Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 436
Aptamer sequence: GGGAUAUCCUCGAGCAUAAGAAACAAGAUAGAUCCUGAAACUGUUUUAAGGUUGGCCGAUCUUCUGCUCGAGAAUGCAUGAAGCGUUCCAUAUUUUU
Target unique ID: Q04206
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_430 | aptamer3 | Protein | TF65_HUMAN | 1 nM | Buffer A (20 mM HEPES (pH 7.5), 0.4 M NaCl, 2 mM EDTA, 5% v/v glycerol, 1 mM DTT, 0.5 mM PMSF, 1 ug/mL pepstatin, 1 ug/mL leupeptin); Buffer B (20 mM HEPES (pH 7.5), 2 mM EDTA, 5% v/v glycerol, 1 mM DTT, 0.5 mM PMSF, 1 ug/mL pepstatin, 1 ug/mL leupeptin) | 10074372 |
Structure information of aptamer
| Aptamer Sequence: | GGGAUAUCCUCGAGCAUAAGAAACAAGAUAGAUCCUGAAACUGUUUUAAGGUUGGCCGAUCUUCUGCUCGAGAAUGCAUGAAGCGUUCCAUAUUUUU |
| 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_430 | Description | aptamer3 |
| Aptamer chemistry | RNA | Length | 97 nt |
| GC content | 41.2% | Molecular weight | 31,122.40 Da |
| Molarity of 1 μg/μl solution | 32.13 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | GGGAUAUCCUCGAGCAUAAGAAACAAGAUAGAUCCUGAAACUGUUUUAAGGUUGGCCGAUCUUCUGCUCGAGAAUGCAUGAAGCGUUCCAUAUUUUU | ||
| Applications | Blocks the ability of NF-κB to bind duplex DNA | ||
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 | 436 |
| Target type | Protein | |
| Target unique ID | Q04206 | |
| Activity | 1 nM | |
| Binding Conditions/Buffer | Buffer A (20 mM HEPES (pH 7.5), 0.4 M NaCl, 2 mM EDTA, 5% v/v glycerol, 1 mM DTT, 0.5 mM PMSF, 1 ug/mL pepstatin, 1 ug/mL leupeptin); Buffer B (20 mM HEPES (pH 7.5), 2 mM EDTA, 5% v/v glycerol, 1 mM DTT, 0.5 mM PMSF, 1 ug/mL pepstatin, 1 ug/mL leupeptin) |
|
| Assay | Estimation of equilibrium dissociation constants for p502 binding to DNA duplex 1 and RNA aptamer 3 |
|
| PubMed ID | 10074372 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_298 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAAACUGGUGUACCUCUUUGCCCUAUCUUAUCUGGAGAUAGUAAGUGCAAUCU | |
| Apta_1289 | RNA | GGGAGAGGAUACUACACGUGGAAAAACCAACAAAUUGGGAAAAAUGUUAAGGGUCCACUUCAUGCCAUUGCAUGUAGCAGAAGCUUCCG | |
| Apta_224 | RNA | GGGGCCACCAACGACAUUGAACCACGUAGGCUCGUUUCUGAGCCGAUCUCGAUGUUGAUAUAAAUAGUGCCCAUGGAUC | |
| Apta_624 | RNA | GGGAAUGGAUCCACAUCUACGAAUUCGAAUUGCCGUAAUUUCCCGUGGAGCGAUGCUUCACUGCAGACUUGACGAAGCUU | |
| Apta_1100 | RNA | GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU | |
| Apta_720 | RNA | GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA | |
| Apta_719 | RNA | GGAAUGGAUCCACAUCUACGAAGGCUUUGAAGGUGAGACCGUGCAAAUGAGGAUGGUGUGGAUGAUUAGGGUUGUCGGUUUUCACUGCAGACUUGACGAAGCUU | |
| Apta_123 | RNA | GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC | |
| Apta_294 | RNA | AUACCAGCUUAUUCAAUUGCCUGAUUAGCGGUAUCACGAUUACUUACCUUCGUUGCUGAGAUAGUAAGUGCAAUCU | |
| Apta_299 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAGACUGGAUAUACUCUUAAGCAUUUCUAUAAUCGAGAUAGUAAGUGCAAUCU | |
| Apta_300 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAACUGCUGCAUCGUCUCCCACGUAUUACACAUGAAGAUAGUAAGUGCAAUCU | |
| Apta_301 | RNA | AUACCAGCUUAUUCAAUUGCCUGAAAAGUUGAACUCCAAAUACGCGCUGAGAUAGUAAGUGCAAUCU | |
| Apta_429 | RNA | GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA | |
| Apta_854 | RNA | GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC | |
| Apta_137 | RNA | GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC | |
| Apta_156 | RNA | GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU | |
| Apta_500 | RNA | GGGAGAAAGGGAAGCUUGAGGUGCUAUGGAGUGGAGGAGUUGAAGGUGUCGGGGUUGGCAGAAGAAGGCGAGCGUACGGAUCCAUC | |
| Apta_522 | RNA | GGGCGACCCUGAUGAGCACACGAGGGGGAAACCCCGGACAAUCAGACACGGUGUUCGAAACGGUGAAAGCCGUAGGUUGCCCUUU | |
| Apta_723 | RNA | GGGAGCUCAGAAUAAACGCUCAAAUCCGUGGACAGGGCGUAAGCGCCUUCGACAUGAGACACGGAUCCUGCGACGAAUUCAGC | |
| Apta_816 | RNA | GGGUUCACUGCAGACUUGACGAAGCUUGAGAGAUGCCCCCUGAUGUGCAUUCUUGUUGUGUUGCGGCAAUGGAUCCACAUCUACGAAUUC |
DEV TOOL
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