Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer Journal Article
| Authors: | Jiang, L.; Majumdar, A.; Hu, W.; Jaishree, T. J.; Xu, W.; Patel, D. J. |
| Article Title: | Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer |
| Abstract: | Background: Aminoglycoside antibiotics can target RNA folds with micromolar affinity and inhibit biological processes ranging from protein biosynthesis to ribozyme action and viral replication. Specific features of aminoglycoside antibiotic-RNA recognition have been probed using chemical, biochemical, spectroscopic and computational approaches on both natural RNA targets and RNA aptamers identified through in vitro selection. Our previous studies on tobramycin-RNA aptamer complexes are extended to neomycin B bound to its selected RNA aptamer with 100 nM affinity. Results: The neamine moiety (rings I and II) of neomycin B is sandwiched between the major groove floor of a 'zippered-up' G·U mismatch aligned segment and a looped-out purine base that flaps over the bound antibiotic. Specific intermolecular hydrogen bonds are observed between the charged amines of neomycin B and base mismatch edges and backbone phosphates. These interactions anchor 2-deoxystreptamine ring I and pyranose ring II within the RNA-binding pocket. Conclusions: The RNA aptamer complexes with tobramycin and neomycin B utilize common architectural principles to generate RNA-binding pockets for the bound aminoglycoside antibiotics. In each case, the 2-deoxystreptamine ring I and an attached pyranose ring are encapsulated within the major groove binding pocket, which is lined with mismatch pairs. The bound antibiotic within the pocket is capped over by a looped-cut base and anchored in place through intermolecular hydrogen bonds involving charged amine groups of the antibiotic. |
| Keywords: | complex formation; rna; anti-bacterial agents; molecular sequence data; magnetic resonance spectroscopy; protons; molecular structure; rna structure; tobramycin; drug binding; carbohydrate sequence; carbohydrate; rna binding; oligosaccharides; nuclear overhauser effect; priority journal; article; framycetin; aminoglycoside antibiotic encapsulation; mismatch-aligned binding pocket; neomycin-rna complex; site-specific intermolecular alignments |
| Journal Title: | Structure |
| Volume: | 7 |
| Issue: | 7 |
| ISSN: | 0969-2126 |
| Publisher: | Cell Press |
| Date Published: | 1999-07-15 |
| Start Page: | 817 |
| End Page: | 827 |
| Language: | English |
| DOI: | 10.1016/s0969-2126(99)80105-1 |
| PUBMED: | 10425683 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | Article -- Export Date: 16 August 2016 -- Source: Scopus |
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