Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 81
Aptamer sequence: GCAAUGGUACGGUACUUCCUUUGGAAGAUAGCUGGAGAACUAACCAAAAGUGCACGCUACUUUGCUAA
Target unique ID: P00735
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_80 | T705 | Protein | THRB_BOVIN | 164 nM | 20 mM Hepes (pH 7.35), 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2 and 0.1% geletin containing 0.05% Tween 20, SHMCK+ buffer containing 0.05% Tween 20 | 12557236 |
Structure information of aptamer
| Aptamer Sequence: | GCAAUGGUACGGUACUUCCUUUGGAAGAUAGCUGGAGAACUAACCAAAAGUGCACGCUACUUUGCUAA |
| 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_80 | Description | T705 |
| Aptamer chemistry | RNA | Length | 68 nt |
| GC content | 44.1% | Molecular weight | 21,242.44 Da |
| Molarity of 1 μg/μl solution | 47.08 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | GCAAUGGUACGGUACUUCCUUUGGAAGAUAGCUGGAGAACUAACCAAAAGUGCACGCUACUUUGCUAA | ||
| Applications | Both RNA aptamers inhibit only bovine thrombin-catalyzed fibrin clot formation in vitro | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P00735 | 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 | 625 |
| Mass | 70,506 | Activity regulation | Inhibited by SERPINA5 |
| Involvement in disease | N/A | Catalytic activity | Reaction=Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B |
| PDB ID(s) | 1A0H;1AVG;1BBR;1ETR;1ETS;1ETT;1HRT;1ID5;1MKW;1MKX;1NL1;1NL2;1TBQ;1TBR;1TOC;1UCY;1UVT;1UVU;1VIT;1YCP;2A1D;2HPP;2ODY;2PF1;2PF2;2SPT;3PMA;3PMB; |
 |
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 | 81 |
| Target type | Protein | |
| Target unique ID | P00735 | |
| Activity | 164 nM | |
| Binding Conditions/Buffer | 20 mM Hepes (pH 7.35), 120 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2 and 0.1% geletin containing 0.05% Tween 20, SHMCK+ buffer containing 0.05% Tween 20 |
|
| Assay | Binding curves for RNA aptamers following seven rounds of SELEX. Binding curves for T-05RNA, T+10RNA and the starting bulk 25N RNA population are shown |
|
| PubMed ID | 12557236 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_81 | RNA | GCAAUGGUACGGUACUUCCAAGUGCGGGGGGGAGGUGGUGGUUCCAAAAGUGCACGCUACUUUGCUAA | |
| Apta_994 | DNA | GCAATGGTACGGTACTTCCGGACAGTGCTGAAAACTGTGACCCCCCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_408 | DNA | GCAATGGTACGGTACTTCCGTCATCAGCTTGTGATGTGGATGCGAACTGCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_995 | DNA | GCAATGGTACGGTACTTCCCCACCCCACGCTGCTCCCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_388 | RNA | GCGGAAGCGUGCUGGGCUAGAAUAAUAAUAAGAAAACCAGUACUUUCGU | |
| Apta_409 | DNA | GCAATGGTACGGTACTTCCGGATGCGGAAACTGGCTAATTGGTGAGGCTGGGGCGGTCGTGCAGCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_400 | RNA | GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_136 | RNA | CGUGUCGUCCUGGUACGAUUUGGUAUAUAACCGUGGCUUUUCGACA | |
| Apta_270 | RNA | CUGUCGAACAUGCUGAGGGUAACGUACUGGCAAGCUCACCUCAGCGUAGCUAa | |
| Apta_396 | RNA | GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_1224 | RNA | GGAGGCGCCAACUGAAUGAAUGUUCUGGAUCUGCUAGAGACUAUCUGCUUCGGCAGCACUCUCCGUUAACAACACGUACAUCCGUAACUAGUCGCGUCAC | |
| Apta_1055 | RNA | CAAGCUUGCGGGUUGGCUUGUAACAAGAUCGCUACGUGUUGAACUCUGCAACACUGGUCGGAUAGCGUAAACGGG | |
| Apta_429 | RNA | GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA | |
| Apta_382 | RNA | GGCGUGACCUGAUGAGUCACGCAGACGCUAGCGAAUUGGUUCCUCGAAAGGGGAAAGCGUUAUUAAGAAACCAAAAUGUGUUACGAAACGUUCCC | |
| Apta_415 | RNA | GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_563 | RNA | GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGAAAGCCAAAGCCGUAGCGCAGAUGAUCUCGCCAUCAGUACCGAAACGGUAGCGAGAGCUC | |
| Apta_613 | RNA | GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC | |
| Apta_624 | RNA | GGGAAUGGAUCCACAUCUACGAAUUCGAAUUGCCGUAAUUUCCCGUGGAGCGAUGCUUCACUGCAGACUUGACGAAGCUU | |
| Apta_1141 | RNA | ACGAGUCUGGUCCUUCCUUUGACGACUAUUGUUUGGUAUCGAUCAACAACAA | |
| Apta_1144 | RNA | ACGAGUCUGGUCCUUCCUCCCUAAUUGCUGUUGAGGUAUCGGCUACAACAA |
DEV TOOL
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