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Interactions of aminoglycosides with RNAs and proteins via carbohydrate microarray

Xueyu Wang1 Xiaoli Wang1 Beilei Zhang1 Jing Hu2 Jian Yin1

(1.Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China 214122)
(2.Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China 214122)

【Abstract】Aminoglycosides are broad-spectrum antibacterials to treat bacterial infections, especially gram-negative bacteria infections. However, aminoglycosides are losing efficacy because of the increase in antibiotic resistance and their inherent toxicity, attracting more interests in developing new aminoglycosides. Several clinically used aminoglycosides are mainly exerted by inhibition of protein synthesis through binding to bacterial rRNA. The bacterial ribosome RNA is the most currently exploited RNA drug target. Identification of new compounds that target RNAs is indispensable to fight with the growing threat that bacteria pose to human safety. In this work, we used carbohydrate microarrays to probe interactions of low molecular weight ligands with RNAs and proteins. Carbohydrate microarrays, comprising hundreds to thousands of different glycan structures on surfaces in a spatially discrete pattern, are sensitive and versatile tools to study the interactions between biological macromolecules. Herein, aminoglycosides have been immobilized onto the modified glass microscope slides and their interactions with RNAs and proteins are then measured through the labeled fluorescence. The results displayed that microarray can be used to detect the binding of aminoglycosides with three types of target molecules, including the small RNA oligonucleotide mimics of aminoglycoside binding sites in the ribosome (rRNA A-site mimics), the large group Ⅰ ribozyme RNA (approximately 400 nucleotide) and certain proteins (toxicity-causing enzymes, such as DNA polymerase and phospholipase C). For rRNA A-site mimics, the fluorescence intensities of 16 S rRNA is stronger than that of 18 S rRNA, illustrating that as a screen technique, the microarray method can not only determine the binding affinity to RNA but also detect the specific binding to bacterial rRNA mimic. The ability to screen group Ⅰ ribozyme RNA can be helpful to the discovery of new RNA therapeutic targets. Binding of immobilized aminoglycosides to toxicity-causing proteins (DNA polymerase and phospholipase C) is a new method to study of aminoglycoside toxicity. These studies lay the foundation for rapid identification of new RNA-binding ligands with strong and specific binding affinity for their desired targets.

【Keywords】 aminoglycoside microarrays; rRNA A-site mimics; group Ⅰ ribozyme; klenow DNA polymerase; phospholipase C; aminoglycoside microarrays; r RNA A-site mimics; group I ribozyme; klenow DNA polymerase; phospholipase C;


【Funds】 National Natural Science Foundation of China (No. 21502071) National Natural Science Foundation of China(No.21502071) Natural Science Foundation of Jiangsu Province, China (Nos. BK20140154, BK20150140) Natural Science Foundation of Jiangsu Province,China(Nos.BK20140154,BK20150140) Fund of the Public Health Research Center at Jiangnan University (No. JUPH201502) the Public Health Research Center at Jiangnan University(No.JUPH201502)

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This Article


CN: 11-1998/Q

Vol 32, No. 10, Pages 1362-1371

October 2016


Article Outline



  • 1 Materials and methods
  • 2 Results and analysis
  • 3 Conclusions
  • References