22Running title: Effect of nanobodies 23 24 2 Summary 25 Advanced fluorescence microscopy studies require specific and monovalent molecular labelling 26 with bright and photostable fluorophores. This necessity led to the widespread use of fluorescently 27 labelled nanobodies against commonly employed fluorescent proteins. However, very little is 28 known how these nanobodies influence their target molecules. Here, we observed clear changes 29 of the fluorescence properties, mobility and organisation of green fluorescent protein (GFP) tagged 30 proteins after labelling with an anti-GFP nanobody. Intriguingly, we did not observe any co-31 diffusion of fluorescently-labelled nanobodies with the GFP-labelled proteins. Our results suggest 32 significant binding of the nanobodies to a non-emissive, oligomerized form of the fluorescent 33 proteins, promoting disassembly into more monomeric forms after binding. Our findings show that 34 great care must be taken when using nanobodies for studying dynamic and quantitative protein 35 organisation. 36 37 38 39 40 41 42 43 44 45 46 47 48 50Labelling a protein of interest with an antibody is a well-established procedure in molecular 51 biology. Rather large size and multivalence of antibodies, however, limit their application as 52 labelling agents in imaging approaches. Over the past years, the popularity of antigen-binding 53