Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

Abstract

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.

A dynamic mode of mitotic bookmarking by transcription factors

“…Imaging experiments were conducted on a custom-built Nikon TI microscope equipped with a 100x/NA 1.49 oil-immersion TIRF objective (Nikon apochromat CFI Apo SR TIRF 100x Oil), EM-CCD camera (Andor iXon Ultra 897), a perfect focusing system (Nikon) and a motorized mirror to achieve HiLo-illumination (Tokunaga et al, 2008). To image PA-JF646 dyes (Grimm et al, 2015; 2016), a multi-band dichroic (405 nm/488 nm/561 nm/633 nm BrightLine quad-band bandpass filter, Semrock) was used to reflect a 633 nm laser (1 W, Coherent, Genesis) and 405 nm laser (140 mW, Coherent, Obis) into the objective, and emission light was filtered using a bandpass emission filter (FF01 676/37 Semrock). To image JF549 (Grimm et al, 2015), the same multi-band dichroic (405 nm/488 nm/561 nm/633 nm quad-band bandpass filter, Semrock) was used to reflect a 561 nm laser (1 W, Coherent, Genesis) into the objective and emission light was filtered using a bandpass emission filter (Semrock 593/40 nm).…”

Hybrid Rhodamine Fluorophores in the Visible/NIR Region for Biological Imaging

“…The tetrahydro‐quinoline structures of some fluorophores still retain a hydrogen atom of the rhodamine 110 amine group (e.g. 11 , λ em =558 nm and 26 , λ em =540 nm); this feature means that these fluorophores have smaller bathochromic shifts than those with julolidine rings (e.g., 12 , λ em =600 nm; 13 , λ em =587 nm; 14 , λ em =580 nm; and 15 , λ em =600 nm) . In the Alexa Fluor dyes, symmetrical rhodamines have longer absorption and emission wavelengths compared to asymmetrical rhodamines with the same modified group.…”

“…[19a, 47] Recently,t he Lavis and Wu groups reported 81 and 82, which have emission wavelengths of 654 and 666 nm, respectively. [31,48] They used 81 to successfully construct af ar-red photoactivatable Si-rhodamine probe that has higher photon counts than the standard…”

Nanoscopic Visualization of Soft Matter Using Fluorescent Diarylethene Photoswitches

“…[1] Therefore,m ethods to directly visualize structures in the nanometer range are of paramount importance for the ongoing evolution of novel materials with specialized and adaptive properties for sophisticated applications.S canning probe microscopy techniques give access to the nanometer range and determine surface properties such as topology and softness, [2,3] while modern electron microscopy methods,s uch as scanning electron microscopy (SEM) [4,5] and transmission electron microscopy (TEM), [6][7][8] can yield structural information even in the subnanometer range when there is sufficient electron density contrast. Despite the success of these methods,t hey are technically demanding and time-consuming.F urthermore,m any softmatter samples possess poor electron contrast, and require non-invasive in situ imaging below the surface as well as the possibility to directly study dynamics.I nr ecent years,s uperresolved fluorescence microscopy has revolutionized optical imaging, [9][10][11][12][13][14] by utilizing the photophysical or photochemical switching of fluorescent dyes in as ophisticated manner in combination with modern optics.Sofar, the life sciences have benefited, in particular, from the new possibilities of resolving structures well beyond the diffraction limit of light. Only af ew examples of the application of super-resolution microscopy to materials science have been reported, [15][16][17][18] since concepts that require,f or example,t he addition of (polar) switching buffers often fail for these systems.T herefore,t he main bottleneck for more universal applications of super-resolution imaging are switchable dyes with suitable (photo-)physical and chemical properties,such as high photostability,adjustable switching rates,minimum interaction with the environment to be probed, and simple design, with the possibility of multiple and straightforward derivatization for the specific labeling of structures or compartments.…”