Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 434
Aptamer sequence: GAAGCUUACAAGAAGGACAGCACGAAUAAAACCUGCGUAAAUCCGCCCCAUUUGUGUAAGGGUAGUGGGUCGAAUUCCGCUCA
Target unique ID: Q04206
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_428 | R1 | Protein | TF65_HUMAN | 11 nM | 10 mM HEPES at pH 7.5, 100 mM NaCl, 1 mM DTT | 18426920 |
Structure information of aptamer
| Aptamer Sequence: | GAAGCUUACAAGAAGGACAGCACGAAUAAAACCUGCGUAAAUCCGCCCCAUUUGUGUAAGGGUAGUGGGUCGAAUUCCGCUCA |
| 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_428 | Description | R1 |
| Aptamer chemistry | RNA | Length | 83 nt |
| GC content | 48.2% | Molecular weight | 26,749.97 Da |
| Molarity of 1 μg/μl solution | 37.38 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | GAAGCUUACAAGAAGGACAGCACGAAUAAAACCUGCGUAAAUCCGCCCCAUUUGUGUAAGGGUAGUGGGUCGAAUUCCGCUCA | ||
| Applications | Anti-NF-kB p65 | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | Q04206 | Protein name | Transcription factor p65 (Nuclear factor NF-kappa-B p65 subunit) (Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3) |
| Gene name(s) | RELA NFKB3 | Organism | Transcription factor p65 (Nuclear factor NF-kappa-B p65 subunit) (Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3) |
| Status | reviewed in uniprot database | Length | 551 |
| Mass | 60,219 | Activity regulation | N/A |
| Involvement in disease | A chromosomal aberration involving ZFTA is found in more than two-thirds of supratentorial ependymomas | Catalytic activity | N/A |
| PDB ID(s) | 1NFI;2LSP;2O61;3GUT;3QXY;3RC0;4KV1;4KV4;5U4K;5URN;6NV2;6QHL;6QHM;6YOW;6YOX;6YOY;6YP2;6YP3;6YP8;6YPL;6YPY;6YQ2;7BI3;7BIQ;7BIW;7BIY;7BJB;7BJF;7BJL;7BJW;7BKH;7LET;7LEU;7LF4;7NJ9;7NJB;7NK3;7NK5;7NLA;7NLE;7NM1;7NM3;7NM9;7NMH;7NQP;7NR7;7NSV;7NV4;7NVI;7NWS;7NXS;7NXT;7NXW;7NXY;7NY4;7NYE;7NYF;7NYG;7NZ6;7NZG;7NZK;7NZV;7O34;7O3A;7O3F;7O3P;7O3Q;7O3R;7O3S;7O57;7O59;7O5A;7O5C;7O5D;7O5F;7O5G;7O5O;7O5P;7O5S;7O5U;7O5X;7O6F;7O6G;7O6I;7O6J;7O6K;7O6M;7O6O; |
 |
Function | NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. |
Activity data
 |
Interaction ID | 434 |
| Target type | Protein | |
| Target unique ID | Q04206 | |
| Activity | 11 nM | |
| Binding Conditions/Buffer | 10 mM HEPES at pH 7.5, 100 mM NaCl, 1 mM DTT |
|
| Assay | Average binding isotherms based on electrophoretic gel mobility shift experiments. Error bars represent the standard error of the mean. Fit values of Kd are shown for indicated R1 truncations. Gray trace corresponds to apamer R1 |
