Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics Using Isothermal Titration Calorimetry

  • Serena BernacchiEmail author
  • Eric EnnifarEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2113)


Isothermal titration calorimetry (ITC) provides a sensitive, powerful, and accurate tool to suitably analyze the thermodynamic of RNA binding events. This approach does not require any modification or labeling of the system under analysis and is performed in solution. ITC is a very convenient technique that provides an accurate determination of binding parameters, as well as a complete thermodynamic profile of the molecular interactions. Here we show how this approach can be used to characterize the interactions between the dimerization initiation site (DIS) RNA localized within the HIV-1 viral genome and aminoglycoside antibiotics. Our ITC study showed that the 4,5-disubstituted 2-desoxystreptamine (2-DOS) aminoglycosides can bind the DIS with a nanomolar affinity and a high specificity.

Key words

HIV-1 Viral RNA Aminoglycosides Dimerization initiation site ITC Thermodynamics RNA–drug interaction 


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Authors and Affiliations

  1. 1.Architecture et Réactivité de l’ARN - CNRS UPR 9002Institut de Biologie Moléculaire et Cellulaire, Université de StrasbourgStrasbourgFrance

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