Selective condensation of DNA by aminoglycoside antibiotics

Abstract

The condensing effect of aminoglycoside antibiotics on the structure of double-stranded DNA was examined. The selective condensation of DNA by small molecules is an interesting approach in biotechnology. Here, we present the interaction between calf thymus DNA and three types of antibiotic molecules: tobramycin, kanamycin, and neomycin. Several techniques were applied to study this effect. Atomic force microscopy, transmission electron microscopy images, and nuclear magnetic resonance spectra showed that the interaction of tobramycin with double-stranded DNA caused the rod, toroid, and sphere formation and very strong condensation of DNA strands, which was not observed in the case of other aminoglycosides used in the experiment. Studies on the mechanisms by which small molecules interact with DNA are important in understanding their functioning in cells, in designing new and efficient drugs, or in minimizing their adverse side effects. Specific interactions between tobramycin and DNA double helix was modeled using molecular dynamics simulations. Simulation study shows the aminoglycoside specificity to bend DNA double helix, shedding light on the origins of toroid formation. This phenomenon may lighten the ototoxicity or nephrotoxicity issues, but also other adverse reactions of aminoglycoside antibiotics in the human body.

Keywords: Aminoglycoside antibiotics; Atomic force microscopy; Deoxyribonucleic acid condensation; Electron microscopy; Molecular dynamics; Toroids.

Fig. 1

Scheme of the aminoglycoside antibiotics used in the study. a Tobramycin, b kanamycin, c neomycin

Fig. 2

¹H-NMR spectra of tobramycin (a, b) and kanamycin (c, d) (1 mg/ml) in the absence (a, c) and in the presence (b, d) of calf thymus DNA (1 mg/ml)

Fig. 3

a AFM and b TEM images of native ct-DNA

Fig. 4

AFM images of DNA on mica after the addition of tobramycin with different concentrations. The ratios of tobramycin:DNA were a 0.2:1, b equimolar (1:1), and c 10:1. d AFM phase image of condensed DNA structures on the mica surface. Yellow arrow indicates toroid as a result of annularization of rod-like structure

Fig. 5

TEM images of DNA on carbon-coated grid after the addition of tobramycin in ratios of tobramycin:DNA a 0.2:1, b high-resolution image of ratio 1:1, and c 10:1. Labeled forms of DNA condensation: toroid, sphere, and rod-like structure

Fig. 6

TEM images of toroids with 1 % phosphotungstate (a), 1 % uranylacetate (b), and without staining solution (c)

Fig. 7

AFM images of native calf thymus DNA with the addition of kanamycin (a), with addition of neomycin (b), and on mica at equimolar-to-base pairs ratio (c). TEM images of calf thymus DNA with the addition of kanamycin (d) and with addition neomycin (e) in the same conditions

Fig. 8

Molecular mechanism of tobramycin interaction with DNA. a Two aminoglycosides acting as a clamp induce DNA curvature. b Zoom on hydrogen bonding between specific hydrogen of tobramycin molecule and oxygen of deoxyribose 5-phosphate