J6f1 aptamer

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Description

In 1995, Wang, Y., & Rando, R. R. reported on the selection of RNA aptamers which were directed against the aminoglycoside tobramycin. In 1998, Hamasaki and Rando were reported here which are designed to reveal the nature of the tobramycin binding domain of J6. Experiments was reported here which was designed to reveal the nature of the tobramycin binding domain of J6 aptamer. A small (40 nts) stem-loop derivative of J6 aptamer, containing a 3 nt and a 1 nt bulge, stoichiometrically binds tobramycin with a dissociation constant of approximately 5 nM. These studies demonstrated that simplified RNA molecules can be generated which bind aminoglycosides specifically and with high affinities. J6f1 is a truncated mutant of J6 aptamer[1,3].



SELEX

Rando, R. R. et al. used SELEX to isolate high-affinity RNA aptamers that specifically bind the aminoglycoside tobramycin. Starting from a 109-nucleotide aptamer (J6) with a dissociation constant of 0.77 ± 0.03 nM for tobramycin, they simplified the construct to a 39-nucleotide aptamer (J6e) that retained high affinity (KD = 58.2 ± 13.1 nM) and specificity for tobramycin. Further modifications led to a 40-nucleotide aptamer (J6f1) with a KD of 5.15 ± 1.52 nM, demonstrating that simplified RNA constructs can maintain high-affinity and specific aminoglycoside binding[3].

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 figures is based on the prediction results of the RNA fold website by ribodraw tool to draw. J6f1 aptamer was named by Rando, R. R. et al[3].

5'-GGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAGCC-3'

drawing

Ligand information

SELEX ligand

Tobramycin is an aminoglycoside antibiotic used to treat cystic fibrosis-associated bacterial, lower respiratory tract, urinary tract, eye, skin, bone, and skin structure infections.-----From Drugbank

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

Drugbank: a comprehensive database with detailed information on drugs and drug targets.

Name Molecular Formula Molecular Weight CAS Solubility PubChem Drugbank ID
Tobramycin C18H37N5O9 467.5 g/mol 32986-56-4 5.37e+01 g/L 36294 DB00684
drawing

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: a compound identifier used by the ZINC database, one of the largest repositories for virtual screening of drug-like molecules.

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

ZINC ID Name CAS Pubchem CID Structure
ZINC8551162 (2R,3S,4R,5S,6S)-4-amino-2-[(1R,2R,3R,4S,6R)-4,6-diamino-3-[(2S,3S,5S,6S)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-dio NA 92331686 drawing
ZINC8551164 (2R,3S,4R,5S,6S)-4-amino-2-[(1R,2R,3R,4S,6R)-4,6-diamino-3-[(2R,3S,5S,6S)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol NA 92331688 drawing
ZINC8551165 (2R,3S,4R,5S,6S)-4-amino-2-[(1R,2R,3R,4S,6R)-4,6-diamino-3-[(2R,3S,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol NA 92331689 drawing
ZINC8551163 (2R,3S,4R,5S,6S)-4-amino-2-[(1R,2R,3R,4S,6R)-4,6-diamino-3-[(2S,3S,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxyoxan-2-yl]oxy-2-hydroxycyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol NA 92331687 drawing
ZINC43562055 (2S,3R,4R,5S,6S)-2-(Aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-3-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2-hydroxycyclohexyl]oxyoxane-3,4,5-triol NA 11274101 drawing
ZINC8214590 Kanamycin 59-01-8 6032 drawing
ZINC53132258 Bekanamycin 4696-76-8 439318 drawing
ZINC8214383 Dibekacin 34493-98-6 470999 drawing


References

[1] Specific binding of aminoglycoside antibiotics to RNA.
Wang, Y., & Rando, R. R.
Chemistry & biology, 2(5), 281–290. (1995)
[2] RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities.
Wang, Y., Killian, J., Hamasaki, K., & Rando, R. R. 
Biochemistry, 35(38), 12338–12346. (1996)
[3] Minimal RNA constructs that specifically bind aminoglycoside antibiotics with high affinities.
Hamasaki, K., Killian, J., Cho, J., & Rando, R. R.
Biochemistry, 37(2), 656–663. (1998)