Docking simulation of polyamines on a kissing-loop RNA dimer

Nucleic Acids Symp Ser (Oxf). 2009:(53):273-4. doi: 10.1093/nass/nrp137.

Abstract

Polyamines, especially branched polyamines such as tetrakis(3-aminopropyl)ammonium (Taa), stabilize the tertiary structure of RNA molecules. In this study, we examined the polyamine binding site of the HIV-1 dimerization initiation site (DIS) in the kissing-loop dimer by the docking simulation. It was found that Taa binds predominantly to the kissing loop interaction site of DIS.

MeSH terms

  • Binding Sites
  • Computer Simulation
  • Dimerization
  • HIV-1 / genetics*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Polyamines / chemistry*
  • Quaternary Ammonium Compounds / chemistry*
  • RNA, Viral / chemistry*

Substances

  • Polyamines
  • Quaternary Ammonium Compounds
  • RNA, Viral
  • tetrakis(3-aminopropyl)ammonium
  • caldopentamine