|
| PubMed ID | 18426920 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_427 | RNA | GAAGCUUUCACACAACAAGGCCCGGGACUGUAUUAGGGAAAUUAGAGUACAGACAGUCGCCGUGGGUCGAAUUCCGCUCA | |
| Apta_1223 | RNA | GGAGGCGCCAACUGAAUGAAAGGUUACGCUUCAACGCCGUGCAGCUGCUUCGGCAGGCUUGUGAGUACAUGGCCCAUUGAUCCGUAACUAGUCGCGUCAC | |
| Apta_1221 | RNA | GGAGGCGCCAACUGAAUGAACGAGUUGAAAUGCGGAUCAAGUUACUGCUUCGGCAGUACCUAGUGGGAAAAGUUCUUGGGUCCGUAACUAGUCGCGUCAC | |
| Apta_723 | RNA | GGGAGCUCAGAAUAAACGCUCAAAUCCGUGGACAGGGCGUAAGCGCCUUCGACAUGAGACACGGAUCCUGCGACGAAUUCAGC | |
| Apta_413 | RNA | GUGAGACCAGCCGAGUGGUGUCUGGCUAUUCACUGGAGCGUGGGUGGAACCCCUGCGCACUCGUUUGGCUGUCCGGGCCUUCGGGCCGGGAUUAUCUCU | |
| Apta_1226 | RNA | GGAGGCGCCAACUGAAUGAAGGUGUAUUUCAGUUAAAGAACUUGCUGCUUCGGCAGCGUUCUGAGUUACUAGUCCAAUAAUCCGUAACUAGUCGCGUCAC | |
| Apta_397 | RNA | GGGAGGACGAUGCGGAUACCAGGAUCACAUCCUGAGGAACCCCGGCUCCCAACCUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_400 | RNA | GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_1168 | RNA | GCGACUACGGUGAGGGUCGGGUCCAGUAGCUUCGGCUACUGUUGAGUAGAGUGUGGGCUCCGUAGUCGC | |
| Apta_522 | RNA | GGGCGACCCUGAUGAGCACACGAGGGGGAAACCCCGGACAAUCAGACACGGUGUUCGAAACGGUGAAAGCCGUAGGUUGCCCUUU | |
| Apta_59 | RNA | GGACCUCGGCGAAAGCUAACGUCUCAUGGCUAAAUUGCCAUGUUGCUACAAAUGAUAUGACUAGAGAGGUUAGGUGCCUCGUGAUGUCCAGUCGC | |
| Apta_936 | RNA | GGAGCUCAGCCUUCACUGCGAUCACCGUGUCGGUGGCUAGUCGAUGUAUCCCGAUCACCAUUGGGGGCAAGUUUAGACAGGCACCACGGUCGGAUCCAC | |
| Apta_280 | RNA | GAUAAUACGACUCACUAUAGGGUUCACUGCAGACUUGACGAAGCUUGCAGAAAAGGGGGAAGAAGAGGGUGAUUCAGGCGAGAGAAUGGAUCCACAUCUACGAAUUC | |
| Apta_720 | RNA | GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA | |
| Apta_157 | RNA | GGGUUCACUGCAGACUUGACGAAGCUUACAAACAAGAGCAAAAAGGGAGUUGACGUAGACUGUGCGGAAUGGAUCCACAUCUACGAAUUC | |
| Apta_719 | RNA | GGAAUGGAUCCACAUCUACGAAGGCUUUGAAGGUGAGACCGUGCAAAUGAGGAUGGUGUGGAUGAUUAGGGUUGUCGGUUUUCACUGCAGACUUGACGAAGCUU | |
| Apta_816 | RNA | GGGUUCACUGCAGACUUGACGAAGCUUGAGAGAUGCCCCCUGAUGUGCAUUCUUGUUGUGUUGCGGCAAUGGAUCCACAUCUACGAAUUC | |
| Apta_549 | RNA | GGAGCUCAGCCUUCACUGCAUGAUAAACCGAUGCUGGGCGAUUCUCCUGAAGUAGGGGAAGAGUUGUCAUGUAUGGGGGCACCACGGUCGGAUCCUG | |
| Apta_724 | RNA | GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC | |
| Apta_299 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAGACUGGAUAUACUCUUAAGCAUUUCUAUAAUCGAGAUAGUAAGUGCAAUCU |
DEV TOOL
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