Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 373
Aptamer sequence: GGTATTGAGGGTCGCATCTCAAAAGGGGTGATTGCTTGCACAATGACAGGGTAGGACAGATGGCTCTAACTCTCCTCT
Target unique ID: P23441
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_368 | A | Protein | NKX21_RAT | 3.36 nM | Ni-NTA magnetic bead (Qiagen) were used with PBS-T (50 mM K2HPO4 pH 7.5, 150 mM NaCl, 0.05% Tween-20) | 12954786 |
Structure information of aptamer
| Aptamer Sequence: | GGTATTGAGGGTCGCATCTCAAAAGGGGTGATTGCTTGCACAATGACAGGGTAGGACAGATGGCTCTAACTCTCCTCT |
| 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_368 | Description | A |
| Aptamer chemistry | DNA | Length | 78 nt |
| GC content | 50.0% | Molecular weight | 24,171.48 Da |
| Molarity of 1 μg/μl solution | 41.37 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | GGTATTGAGGGTCGCATCTCAAAAGGGGTGATTGCTTGCACAATGACAGGGTAGGACAGATGGCTCTAACTCTCCTCT | ||
| Applications | Enzyme-linked assays, western blots and affinity purification | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P23441 | Protein name | Homeobox protein Nkx-2.1 (Thyroid nuclear factor 1) (Thyroid transcription factor 1) (TTF-1) |
| Gene name(s) | Nkx2-1 Nkx-2.1 Titf1 Ttf-1 Ttf1 | Organism | Homeobox protein Nkx-2.1 (Thyroid nuclear factor 1) (Thyroid transcription factor 1) (TTF-1) |
| Status | reviewed in uniprot database | Length | 372 |
| Mass | 38,554 | Activity regulation | N/A |
| Involvement in disease | N/A | Catalytic activity | N/A |
| PDB ID(s) | 1FTT; |
 |
Function | Transcription factor that binds and activates the promoter of thyroid specific genes such as thyroglobulin, thyroperoxidase, and thyrotropin receptor. |
Activity data
 |
Interaction ID | 373 |
| Target type | Protein | |
| Target unique ID | P23441 | |
| Activity | 3.36 nM | |
| Binding Conditions/Buffer | Ni-NTA magnetic bead (Qiagen) were used with PBS-T (50 mM K2HPO4 pH 7.5, 150 mM NaCl, 0.05% Tween-20) |
|
| Assay | Plot of the steady-state affinity for 'A' using the Req values derived from sensorgrams in (A) fitted locally. The KD = 5.14 × 10**-9 M as determined from the steady-state affinity model |
|
| PubMed ID | 12954786 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_128 | DNA | GGTATTGAGGGTCGCATCCCGTAGTGTGTTCTTATTCGTGTCTGTGTGTGTTCTGTCGGATGGCTCTAACTCTCCTCT | |
| Apta_127 | DNA | GGTATTGAGGGTCGCATCCACTGGTCGTTGTTGTCTGTTGTCTGTTATGTTGTTTCGTGATGGCTCTAACTCTCCTCT | |
| Apta_811 | DNA | ATAGGAGTCACGACGACCAGAATCTAAAAATGGGCAAAGAAACAGTGACTCGTTGAGATACTTATGTGCGTCTACCTCTTGACTAAT | |
| Apta_812 | DNA | ATAGGAGTCACGACGACCAGAATAGAGATATGACAGCGGGGAAGGTTAAGAGGCGCTAGGAGTATGTGCGTCTACCTCTTGACTAAT | |
| Apta_1120 | DNA | GGGAATGGATCCACATCTACGAATTCGGAATGAGTGCCCTGCAAGCGAGGGCTAGCTTCACTGCAGACTTGACGAAGCTT | |
| Apta_78 | DNA | ATCTCGACTAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACAATACTCGT | |
| Apta_79 | DNA | ATCTCGAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACTCGT | |
| Apta_369 | DNA | GGCTGTTGTGAGCCTCCTCCCAGAGGGAAGACTTTAGGTTCGGTTCACGTCCCGCTTATTCTTACTCCC | |
| Apta_408 | DNA | GCAATGGTACGGTACTTCCGTCATCAGCTTGTGATGTGGATGCGAACTGCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_508 | DNA | GCGGGCGATCGGCGGGGGGTGCGTGCGCTCTGTGCCAGGGGGTGGGACAGATCATATGGGGGTGCT | |
| Apta_535 | DNA | ATCCGTCACACCTGCTCTTGGGGTTATTACTCGTGAGATTGGGAATAGGTTACATGGTGTTGGCTCCCGTAT | |
| Apta_570 | DNA | GGCAAGATGTGCCCAGAACAGTTGCTTGTATGGTGGGGAGCGTCCATATTGGCTTAAAC | |
| Apta_1115 | DNA | CGTACGGAATTCGCTAGCGGTGACGGACGTGGGGTGCACGAAGGGAGGGGATCCGAGCTCCACGTG | |
| Apta_1117 | DNA | CGTACGGAATTCGCTAGCGGACTGGAGTCTAGACCGGGTAGCTGTGGTGGATCCGAGCTCCACGTG | |
| Apta_774 | DNA | GAATTCAGTCGGACAGCGAGGAAAATTTCGTTATTTTCGTTTCCGGGAACTCGGGCATTTAGAGATGGACGAATATCGTCTCCC | |
| Apta_409 | DNA | GCAATGGTACGGTACTTCCGGATGCGGAAACTGGCTAATTGGTGAGGCTGGGGCGGTCGTGCAGCAAAAGTGCACGCTACTTTGCTAA | |
| Apta_767 | DNA | GAATTCAGTCGGACAGCGACGGTGGGAGCCCCAAATAATTCTTGCGATTATTAGTGTAAGCGGATGGACGAATATCGTCTCCC | |
| Apta_1180 | DNA | GAATTCAGTCGGACAGCGCAATTGTGGTTCTTACCCTATCCCTTGTGTTTGGCGTTCGTTGCGATGGACGAATATCGTCTCCC | |
| Apta_1031 | DNA | GGAGACCGCTTAAGCTTAAAGGAGCGGTTACGAATGCGATGACTTAGGTACCATTGCACTACGGTACCTAAACAGTTCCTTTGGATCCGAATTCGCCGC | |
| Apta_277 | DNA | TTTTTTGGTCAGATGAGGCCTGGTGATCGTGCCCAGGCCATATGAGCAAGGAACCCCTATGCGTGCT |
DEV TOOL
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