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Decoding region bubble size and aminoglycoside antibiotic binding.

Do Hyun Ryu1, Robert R Rando

  • 1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 45 Shattuck Street, Boston, MA 02115, USA.

Bioorganic & Medicinal Chemistry Letters
|July 20, 2002
PubMed
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Aminoglycoside antibiotics bind to RNA with internal bubbles. However, they do not bind to the human mitochondrial 12S decoding region, acting like a chemical switch when mutations alter bubble size.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Genetics

Background:

  • Aminoglycoside antibiotics are known to bind to various RNA structures, including those with internal bubbles and bulges.
  • This binding interaction is typically observed with bacterial, cytoplasmic, and other human RNA molecules.

Purpose of the Study:

  • To investigate the absence of aminoglycoside binding in the human 12S mitochondrial decoding region.
  • To explore the structural basis for this exception and its potential modulation.

Main Methods:

  • Comparative analysis of aminoglycoside-RNA interactions across different cellular compartments (mitochondrial, bacterial, cytoplasmic).
  • Site-directed mutagenesis of the human 12S mitochondrial decoding region to alter bubble structure.
  • Assessment of aminoglycoside binding affinities to wild-type and mutant RNA sequences.

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Main Results:

  • Aminoglycoside antibiotics exhibit promiscuous binding to diverse RNA structures with internal bubbles and bulges.
  • Binding of aminoglycosides to the human 12S mitochondrial decoding region was notably absent.
  • Mutations reducing the size of the bubble in the 12S decoding region restored aminoglycoside binding.

Conclusions:

  • The human 12S mitochondrial decoding region represents an exception to the general aminoglycoside-RNA binding rule.
  • The size of the internal bubble in the 12S decoding region is a critical determinant for aminoglycoside interaction.
  • This interaction exhibits a chemical switch-like behavior, suggesting potential for targeted modulation.