Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 435
Aptamer sequence: GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA
Target unique ID: Q04206
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_429 D1 Protein TF65_HUMAN 149 nM 10 mM HEPES at pH 7.5, 100 mM NaCl, 1 mM DTT 18426920
Structure information of aptamer
Aptamer Sequence: GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA
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_429 Description D1
Aptamer chemistry RNA Length 85 nt
GC content 49.4% Molecular weight 27,468.30 Da
Molarity of 1 μg/μl solution 36.41 μM Number of G-quadruplexes 2
G-Score 17 Function Targeted binding
Sequence GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA
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 435
Target type Protein
Target unique ID Q04206
Activity 149 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_256 RNA GGGCGCUAAGUCCUCGCUCAUGCGCGUCCCAUGGGGUAUAGAGGGGUCGAAGUGGACGCGCGACUCGGAUCCU 56.47%
Apta_551 RNA GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGCGGUGCUAGUUAGUUGCAGUUUCGGUUGUUACGCGAAACGGUGAAAGCCGUAGGUCU 54.55%
Apta_130 RNA GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA 54.12%
Apta_563 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGAAAGCCAAAGCCGUAGCGCAGAUGAUCUCGCCAUCAGUACCGAAACGGUAGCGAGAGCUC 54.08%
Apta_81 RNA GCAAUGGUACGGUACUUCCAAGUGCGGGGGGGAGGUGGUGGUUCCAAAAGUGCACGCUACUUUGCUAA 52.94%
Apta_453 RNA GGGCUAGCUGAUCGUACCAGUAGCGUGGCCUGGGGGGCCUAGUCGUGCGAUACUAACAGCUAACACCC 52.94%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 52.63%
Apta_557 RNA GGAACACUAUCCGAUGGCACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGCUAGGCAAUGACAUGGACUCCUUGGUCAUUAGGAUCG 51.82%
Apta_496 RNA GGGCUAGCUGAUCGUACCCAGUAGCGUGGCAUGGGGUGCCUAGUCGGGCGAUACUAACAGCUAACACCC 51.76%
Apta_718 RNA GGGUUGUGAGCUCCCGGCUCGCAUUGUGAGGUGGAGGGGGACGUGCUGCAGGUCGACGCAUGCGCCG 51.76%
Apta_337 RNA GGGAGGAUAUUUUCUCAGACCGUAAGUACCGAAUGUGCUUUUGGCCGAUUUUUGGCCCCUGCAGUUGCAGCAUCGUGAACUAGGAUCCGGG 51.65%
Apta_430 RNA GGGAUAUCCUCGAGCAUAAGAAACAAGAUAGAUCCUGAAACUGUUUUAAGGUUGGCCGAUCUUCUGCUCGAGAAUGCAUGAAGCGUUCCAUAUUUUU 51.55%
Apta_895 RNA ACCGAGUCCAGAAGCUUGUAGUACUACCGCAACGUUGGCGUUCGGCGUUGGCCGCGUCAUCGCUAGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC 51.40%
Apta_500 RNA GGGAGAAAGGGAAGCUUGAGGUGCUAUGGAGUGGAGGAGUUGAAGGUGUCGGGGUUGGCAGAAGAAGGCGAGCGUACGGAUCCAUC 51.16%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 51.14%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 51.11%
Apta_2 RNA GGGCUUCUCUGGUUAGACCAGAUUUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCC 50.59%
Apta_55 RNA GACAUCUGUAAGUAAGAUUCUAUCUGCAAAGCGGUUAGGAGGGCUCGGACUCUGAUUGCCUCCCCGCACC 50.59%
Apta_80 RNA GCAAUGGUACGGUACUUCCUUUGGAAGAUAGCUGGAGAACUAACCAAAAGUGCACGCUACUUUGCUAA 50.59%
Apta_129 RNA GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA 50.59%

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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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