Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_1146 | Antibac1 | Molecule | Peptidoglycan Pentapeptide-mdap3 | 0.415 μM | 0.15 M NaCl, 20 mM Tris-HCl, and 1 mM EDTA, pH 7.5 | 25185503 |
Structure information of aptamer
| Aptamer Sequence: | GGGACAGGGAGTGCGCTGCTCCCC |
| 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_1146 | Description | Antibac1 |
| Aptamer chemistry | DNA | Length | 24 nt |
| GC content | 75.0% | Molecular weight | 7,395.75 Da |
| Molarity of 1 μg/μl solution | 135.21 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Aptasensor |
| Sequence | GGGACAGGGAGTGCGCTGCTCCCC | ||
| Applications | Bacterial infections identification | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| PubChem ID | 3035036 | Molecular name | Peptidoglycan Pentapeptide-mdap3 |
| Molecular formula | C40H67N9O21 | Molecular weight | 1010 |
| IUPAC name | (2S,6S)-6-[[(2R)-2-[[(2S)-2-[[(2R)-2-[(2S,3R,4R,5S,6R)-3-acetamido-5-[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxypropanoyl]amino]propanoyl]amino]-5-amino-5-oxopentanoyl]amino]-2-amino-7-[[(2R)-1-[[(1R)-1-carboxyethyl]amino]-1-oxopropan-2-yl]amino]-7-oxoheptanoic acid | InChIKey | IFUAEVRHOAQERC-BQZBOJCTSA-N |
| LogP | -8.281 | Topological polar surface area | 485.48 |
| Hydrogen bond acceptor | 20 | Hydrogen bond donor | 16 |
Synonym(s): Peptidoglycan Pentapeptide-mdap3; 73715-37-4; (2S,6S)-6-[[(2R)-2-[[(2S)-2-[[(2R)-2-[(2S,3R,4R,5S,6R)-3-acetamido-5-[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxypropanoyl]amino]propanoyl]amino]-5-amino-5-oxopentanoyl]amino]-2-amino-7-[[(2R)-1-[[(1R)-1-carboxyethyl]amino]-1-oxopropan-2-yl]amino]-7-oxoheptanoic acid; Peptidoglycan monomer-mDap3; N-Acetylglucosaminyl-N-acmu-ala-iso-gln-meso-diaminopimelic acid-ala-ala; N-Acetylglucosaminyl-N-acetylmuramyl-L-alanyl-D-isoglutaminyl-meso-diaminopimelic acid-D-alanyl-D-alanine; D-Alanine, N-(N-(N2-(N2-(N-(N-acetyl-4-O-(2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl)muramoyl)-L-alanyl)-D-alpha-glutaminyl)-(R*,S*)-6-carboxylysyl)-D-alanyl)-; D-Alanine, N-(N-acetyl-4-O-(2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl)muramoyl)-L-alanyl-D-alpha-glutaminyl-meso-alpha,epsilon-diaminopimelyl-D-alanyl-
Activity data
 |
Interaction ID | 1206 |
| Target type | Molecule | |
| Target unique ID | 3035036 | |
| Activity | 0.415 μM | |
| Binding Conditions/Buffer | 0.15 M NaCl, 20 mM Tris-HCl, and 1 mM EDTA, pH 7.5 |
|
| Assay | Antibac1 saturation curves |
|
| PubMed ID | 25185503 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_73 | DNA | GGGGAGTAGGTTGGTGTGGTTGGGGCTCCCC | |
| Apta_631 | DNA | GGGATCGAAACGTAGCGCCTTCGATCCC | |
| Apta_1147 | DNA | GGGGACTAGAGGACTTGTGCGGCC | |
| Apta_71 | DNA | GGCGAGTAGGTTGGTGTGGTTGGGGCTCGCC | |
| Apta_359 | DNA | GGGAACGCGTTATTGGGTAACTTCCC | |
| Apta_361 | DNA | GGGAACGCCCGTATTGCTCGGTTCCC | |
| Apta_362 | DNA | GGGAACGCACCGATCGCAGGTTTCCC | |
| Apta_1027 | DNA | GGAGCTACGTTTAGCGAGTCCGACGCTCGGTGCCTCTTC | |
| Apta_17 | DNA | AGGGGGGGGGGTGGGGGTGGGTCCC | |
| Apta_1194 | DNA | GGGAGAGGTGGGAGCGGGGCCAGGG | |
| Apta_360 | DNA | GGGAACGCATACGCCGCAGTATTTCCC | |
| Apta_74 | DNA | GGACAGTAGGTTGGTGTGGTTGGGGCTGTCC | |
| Apta_672 | DNA | GGGGTGAAACGGGTCCCG | |
| Apta_602 | DNA | GGGCGAGAACAGTGTCCCAGTCGCTAGTTTTCTCTGCCC | |
| Apta_778 | DNA | GAAGACGAGCGGCGAGTGTTATTACGCTTGGAAACAACCCC | |
| Apta_778 | DNA | GAAGACGAGCGGCGAGTGTTATTACGCTTGGAAACAACCCC | |
| Apta_543 | DNA | GGCACGTGTTGTCTCTCTGTGTCTCGTGCC | |
| Apta_960 | DNA | CCCGAGGCACGAGGGGGAACGTATCGTCATGTGCCGGCCA | |
| Apta_15 | DNA | TGAGGGGGGGGGAGGGCGGGGCTGC | |
| Apta_24 | DNA | TGTGGGGATGGATGGGCCGGGCTGC |
DEV TOOL
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