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[Preprint]. 2024 Sep 23:2024.09.20.614087.
doi: 10.1101/2024.09.20.614087.

A one-step protocol to generate impermeable fluorescent HaloTag substrates for in situ live cell application and super-resolution imaging

Affiliations

A one-step protocol to generate impermeable fluorescent HaloTag substrates for in situ live cell application and super-resolution imaging

Kilian Roßmann et al. bioRxiv. .

Abstract

Communication between cells is largely orchestrated by proteins on the cell surface, which allow information transfer across the cell membrane. Super-resolution and single-molecule visualization of these proteins can be achieved by genetically grafting HTP (HaloTag Protein) into the protein of interest followed by brief incubation of cells with a dye-HTL (dye-linked HaloTag Ligand). This approach allows for use of cutting-edge fluorophores optimized for specific optical techniques or a cell-impermeable dye-HTL to selectively label surface proteins without labeling intracellular copies. However, these two goals often conflict, as many high-performing dyes exhibit membrane permeability. Traditional methods to eliminate cell permeability face synthetic bottlenecks and risk altering photophysical properties. Here we report that dye-HTL reagents can be made cell-impermeable by inserting a charged sulfonate directly into the HTL, leaving the dye moiety unperturbed. This simple, one-step method requires no purification and is compatible with both the original HTL and second-generation HTL.2, the latter offering accelerated labeling. We validate such compounds, termed dye-SHTL ('dye shuttle') conjugates, in live cells via widefield microscopy, demonstrating exclusive membrane staining of extracellular HTP fusion proteins. In transduced primary hippocampal neurons, we label mGluR2, a neuromodulatory G protein-coupled receptor (GPCR), with dyes optimized for stimulated emission by depletion (STED) super-resolution microscopy, allowing unprecedented accuracy in distinguishing surface and receptors from those in internal compartments of the presynaptic terminal, important in neural communication. This approach offers broad utility for surface-specific protein labelling.

Keywords: ATTO 647N; HaloTag; STED; fluorescence microscopy; impermeability; mGluR2.

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Conflict of interest statement

COMPETING INTERESTS NL is a member of the scientific advisory board of Trace Neuroscience. MRT and BCS are on patent applications describing HTL.2. All other authors declare no competing interests.

Figures

Figure 1:
Figure 1:. Logic for impermeable dyes to label cell surface proteins.
A-B) Known strategies to address extracellularly exposed self-labelling tags with cartoons and chemical structures indicating where anionic charges have previously been introduced. C-D) Our new strategy to install a sulfonate charge on the HaloTag Ligand (HTL). E) Modelling of the HaloTag Protein (HTP) bound to TMR-SHTL. F) Synthesis of TMR-d12-SHTL and SiR-d12-SHTL. G) Excitation and emission profiles of TMR-d12 comparing HTL to SHTL conjugates. H) In vitro protein labelling of apo-HTP confirms binding by full protein mass spectrometry. I) Labelling kinetics of apo-HTP with TMR-d12-HTL and TMR-d12-SHTL. J) Fluorescence quantum yields of TMR/SiR-d12 conjugated to HTL/SHTL with or without HTP-bound. K) Fluorescence lifetimes of the same reagents. L) Table summarizing values from G, J, K.
Figure 2:
Figure 2:. Live cell imaging in transfected HE293 cells.
A-E) HEK293 expressing HTP-TM-SNAP. Intracellular SNAP labelled with BG-JF646; extracellular HTP labelled with TMR-d12-HTL or TMR-d12-SHTL. Widefield imaging (A), zoom-ins (B, D) and line scans (C, E). F-J) HEK293 cells expressing SNAP-TM-HTP. Extracellular SNAP labelled with BG-SulfoJF646; intracellular HTP labelled with TMR-d12-HTL or TMR-d12-SHTL. Widefield (F), zoom-in (G, I) and line scans (H, J). K-O) As for A-E but staining with BG-JF549 and SiR-d12-(S)HTL. P-T) As for F-J but staining with BG-SulfoJF549 and SiR-d12-(S)HTL.
Figure 3:
Figure 3:. Revealing HTP-mGluR2 localization in hippocampal neurons.
A) Viral DNA expression cassette with HTP-mGluR under hSyn promoter. B) Neural connection via synapses and localization of axonal MAP2, presynaptic Bassoon and postsynaptic Shank proteins (created in biorender.com). C) Confocal imaging of HTP-mGluR2 transduced mouse hippocampal neurons with SiR-d12-SHTL (left) and SiR-d12-HTL (right), co-stained with an antibody against MAP2 for dendrite identification. D-G) Quantification of HTP-mGluR2 labelling in the soma (D), in dendrites (MAP2 positive, E) and in axons (MAP2 negative, F) reveals significantly less signal using SiR-d12-SHTL, while no difference in axonal MAP2 intensity is observed (G). Mean±SD. Student’s t-test. H) Confocal imaging of HTP-mGluR2 transduced mouse hippocampal neurons cells with SiR-d12-SHTL (500 nM), and the pre- and postsynaptic markers Bassoon and Shank, respectively. I) Overlay of images in H. J) Representative line scan of a synapse shows mGluR2 co-localization primarily with the presynaptic marker Bassoon. K) Quantification of mGluR2 localization with respect to Bassoon and Shank. Mean±SD. Student’s t-test. L-M) As for I-K but labelling with SiR-d12-HTL.
Figure 4:
Figure 4:. STED super-resolution imaging of surface HTP(:S-SiR-d12)-mGluR2.
A) Confocal and STED images of HTP(:S-SiR-d12)-mGluR2 transduced neurons. B) Line scan profile of a process comparing confocal to STED performance, yielding a resolution of 134 nm across the ultrastructure. C) Confocal and dual color STED with zoom in of the process reported in (B).
Figure 5:
Figure 5:. Sulfonation on the HaloTag ligand v2.0 (HTL.2) for improved labelling with sticky ATTO 647N.
A) Chemical structure of ATTO 647N, with a N-methyl amidated additional four carbon linker on the 3 position, which disallows proper dye:HTP secondary interactions. B) Sulfonation protocol on second version HaloTag ligand HTL.2 yields double sulfonated S2HTL.2. C) qTOF full protein mass spectrometry of recombinant HTP labelled with ATTO 647N-HTL.2 and ATTO 647N-S2HTL.2. E) HTP-SNAP- mGluR2 transfected HEK293 cells, labelled with BG-Sulfo549 (1 uM) and different concentrations of ATTO 647N-HTL.2 for 10 minutes prior to fixation and imaging gives rise to unspecific signal. F, G) Zoom ins and brightness contrast adjusted images from (E). H-J) As for (E-G) but with different concentrations of ATTO 647N-SHTL leads to image improvements by removing unspecific signals. K-M) As for (E-G) but with different concentrations of ATTO 647N-S2HTL.2 allows clear membrane labelling even at 1 nM.
Figure 6:
Figure 6:. One step protocol on small scale to synthesize and apply dye-SHTL.
A) Required stock solutions. B) Outlined 5-minute synthetic protocol (partly created in biorender.com). C) Structures of JF549/646-SHTL. D) LCMS traces of the reaction for TMR-d12-HTL and JF646-HTL. E) Confocal imaging of HEK293:SNAP-HTP-mGluR2 transfected cells with TMR-d12-(S)HTL (50 nM) and BG-Sulfo646 (50 nM) including line scans. F) As for E, but with JF549-SHTL, SiR-d12-SHTL and JF646-SHTL.

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