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Direct observation of aminoglycoside-RNA interactions by surface plasmon resonance

Academic Article
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Overview

related to degree

  • Hendrix, Martin, Ph.D. in Chemistry, Scripps Research 1993 - 1997

authors

  • Hendrix, Martin
  • Priestley, E. S.
  • Joyce, Gerald
  • Wong, Chi-Huey

publication date

  • 1997

journal

  • Journal of the American Chemical Society  Journal

abstract

  • The specificity of neomycin B and related aminoglycoside antibiotics in their interaction with the Rev responsive element (RRE) of HIV-1 mRNA has been studied by directly observing the aminoglycoside-RNA complexes using surface plasmon resonance. Several different RNA sequences, each with a biotin tag, have been prepared using T7 RNA polymerase-catalyzed transcription of synthetic DNA templates and have been immobilized on a streptavidin-coated surface for the binding study. The results indicate that neomycin B is not specific for the G-rich bubble region in RRE. Rather, it appears to interact with three different sites, each with a submicromolar dissociation constant, within the 67-nucleotide domain II of RRE. Further analysis of neomycin B binding with three short synthetic RNA hairpins showed binding with submicromolar affinity and 1:1 stoichiometry in each case. This suggests that neomycin B may generally bind with this affinity to regular A-form RNA or hairpin loops. The approach described here is generally useful for understanding the fundamental interactions involved in the specific recognition of nucleic acids by small molecules which is the basis of rational drug design.

subject areas

  • Anti-Bacterial Agents
  • Antibody Affinity
  • Base Sequence
  • Binding Sites
  • Biotinylation
  • Chemistry, Pharmaceutical
  • Framycetin
  • Gene Products, rev
  • Genes, env
  • HIV-1
  • Paromomycin
  • Protein Binding
  • RNA, Messenger
  • RNA, Viral
  • Structure-Activity Relationship
  • rev Gene Products, Human Immunodeficiency Virus
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Identity

International Standard Serial Number (ISSN)

  • 0002-7863

Digital Object Identifier (DOI)

  • 10.1021/ja964290o

PubMed ID

  • 11540136
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Additional Document Info

start page

  • 3641

end page

  • 3648

volume

  • 119

issue

  • 16

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