Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 78
Aptamer sequence: GGTTGGTGTGGTTGG
Target unique ID: P00734
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_211 TBA (thrombin aptamer) Protein THRB_HUMAN 25 nM 50 mM HEPES, 100 mM NaCl, 1 mM MgCl2, 5 mM KCl, 1 mM,CaCl2, pH 7.4 31580650
Structure information of aptamer
Aptamer Sequence: GGTTGGTGTGGTTGG
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_211 Description TBA (thrombin aptamer)
Aptamer chemistry DNA Length 15 nt
GC content 60.0% Molecular weight 4,965.99 Da
Molarity of 1 μg/μl solution 201.37 μM Number of G-quadruplexes 2
G-Score 20 Function Targeted binding
Sequence GGTTGGTGTGGTTGG
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

No relevant experimental diagram

 Interaction ID 78
Target type Protein
Target unique ID P00734
Activity 25 nM
Binding Conditions/Buffer

50 mM HEPES, 100 mM NaCl, 1 mM MgCl2, 5 mM KCl, 1 mM,CaCl2, pH 7.4
Assay

N/A
PubMed ID 31580650

No relevant experimental diagram

 Interaction ID 215
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_210 DNA AGGTTGGTTGGTTGGAAT 72.22%
Apta_757 DNA GGTGGTGGTGGTTGTGGTGGTGG 65.22%
Apta_545 DNA TTAGTTGGGGTTCAGTTGG 63.16%
Apta_198 DNA AGGAAGGCTTTAGGTCTGAG 60.00%
Apta_806 DNA GGTTGGATGTAAGGTTGGAGGGGGG 60.00%
Apta_1196 DNA GGGGGATGGGGG 60.00%
Apta_1197 DNA GGGGGCATGGGGG 60.00%
Apta_1038 DNA CCCGTCCGTATGGTGGG 58.82%
Apta_1039 DNA GCCCGTCCGTATGGTGGGT 57.89%
Apta_350 DNA GGTGGTGGTGGTTGTGGTGGTGGTGG 57.69%
Apta_546 DNA CACGGCATGGTGGGCGTCGTG 57.14%
Apta_197 DNA GGCTTTAGGTCTGAGATCTCGGAAT 56.00%
Apta_539 DNA CGTGTTGTCTCTCTGTGTCTCG 54.55%
Apta_389 DNA GCCTGTGGTGTTGGGGCGGGTGCG 54.17%
Apta_390 DNA GGTGCGGCGGGACTAGTGGGTGTG 54.17%
Apta_203 DNA GGAAGGCTTTAGGTCTGAGATCTCGG 53.85%
Apta_1193 DNA GGGTTGGAGGTGGAGGGGAGTTGAGG 53.85%
Apta_147 DNA TGCGGTTGTAGTACTCGTGGCCG 52.17%
Apta_12 DNA TGAGGGGGTGGGTGGGACGGGTTGG 52.00%
Apta_1086 DNA GCAGTTGATCCTTTGGATACCCTGG 52.00%

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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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