Selected Papers

SiR-actin Kit & SiR-tubulin Kit

“Fluorogenic probes for live-cell imaging of the cytoskeleton”; G. Lukinavičius, et. al.; Nature Methods 11, 731–733, 2014.
The landmark paper introducing the probes SiR-actin and SiR-tubulin. This article contains a thorough evaluation of the probes in live-cell imaging conditions, including SIM and STED imaging. A must read!

“Polarized endosome dynamics by spindle asymmetry during asymmetric cell division”; E. Derivery, et. al.; Nature, 528(7581): 280-2851, 2015.
An excellent Nature article in which the authors show the mechanism of specific endosome segregation during asymmetric division. With the help of SiR-tubulin and other reporters fused to FPs, robust evidence of an asymmetric distribution of microtubules along the mitotic axis is shown. This uneven microtubule density is at the basis of segregation.

“STED Nanoscopy Reveals the Ubiquity of Subcortical Cytoskeleton Periodicity in Living Neurons”; E. D’Este, et. al.; Cell Reports, Volume 10 , Issue 8 , 1246 – 1251, 2015.
A remarkable article from the group of the Nobel Prize winner Stefan Hell showing how actin organizes into ring-like structures in living neurons using STED nanoscopy. SiR-actin is the key reagent that allowed to images these periodic structures that are below the conventional diffraction limit.

“Subcortical cytoskeleton periodicity throughout the nervous system”; E. D’Este, et. al.; Scientific Reports, 6, 22741, 2016.
In this article, which was built on the previous article in this list, D’Este et. al. (group of Nobel prize winner Stefan Hell) brilliantly used SiR-actin to systematically look by STED nanoscopy for ring-like structures of actin within many cell types of the nervous system. They showed that this particular actin organization is found in almost all neural cells. Stunning images with impressive resolution.

“Dynamic actin filaments control the mechanical behavior of the human red blood cell membrane”; D. S. Gokhin, et. al.; Mol. Biol. Cell; February 25, 2015.
This article challenges the idea that actin filaments under the plasma membrane of red blood cells (RBC) are not dynamic. Further, evidence is shown that these dynamic actin filaments play a role in the mechanical properties of the RBCs. SiR-actin was successfully used in a FRAP experiment to demonstrate the dynamic behavior of F-actin in live RBCs. 

“A marginal band of microtubules transports and organizes mitochondria in retinal bipolar synaptic terminals”; M. Graffe, et. al.; J. Gen Physiol. Vol. 146 No.1: 109-117, 2015.
This paper features amazing images of retina bipolar cells of goldfish containing giant synaptic terminals stained with SiR-tubulin. The authors show an unusual arrangement of a thick band of microtubules emerging from the axon and that loop around the terminal periphery throughout the presynaptic space of the synaptic terminal.

“A cleavable cytolysin-neuropeptide Y bioconjugate enables specific drug delivery and demonstrates intracellular mode of action”; V. M. Ahrens, et. al.; J. Control. Release; 209:170-178, 2015.
The authors report a cleavable cytolysin–neuropeptide Y bioconjugate that specifically targets receptors overexpressed by cancer cells. The conjugate internalizes and releases intracellularly a microtubule poison. The treated cells were subsequently stained with SiR-tubulin and it was shown that their microtubules depolymerized and nuclei fragmented.

“A Bright Dye for Live-Cell STED Microscopy”; S. Pitsch, I. Köster, 2015.
A joint application note from Spirochrome and the world leading microscope manufacturer Leica that underscores the use of SiR-tubulin and SiR-actin in live cell STED microscopy .


“SiR–Hoechst is a far-red DNA stain for live-cell nanoscopy”; G. Lukinavičius et. al.; Nat. Commun. 6:8497 doi: 10.1038/ncomms9497 (2015).
This article introduces the probe SiR-DNA (named SiR-hoechst in the article). It shows how SiR-DNA outperforms other live cells DNA stains both in terms of toxicity and specificity in live-cell imaging conditions.

“Back to the roots: segregation of univalent sex chromosomes in meiosis”; G. Fabig et. al.; Chromosoma, 1-10 (2015).
Here SiR-DNA was used to track sexual chromosomes during meiosis in different„ nematode species, including C. elegans.

SiR-COOH, SiR-NHS, SiR-tetrazine, SiR-azide & SiR-alkyne reagents

“A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins”; G. Lukinavičius, et. al.; Nature Chemistry 5, 132–139, 2013.
Another landmark paper introducing the carboxylated SiR-fluorophore SiR-COOH and its use for the the generation of fluorogenic substrates for the self labeling tags SNAP-tag, CLIP-tag and Halo-tag as well as SiR-tetrazine.

“Superresolution imaging of the Golgi in live cells with a bioorthogonal ceramide probe”;R. S. Erdmann et al.; Angew. Chem. Int. Ed.; 53: 10242–10246 (2014).
In this article SiR-tetrazine is used together with a novel clickable ceramide probe. This combination allowed to record superresolution images (STED) of the golgi in live cells.

“Genetic Code Expansion Enables Live-Cell and Super-Resolution Imaging of Site-Specifically Labeled Cellular Proteins”; C. Uttamapinant , et. al.; J. Am. Chem. Soc., 2015, 137 (14), pp 4602–4605.
A bright application of SiR-tetrazine which, in combination with unnatural amino acid incorporation technology, yields amazing superresolution images (STORM) of proteins in live cells.

“Red Si–rhodamine drug conjugates enable imaging in GFP cells”; E. Kim, et. al.; Chem. Commun., 50, 4504-4507, 2014.
This article underscores the superiority of carboxylated SiR fluorophore to create custom fluorescent probes that are cell permeable, in the far-red, fluorogenic and highly specific. Conjugation of SiR-COOH and the PARP inhibitor Olaparib produced a fluorescent probe to report on the localization of PARP1 and PARP2 in live cells.

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