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Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments

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Grotz,  Kara K.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Heinz,  Marcel
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Stelzl,  Lukas S.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Hummer,  Gerhard       
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;
Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany;

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Citation

Grotz, K. K., Nueesch, M. F., Holmstrom, E. D., Heinz, M., Stelzl, L. S., Schuler, B., et al. (2018). Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments. The Journal of Physical Chemistry B, 122(49), 11626-11639. doi:10.1021/acs.jpcb.8b07537.


Cite as: https://hdl.handle.net/21.11116/0000-0003-8FD1-0
Abstract
We combine single-molecule Förster resonance energy transfer (single-molecule FRET) experiments with extensive all-atom molecular dynamics (MD) simulations (>100 μs) to characterize the conformational ensembles of single-stranded (ss) DNA and RNA in solution. From MD simulations with explicit dyes attached to single-stranded nucleic acids via flexible linkers, we calculate FRET efficiencies and fluorescence anisotropy decays. We find that dispersion-corrected water models alleviate the problem of overly abundant interactions between fluorescent dyes and the aromatic ring systems of nucleobases. To model dye motions in a computationally efficient and conformationally exhaustive manner, we introduce a dye-conformer library, built from simulations of dinucleotides with covalently attached dye molecules. We use this library to calculate FRET efficiencies for dT19, dA19, and rA19 simulated without explicit labels over a wide range of salt concentrations. For end-labeled homopolymeric pyrimidine ssDNA, MD simulations with the parmBSC1 force field capture the overall trend in salt-dependence of single-molecule FRET based distance measurements. For homopolymeric purine ssRNA and ssDNA, the DESRES and parmBSC1 force fields, respectively, provide useful starting points, even though our comparison also identifies clear deviations from experiment.