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Lividomycin aptamer
Description
In 1996, Lato, S. M., & Ellington, A. D prepared levidomycin affinity columns and screened RNA molecules by an in vitro selection process. By increasing the stringency of the selection, the concentration of Levidomycin on the affinity column was reduced and the wash volume was increased. RNA molecules capable of binding Levidomycin were successfully screened by in vitro selection. After several rounds of selection and amplification, the screened SLB10-1 showed high affinity and specificity for levidomycin with an affinity of approximately 300 nM[1].SELEX
Lato, S. M., & Ellington, A. D. used in vitro screening from a pool of RNAs that would contain 30 random sequence positions, after which 10 aptamers were cloned, 13 clones were sequenced, and 12 proved to be identical aptamers, one being an unrelated species[1].
Detailed information are accessible on SELEX page.
Structure
The sequence and secondary prediction structure of the aptamer will be shown here, here we used ribodraw to complete the figure. The 2D structure of the figure is based on the article by ribodraw tool to draw.5'-GGGAAUGGAUCCACAUCUACGAAUUCAACGAGUGCAGUGGGAAACAGGUCUUUGGCUUCACUGCAGACUUGACGAAGCUU-3'
Ligand information
SELEX ligand
This compound belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions.-----From drugbank
| Name | Molecular Formula | MW | CAS | Solubility | PubChem | Drug ID |
|---|---|---|---|---|---|---|
| lividomycin | C29H55N5O18 | 761.8 g/mol | 36441-41-5 | Difficult to dissolve in water | 72394 | DB04728 |
Similar compound
We screened the compounds with great similarity to by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available, we will supplement them with Pubchem CID. For another compound, we used a similar compound query method from the PubChem database.
| Zinc_id | Named | CAS | Pubchem CID | Structure |
|---|---|---|---|---|
| ZINC253673980 | lividomycin A | 36441-41-5 | 72394 |  |
| ZINC255211892 | (2R,3S,4R,5S,6R)-2-[(2R,3S,4R,5S,6R)-5-amino-2-(aminomethyl)-6-[(2S,3R,4S,5S)-5-[(1R,2S,3R,5S,6S)-3,5-diamino-2-[(2R,3S,4R,5S,6S)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol | NA | 162929092 |  |
| ZINC257402766 | (2R,3S,4R,5R,6S)-2-[(2S,3R,4S,5R,6R)-5-amino-2-(aminomethyl)-6-[(2S,3S,4R,5R)-5-[(1R,2S,3S,5R,6R)-3,5-diamino-2-[(2R,3S,5R,6R)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol | NA | 125038099 |  |
| ZINC257402767 | (2R,3S,4R,5R,6S)-2-[(2S,3R,4S,5R,6R)-5-amino-2-(aminomethyl)-6-[(2S,3S,4R,5R)-5-[(1R,2S,3S,5R,6R)-3,5-diamino-2-[(2R,3S,5S,6R)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol | NA | 125038100 |  |
| ZINC257402768 | (2R,3S,4R,5R,6S)-2-[(2S,3R,4S,5R,6R)-5-amino-2-(aminomethyl)-6-[(2S,3S,4R,5R)-5-[(1R,2S,3S,5R,6R)-3,5-diamino-2-[(2R,3S,5S,6S)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol | NA | 125038101 |  |
| ZINC257402769 | (2R,3S,4R,5R,6S)-2-[(2S,3R,4S,5R,6R)-5-amino-2-(aminomethyl)-6-[(2S,3S,4R,5R)-5-[(1R,2S,3S,5R,6R)-3,5-diamino-2-[(2R,3S,5R,6S)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol | NA | 125038102 |  |
References
[1] Screening chemical libraries for nucleic-acid-binding drugs by in vitro selection: a test case with lividomycin.Lato, S. M., & Ellington, A. D.
Molecular diversity, 2(1-2), 103–110. (1996)
[2] Thermodynamics of aminoglycoside-rRNA recognition.
Pilch, D. S., Kaul, M., Barbieri, C. M., & Kerrigan, J. E.
Biopolymers,70(1), 58–79. (2003)