Fiche publication
Date publication
avril 2016
Journal
Nucleic acids research
Auteurs
Membres identifiés du Cancéropôle Est :
Dr DEJAEGERE Annick
,
Pr MELY Yves
Tous les auteurs :
Voltz K, Léonard J, Touceda PT, Conyard J, Chaker Z, Dejaegere A, Godet J, Mély Y, Haacke S, Stote RH
Lien Pubmed
Résumé
Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies.
Mots clés
2-Aminopurine, DNA, chemistry, DNA, Viral, chemistry, HIV-1, genetics, Models, Molecular, Molecular Dynamics Simulation, Nucleic Acid Conformation, Spectrometry, Fluorescence
Référence
Nucleic Acids Res.. 2016 Apr;44(7):3408-19
