FRET-guided modeling of nucleic acids Preprint uri icon

 

Abstract

  • The functional diversity of RNA is encoded in their innate conformational heterogeneity. The
    combination of single-molecule spectroscopy and computational modeling offers new,
    attractive opportunities to map structural transitions within nucleic acid ensembles. Here, we
    describe a framework to harmonize single-molecule FRET measurements with molecular
    dynamics simulations and de novo structure prediction. Using either all-atom or implicit
    fluorophore modeling we recreate FRET experiments in silico, visualize the underlying
    structural dynamics and quantify the simulated reaction coordinates. Using multiple
    accessible-contact volumes (multi-ACV) as a post-hoc scoring method for fragment-assembly
    in Rosetta, we demonstrate that FRET effectively refines de novo RNA structure prediction
    without the need of explicit dye labeling. We benchmark our FRET-assisted modeling
    approach on double-labeled DNA strands and validate it against an intrinsically dynamic
    manganese(II)-binding riboswitch. We show that a FRET coordinate describing the assembly
    of a four-way junction allows our pipeline to recapitulate the global fold of the riboswitch with
    sub-helical accuracy to the crystal structure. We conclude that computational fluorescence
    spectroscopy facilitates the interpretability of dynamic structural ensembles and improves the
    mechanistic understanding of nucleic acid interactions.

Veröffentlichungszeitpunkt

  • 2023

veröffentlicht in

  • bioRxiv  Integrierende Ressource

Zugangsrechte

  • Open Access

Seitenzahl

  • 18