FRET-guided modeling of nucleic acids Preprint
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Abstract
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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.
AutorInnen
Veröffentlichungsjahr
- 2023
Beitrag veröffentlicht in
- bioRxiv Integrierende Ressource
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- Open Access
Seitenzahl
- 18