215 | DNA | AGGAAGGCTTTAGGTCCGAGATCTCGGAAT | |
| Apta_1256 | DNA | GATCGGGTGTGGGTGGCGTAAAGGGAGCATCGGACA | |
| Apta_729 | DNA | AACACCGTGGAGGATAGTTCGGTGGCTGTTCAGGGTCTCCTCCCGGTG | |
| Apta_239 | DNA | CCCAGATTACTGTGGAGTGGTTGTCTGCGAATCCTTCGTCCACCCAATAG | |
| Apta_33 | DNA | GCGGTAAACTGCGTCCGAAGGGGCTGCAGTGACCCGAATGGGTCCGCCGCGAAGCG | |
| Apta_1273 | DNA | TCCCTCCTGTTGGTTTGGGATGGTGGCGACTATCTGATTGTTTGACTCCCCGTAGGGG | |
| Apta_733 | DNA | TAGGCAGTGGTTTGACGTCCGCATGTTGGGAATAGCCACGCCT |
DEV TOOL
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