Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 76
Aptamer sequence: CAGCGCTAGGGCTTTTAGCGTAATGGGTAGGGTGGTGCGGTGCAGATATCGGAATTGGTG
Target unique ID: P00734
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_76 Thrombin 03 Protein THRB_HUMAN 7.04 pM DPBS with 2.5 mM MgCl2, 1 mM CaCl2, 0.05% TWEEN-20 24644057
Structure information of aptamer
Aptamer Sequence: CAGCGCTAGGGCTTTTAGCGTAATGGGTAGGGTGGTGCGGTGCAGATATCGGAATTGGTG
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_76 Description Thrombin 03
Aptamer chemistry DNA Length 60 nt
GC content 55.0% Molecular weight 19,033.94 Da
Molarity of 1 μg/μl solution 52.54 μM Number of G-quadruplexes 2
G-Score 20 Function Targeted binding
Sequence CAGCGCTAGGGCTTTTAGCGTAATGGGTAGGGTGGTGCGGTGCAGATATCGGAATTGGTG
Applications Binds specifically to thrombin
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 76
Target type Protein
Target unique ID P00734
Activity 7.04 pM
Binding Conditions/Buffer

DPBS with 2.5 mM MgCl2, 1 mM CaCl2, 0.05% TWEEN-20
Assay

Highest affinity aptamers obtained via particle display for four protein targets
PubMed ID 24644057
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_464 DNA GTCAGATTCCACTATAGTAGGTTGGGTAGGGTGGTCGCAGTGGATGATATGTCGTAGGGG 58.33%
Apta_449 DNA CGCACTATGTTTTACGAGCCGTTTCCTCGGCAGATAGTAAGTGCG 56.67%
Apta_67 DNA AGATGCCTGTCGAGCATGCTGTTGTGGTAGGGTTAGGGATGGTAGCGGTTGTAGCTAAACTGCTTTGTCGACGGG 56.00%
Apta_1229 DNA CACGGGCAGAGGGATAGGTTGTTGACGGGGCTGGTGGGTGGGTGCGCTCGCGCTATCGTGG 55.74%
Apta_759 DNA GAGGCATACCAGCTTATTATTGGGGCCGGGGCAAGGGGGGGGTACCGTGGTAGGACAGATAGTAAGTGCAATCTGCGAA 55.70%
Apta_149 DNA CCGTAGGTTCGGGGTCGGAGTGGTCCGGAAGATGGCGTGG 55.00%
Apta_287 DNA CAGCACCGACCTTGTGCTTTGGGAGTGCTGGTCCAAGGGCGTTAATGGACA 55.00%
Apta_830 DNA GACGGTGGCAGGGAAAGGGGTCGGGCATATGGCGGAGGGG 55.00%
Apta_930 DNA TTGCACTATGTTTTAGCTAGGGTTCCCTCCGGAGATAGTAAGTGCAA 55.00%
Apta_942 DNA AGTGGGTAAGGTCTGGTGGATTGTGGACGGGGGGCGGGGCAGTGGCTTGA 55.00%
Apta_1185 DNA CAGGGGGTTTTGGTGGGGGGGGCTGGGTTGTCTTGGGGGTGGGCT 55.00%
Apta_589 DNA GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG 53.75%
Apta_589 DNA GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG 53.75%
Apta_68 DNA AGATGCCTGTCGAGCATGCTGTGAATAGGTAGGGTCGGATGGGCTACGGTGTAGCTAAACTGCTTTGTCGACGGG 53.33%
Apta_148 DNA CCGTAGGTTCGGGGTCGGAGTGGTCCGGAAGGTGGCGTGG 53.33%
Apta_217 DNA CGCCTGATTAGCGATACTCAGGCGTTGGGTGGGTGGGTGGG 53.33%
Apta_255 DNA TAGCGATACTGCGTGGGTTGGGGCGGGTAGGGCCAGCAGTCTCGT 53.33%
Apta_282 DNA ATCCATGGGGCGGAGATGAGGGGGAGGAGGGCGGGTACCCGGTTGAT 53.33%
Apta_411 DNA AGACGTAAGTTAATTGGACTTGGTCGTGTGCGGCACAGCGATTGAAAT 53.33%
Apta_482 DNA AGCAAGGTTTGGTGTTGGTTGGTTGCTGGTTTTGGTTTC 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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