Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 80
Aptamer sequence: ATCTCGAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACTCGT
Target unique ID: P00734
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_79 | CTBA4T-B1 | Protein | THRB_HUMAN | 19 pM | 1× PBSMT, pH 7.2, contains 137 mM NaCl, 2.68 mM KCl, 8.1 mM Na2HPO4, 1.76 mM KH2PO4, 1 mM MgCl2, and 0.025% Tween-20 | 33021630 |
Structure information of aptamer
| Aptamer Sequence: | ATCTCGAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACTCGT |
| 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_79 | Description | CTBA4T-B1 |
| Aptamer chemistry | DNA | Length | 55 nt |
| GC content | 58.2% | Molecular weight | 17,349.87 Da |
| Molarity of 1 μg/μl solution | 57.64 μM | Number of G-quadruplexes | 2 |
| G-Score | 20 | Function | Targeted therapy |
| Sequence | ATCTCGAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACTCGT | ||
| Applications | Excellent anticoagulation activity | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P00734 | Protein name | Prothrombin (EC 3.4.21.5) (Coagulation factor II) [Cleaved into: Activation peptide fragment 1; Activation peptide fragment 2; Thrombin light chain; Thrombin heavy chain] |
| Gene name(s) | F2 | Organism | Prothrombin (EC 3.4.21.5) (Coagulation factor II) [Cleaved into: Activation peptide fragment 1; Activation peptide fragment 2; Thrombin light chain; Thrombin heavy chain] |
| Status | reviewed in uniprot database | Length | 622 |
| Mass | 70,037 | Activity regulation | Inhibited by SERPINA5 |
| Involvement in disease | Factor II deficiency (FA2D) | Catalytic activity | Reaction=Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B |
| PDB ID(s) | 1A2C;1A3B;1A3E;1A46;1A4W;1A5G;1A61;1ABI;1ABJ;1AD8;1AE8;1AFE;1AHT;1AI8;1AIX;1AWF;1AWH;1AY6;1B5G;1B7X;1BA8;1BB0;1BCU;1BHX;1BMM;1BMN;1BTH;1C1U;1C1V;1C1W;1C4U;1C4V;1C4Y;1C5L;1C5N;1C5O;1CA8;1D3D;1D3P;1D3Q;1D3T;1D4P;1D6W;1D9I;1DE7;1DIT;1DM4;1DOJ;1DWB;1DWC;1DWD;1DWE;1DX5;1E0F;1EB1;1EOJ;1EOL;1FPC;1FPH;1G30;1G32;1G37;1GHV;1GHW;1GHX;1GHY;1GJ4;1GJ5;1H8D;1H8I;1HAG;1HAH;1HAI;1HAO;1HAP;1HBT;1HDT;1HGT;1HLT;1HUT;1HXE;1HXF;1IHS;1IHT;1JMO;1JOU;1JWT;1K21;1K22;1KTS;1KTT;1LHC;1LHD;1LHE;1LHF;1LHG;1MH0;1MU6;1MU8;1MUE;1NM6;1NO9;1NRN;1NRO;1NRP;1NRQ;1NRR;1NRS;1NT1;1NU7;1NU9;1NY2;1NZQ;1O0D;1O2G;1O5G;1OOK;1OYT;1P8V;1PPB;1QBV;1QHR;1QJ1;1QJ6;1QJ7;1QUR;1RD3;1RIW;1SB1;1SFQ;1SG8;1SGI;1SHH;1SL3;1SR5;1T4U;1T4V;1TA2;1TA6;1TB6;1TBZ;1THP;1THR;1THS;1TMB;1TMT;1TMU;1TOM;1TQ0;1TQ7;1TWX;1UMA;1UVS;1VR1;1VZQ;1W7G;1WAY;1WBG;1XM1;1XMN;1YPE;1YPG;1YPJ;1YPK;1YPL;1YPM;1Z71;1Z8I;1Z8J;1ZGI;1ZGV;1ZRB;2A0Q;2A2X;2A45;2AFQ;2ANK;2ANM;2B5T;2BDY;2BVR;2BVS;2BVX;2BXT;2BXU;2C8W;2C8X;2C8Y;2C8Z;2C90;2C93;2CF8;2CF9;2CN0;2FEQ;2FES;2GDE;2GP9;2H9T;2HGT;2HNT;2HPP;2HPQ;2HWL;2JH0;2JH5;2JH6;2OD3;2PGB;2PGQ;2PKS;2PW8;2R2M;2THF;2UUF;2UUJ;2UUK;2V3H;2V3O;2ZC9;2ZDA;2ZDV;2ZF0;2ZFF;2ZFP;2ZFQ;2ZFR;2ZG0;2ZGB;2ZGX;2ZHE;2ZHF;2ZHQ;2ZHW;2ZI2;2ZIQ;2ZNK;2ZO3;3B23;3B9F;3BEF;3BEI;3BF6;3BIU;3BIV;3BV9;3C1K;3C27;3D49;3DA9;3DD2;3DHK;3DT0;3DUX;3E6P;3EE0;3EGK;3EQ0;3F68;3GIC;3GIS;3HAT;3HKJ;3HTC;3JZ1;3JZ2;3K65;3LDX;3LU9;3NXP;3P17