Supramolecular hydrogel of kanamycin selectively sequesters 16S rRNA

Abstract

As the first example of hydrogelator derived from aminoglycoside antibiotics, the hydrogel of kanamycin indicates that the hydrogel of aminoglycosides preserve the specific interaction with their macromolecular targets (e.g., 16S rRNA), thus illustrating a simple approach to explore and identify possible biological targets of supramolecular nanofibers/hydrogels.

Figure 1

Optical images of (A) Gel I formed by 1 (0.5 wt%, pH7.0); (B) Gel II formed by 2 (1.0 wt%, pH7.0); TEM of (C) Gel I and (D) Gel II.

Figure 2

(A) A possible molecular arrangement of the hydrogelator (1) in the gel phase (some hydrogen bonds are shown as the dot lines). (B) A hypothetical binding between two self-assembled molecules of 1 and their receptor (A-site of 16S rRNA) derived from the crystal structure of kanamycin A.

Figure 3

(A) Fluorescence spectra of solution of 1 (1 μg/mL) and mixtures of 1 with different equivalent of oligonucleotide (A site of 16S rRNA) in pbs buffer solution. (B) Gel electrophoresis of 16S rRNA and 23S rRNA in the extract before and after incubation with hydrogel of 1 for 4 hours.

Scheme 1

Supramolecular nanofibers sequester the potential targets (e.g., 16S rRNA (in red color)) in the gel phase.

Scheme 2

Structures of the hydrogelators based on kanamycin A.