Organic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure and dynamics, and it is not obvious that the properties of lipid analogs would match those of non-labeled host lipids. In this work, we bridged atomistic simulations with super-resolution imaging experiments and biomimetic membranes to assess the performance of commonly used sphingomyelin-based lipid analogs. The objective was to compare, on equal footing, the relative strengths and weaknesses of acyl chain labeling, headgroup labeling, and labeling based on poly-ethyl-glycol (PEG) linkers in determining biomembrane properties. We observed that the most appropriate strategy to minimize dye-induced membrane perturbations and to allow consideration of Brownian-like diffusion in liquid-ordered membrane environments is to decouple the dye from a membrane by a PEG linker attached to a lipid headgroup. Yet, while the use of PEG linkers may sound a rational and even an obvious approach to explore membrane dynamics, the results also suggest that the dyes exploiting PEG linkers interfere with molecular interactions and their dynamics. Overall, the results highlight the great care needed when using fluorescent lipid analogs, in particular accurate controls.

Department of Physics University of Helsinki P O Box 64 FI 00014 Helsinki Finland

Department of Physics University of Helsinki P O Box 64 FI 00014 Helsinki Finland; Laboratory of Physics Tampere University of Technology P O Box 692 FI 33101 Tampere Finland

Department of Physics University of Helsinki P O Box 64 FI 00014 Helsinki Finland; Laboratory of Physics Tampere University of Technology P O Box 692 FI 33101 Tampere Finland; Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague Czech Republic

Department of Physics University of Helsinki P O Box 64 FI 00014 Helsinki Finland; Laboratory of Physics Tampere University of Technology P O Box 692 FI 33101 Tampere Finland; MEMPHYS Center for Biomembrane Physics

Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstr 108 01307 Dresden Germany

MRC Human Immunology Unit Weatherall Institute of Molecular Medicine University of Oxford Headley Way OX3 9DS Oxford United Kingdom

MRC Human Immunology Unit Weatherall Institute of Molecular Medicine University of Oxford Headley Way OX3 9DS Oxford United Kingdom; Institute of Applied Optics Friedrich Schiller University Jena Max Wien Platz 4 07743 Jena Germany; Leibniz Institute of Photonic Technology e 5 Albert Einstein Straße 9 07745 Jena Germany

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