;3P6Z;3P70;3PMH;3PO1;3QDZ;3QGN;3QLP;3QTO;3QTV;3QWC;3QX5;3R3G;3RLW;3RLY;3RM0;3RM2;3RML;3RMM;3RMN;3RMO;3S7H;3S7K;3SHA;3SHC;3SI3;3SI4;3SQE;3SQH;3SV2;3T5F;3TU7;3U69;3U8O;3U8R;3U8T;3U98;3U9A;3UTU;3UWJ;3VXE;3VXF;4AX9;4AYV;4AYY;4AZ2;4BAH;4BAK;4BAM;4BAN;4BAO;4BAQ;4BOH;4CH2;4CH8;4DIH;4DII;4DT7;4DY7;4E05;4E06;4E7R;4H6S;4H6T;4HFP;4HTC;4HZH;4I7Y;4LOY;4LXB;4LZ1;4LZ4;4MLF;4NZQ;4O03;4RKJ;4RKO;4RN6;4THN;4UD9;4UDW;4UE7;4UEH;4UFD;4UFE;4UFF;4UFG;4YES;5A2M;5AF9;5AFY;5AFZ;5AHG;5CMX;5DO4;5E8E;5EDK;5EDM;5EW1;5EW2;5GDS;5GIM;5JDU;5JFD;5JZY;5L6N;5MJT;5MLS;5MM6;5NHU;5TO3;5Z5W;5Z5X;6BJR;6C2W;6EO6;6EO7;6EO8;6EO9;6V5T;7KME;8KME; |
 |
Function | Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. |
Activity data
 |
Interaction ID | 80 |
| Target type | Protein | |
| Target unique ID | P00734 | |
| Activity | 19 pM | |
| Binding Conditions/Buffer | 1× PBSMT, pH 7.2, contains 137 mM NaCl, 2.68 mM KCl, 8.1 mM Na2HPO4, 1.76 mM KH2PO4, 1 mM MgCl2, and 0.025% Tween-20 |
|
| Assay | Fraction of the shifted band (aptamer/thrombin complex) vs. [thrombin] for CTBA4T, CTBA4T-B1, and CTBA4MT, respectively. The data was fitted with the Origin software to a saturation 1:1 binding curve using nonlinear regression, resulting in a Kd value provided in each graph |
|
| PubMed ID | 33021630 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_78 | DNA | ATCTCGACTAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACAATACTCGT | |
| Apta_266 | DNA | TGGATGGTAGCTCGGTCGGGGTGGGTGGGTTGGCAAGTCT | |
| Apta_223 | DNA | CATTGAGATAGCTAGTTGTAGCTGCGTCATAGGCTGGGTTGGGTCTAGTGGTTGGGTGTG | |
| Apta_1088 | DNA | ATCCAGAGTGACGCAGCATCGAGTGGCTTGTTTGTAATGTAGGGTTCCGGTCGTGGGTTGGACACGGTGGCTTAGT | |
| Apta_887 | DNA | ACGCTCGGATGCCACTACAGGGGGGTGGTCCTGAGGGTGGTGTGGTTGGTTTGGTTTCCTCATGGACGTGCTGGTGAC | |
| Apta_738 | DNA | ATCGTCTGCTCCGTCCAATACCTGCATATACACTTTGCATGTGGTTTGGTGTGAGGTCGTGC | |
| Apta_590 | DNA | ACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCT | |
| Apta_697 | DNA | CTCTCGGGACGACGGACGCTAATCTTACAAGGGCGTAGTGTATGTCGTCCC | |
| Apta_750 | DNA | ATGCGAACAGGTGGGTGGGTTGGGTGGATTGTTCGGCTTCTTGAT | |
| Apta_1013 | DNA | ATCACGTATGGGGGGCCGGCATGAGGGCCGCGCGTGACA | |
| Apta_1042 | DNA | ATCACGATATGCCCGGCTCATCGGGGTTCAGTTGGGCGGTCACATGGAAA | |
| Apta_1080 | DNA | CTTACGACCCAGGGGGGTGGACAGGCGGGGGTTAGGGGGGTCGTAAG | |
| Apta_1117 | DNA | CGTACGGAATTCGCTAGCGGACTGGAGTCTAGACCGGGTAGCTGTGGTGGATCCGAGCTCCACGTG | |
| Apta_1259 | DNA | GGCGCGGCATGGTGTGGACTCCAGGCGGTAGGGATGTCGT | |
| Apta_979 | DNA | ATGAGTAGTGCGGAGGGATGTGAATACTGACGCGGTCATAGTCGCTGTTGTACCATTGA | |
| Apta_742 | DNA | ATCGTCTGCTCCGTCCAATAGGACCGATAGGAACCACGGACTGCATGTTTCTGCATTTGACGTGGTTTGGTGTGAGGTCGTGC | |
| Apta_417 | DNA | GGCAGGAAGACAAACACCAGGTGAGGGAGACGACGCGAGTGTTAGATGGTAGCTGTTGGTCTGTGGTGCTGT | |
| Apta_1229 | DNA | CACGGGCAGAGGGATAGGTTGTTGACGGGGCTGGTGGGTGGGTGCGCTCGCGCTATCGTGG | |
| Apta_1178 | DNA | AGCGTCGAATACCACTACAGGGGATGCGAAGTTCCGCGGTCGAGTATATGATACATCCATCTAATGGAGCTCGTGGTCAG | |
| Apta_609 | DNA | GCTGCGAGGTGGGTGGGTGGGAGCAATTGGTCCTCGCTTAGCTTCTACGGTGGGCTATCT |
DEV TOOL
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