RNA Sequence Determinants for Aminoglycoside Binding to an A-site rRNA Model Oligonucleotide

Authors

Kam D. Dahlquist, Loyola Marymount UniversityFollow
Michael I. Recht
Dominique Fourmy
Scott C. Blanchard
Joseph D. Puglisi

Document Type

Article

Publication Date

1996

Abstract

The codon-anticodon interaction on the ribosome occurs in the A site of the 30 S subunit. Aminoglycoside antibiotics, which bind to ribosomal RNA in the A site, cause misreading of the genetic code and inhibit translocation. Biochemical studies and nuclear magnetic resonance spectroscopy were used to characterize the interaction between the aminoglycoside antibiotic paromomycin and a small model oligonucle otide that mimics the A site ofEscherichia coli16 S ribosomal RNA. Upon chemical modification, the RNA oligonucleotide exhibits an accessibility pattern similar to that of 16 S rRNA in the 30 S subunit. In addition, the oligonucleotide binds specifically aminoglycoside antibiotics. The anti biotic binding site forms an asymmetric internal loop, caused by non-canonical base-pairs. Nucleotides that are important for binding of paromomycin were identified by performing quantitative footprinting on oligonucleotide sequence variants and include the C1407·G1494 base-pair, and A·U base-pair at positions 1410/1490, and nucleotides A1408, A1493 and U1495. The asymmetry of the internal loop, which requires the presence of a nucleotide in position 1492, is also crucial for antibiotic binding. Introduction into the oligonucleotide of base changes that are known to confer aminoglycoside resistance in 16 S rRNA result in weaker binding of paromomycin to the oligonucleotide. Oligonucleotides homologous to eukaryotic rRNA sequences show reduced binding of paromomycin, suggesting a physical origin for the species-specific action of aminoglycosides.

Comments

LMU users: use the following link to login and access the article via LMU databases.

Original Publication Citation

Recht, M. I., et al. “RNA Sequence Determinants for Aminoglycoside Binding to an A-Site RRNA Model Oligonucleotide.” Journal of Molecular Biology, vol. 262, no. 4, Oct. 1996, pp. 421–436.

Digital Commons @ LMU & LLS Citation

Dahlquist, Kam D.; Recht, Michael I.; Fourmy, Dominique; Blanchard, Scott C.; and Puglisi, Joseph D., "RNA Sequence Determinants for Aminoglycoside Binding to an A-site rRNA Model Oligonucleotide" (1996). Biology Faculty Works. 136.
https://digitalcommons.lmu.edu/bio_fac/136