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DNA-aptamers binding aminoglycoside antibiotics.

Nikolaus N, Strehlitz B - Sensors (Basel) (2014)

Bottom Line: The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics.Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated.Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range.

View Article: PubMed Central - PubMed

Affiliation: Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Germany. nadia.nikolaus@ufz.de.

ABSTRACT
Aptamers are short, single stranded DNA or RNA oligonucleotides that are able to bind specifically and with high affinity to their non-nucleic acid target molecules. This binding reaction enables their application as biorecognition elements in biosensors and assays. As antibiotic residues pose a problem contributing to the emergence of antibiotic-resistant pathogens and thereby reducing the effectiveness of the drug to fight human infections, we selected aptamers targeted against the aminoglycoside antibiotic kanamycin A with the aim of constructing a robust and functional assay that can be used for water analysis. With this work we show that aptamers that were derived from a Capture-SELEX procedure targeting against kanamycin A also display binding to related aminoglycoside antibiotics. The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics. Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated. Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range. Finally, the proof of principle of an assay for detection of kanamycin A in a real water sample is given.

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Related in: MedlinePlus

(a) Chemical structures of the selection targets. Numbering of the rings and pKa values of amino groups according to [13]; (b) Chemical structures of aminoglycoside antibiotics other than kanamycin A. Differences in the structure compared to kanamycin A are marked in yellow. Numbering of the rings and pKa values of amino groups according to [13]; (c) Chemical structures of amino sugars. Differences in the structure compared to kanamycin A are marked in yellow.
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f1-sensors-14-03737: (a) Chemical structures of the selection targets. Numbering of the rings and pKa values of amino groups according to [13]; (b) Chemical structures of aminoglycoside antibiotics other than kanamycin A. Differences in the structure compared to kanamycin A are marked in yellow. Numbering of the rings and pKa values of amino groups according to [13]; (c) Chemical structures of amino sugars. Differences in the structure compared to kanamycin A are marked in yellow.

Mentions: All chemicals for preparing buffers and solutions were obtained from Merck (Darmstadt, Germany). Kanamycin A disulfate salt dihydrate, gentamicin sulfate salt hydrate, glucosamine, N-acetyl-D-glucosamine, neomycin trisulfate hydrate, sisomicin sulfate salt, streptomycin sulfate salt, sulfacarbamide, sulfamethoxazole, sotalol hydrochloride, and tobramycin were purchased from Sigma-Aldrich (Seelze, Germany). Kanamycin B and netilmicin sulfate were purchased from LKT Laboratories (St Paul, MN, USA), paromomycin sulfate was purchased from U.S. Pharmacopeia (Rockville, MD, USA), and apramycin sulfate from Applichem (Darmstadt, Germany). For an overview of the pharmaceuticals and their chemical structures see Figure 1. Four of the pharmaceuticals (kanamycin A disulfate salt dihydrate, sulfacarbamide, sulfamethoxazole, and sotalol hydrochloride), were used as aptamer selection target mixture. Individual stock solutions of the pharmaceuticals were prepared, diluted in selection buffer and mixed to the final concentration of 1 mmol L−1 for each substance. The pH value was adjusted to ∼7.6 and the mixture was sterile-filtered using a syringe filter with the pore size of 0.22 μm (VWR, Dresden, Germany), aliquoted and stored at −18 °C.


DNA-aptamers binding aminoglycoside antibiotics.

Nikolaus N, Strehlitz B - Sensors (Basel) (2014)

(a) Chemical structures of the selection targets. Numbering of the rings and pKa values of amino groups according to [13]; (b) Chemical structures of aminoglycoside antibiotics other than kanamycin A. Differences in the structure compared to kanamycin A are marked in yellow. Numbering of the rings and pKa values of amino groups according to [13]; (c) Chemical structures of amino sugars. Differences in the structure compared to kanamycin A are marked in yellow.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3958260&req=5

f1-sensors-14-03737: (a) Chemical structures of the selection targets. Numbering of the rings and pKa values of amino groups according to [13]; (b) Chemical structures of aminoglycoside antibiotics other than kanamycin A. Differences in the structure compared to kanamycin A are marked in yellow. Numbering of the rings and pKa values of amino groups according to [13]; (c) Chemical structures of amino sugars. Differences in the structure compared to kanamycin A are marked in yellow.
Mentions: All chemicals for preparing buffers and solutions were obtained from Merck (Darmstadt, Germany). Kanamycin A disulfate salt dihydrate, gentamicin sulfate salt hydrate, glucosamine, N-acetyl-D-glucosamine, neomycin trisulfate hydrate, sisomicin sulfate salt, streptomycin sulfate salt, sulfacarbamide, sulfamethoxazole, sotalol hydrochloride, and tobramycin were purchased from Sigma-Aldrich (Seelze, Germany). Kanamycin B and netilmicin sulfate were purchased from LKT Laboratories (St Paul, MN, USA), paromomycin sulfate was purchased from U.S. Pharmacopeia (Rockville, MD, USA), and apramycin sulfate from Applichem (Darmstadt, Germany). For an overview of the pharmaceuticals and their chemical structures see Figure 1. Four of the pharmaceuticals (kanamycin A disulfate salt dihydrate, sulfacarbamide, sulfamethoxazole, and sotalol hydrochloride), were used as aptamer selection target mixture. Individual stock solutions of the pharmaceuticals were prepared, diluted in selection buffer and mixed to the final concentration of 1 mmol L−1 for each substance. The pH value was adjusted to ∼7.6 and the mixture was sterile-filtered using a syringe filter with the pore size of 0.22 μm (VWR, Dresden, Germany), aliquoted and stored at −18 °C.

Bottom Line: The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics.Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated.Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range.

View Article: PubMed Central - PubMed

Affiliation: Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, Leipzig 04318, Germany. nadia.nikolaus@ufz.de.

ABSTRACT
Aptamers are short, single stranded DNA or RNA oligonucleotides that are able to bind specifically and with high affinity to their non-nucleic acid target molecules. This binding reaction enables their application as biorecognition elements in biosensors and assays. As antibiotic residues pose a problem contributing to the emergence of antibiotic-resistant pathogens and thereby reducing the effectiveness of the drug to fight human infections, we selected aptamers targeted against the aminoglycoside antibiotic kanamycin A with the aim of constructing a robust and functional assay that can be used for water analysis. With this work we show that aptamers that were derived from a Capture-SELEX procedure targeting against kanamycin A also display binding to related aminoglycoside antibiotics. The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics. Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated. Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range. Finally, the proof of principle of an assay for detection of kanamycin A in a real water sample is given.

Show MeSH
Related in: MedlinePlus