Cyanine rotaxanated

Analysis of the available literature data on host-guest complexes based on cyanine and styryl dyes with CDs shows that rotaxane formation in general... 

References [52-54] do not include any data directly comparing squaraine rotaxanes with common cyanine dyes such as Cy5 (GE Healthcare) and Alexa 647 (Life Technologies). Nevertheless, from the available data it can be concluded that squaraine rotaxanes are remarkably resistant to chemical and photochemical degradation, and likely to be very useful as a versatile fluorescent scaffold for constructing various types of highly stable, red and near infrared (NIR) imaging probes and labels. 

With the example of stained E. coli cells, the squaraine rotaxane 15b containing a zinc(II)-dipicolylamine (Zn-DPA) ligand, which is known to selectively associate with the anionic surfaces of bacterial cells, was found to be almost 100 times more photostable as compared to Cy5-Zn-DPA [55]. This can be attributed to stronger cell-surface affinity of 15b, leading to a slower off rate for the probe. The remarkable stability of 15b permits fluorescence imaging experiments that are impossible with probes based on conventional NIR cyanine dyes such as Cy5. Squaraine rotaxanes are likely to be superior substitutes for conventional cyanine dyes for biomedical imaging applications that require NIR fluorescent probes. 

Squaraines 17a-17c were encapsulated in these macrocyles to form the corresponding pseudorotaxanes. Squaraine rotaxanes 14 and 15 with a phenylene tetralactam macrocycle have absorption/emission profiles (Table 3) that closely match those of Cy5, whereas squaraine rotaxanes 16 D 17 with an anthrylene macrocycle have a red-shifted absorption/emission that matches that of the homologous cyanine Cy5.5 (Table 4). These rotaxanes should be useful for fluorescence microscopy imaging applications. 

An overview of the synthesis, structure, photophysical properties, and applications of squaraine rotaxanes as fluorescent imaging probes and chemosensors is provided in a recent review [67]. Although a variety of squaraine dyes form rotaxanes with the molecular cage 25 or with a tetralactam macrocyclic system introduced by Leigh and co-workers [16, 17], there is no evidence in the literature that conventional cyanine dyes can be embedded in these macrocycles. 

Buston JEH, Young JR, Anderson HL (2000) Rotaxane-encapsulated cyanine dyes enhanced fluorescence efficiency and photostability. Chem Commun 11 905-906... 

Yau CMS, Pascu SI, Odom SA, Warren JE, Klotz EJF, Frampton MJ, Williams CC, Coropceanu V, Kuimova MK, Phillips D, Barlow S, Bredas JL, Marder SR, Millar V, Anderson HL (2008) Stabilisation of a heptamethine cyanine dye by rotaxane encapsulation. Chem Commun 25 2897-2899... 

Buston JEH, Marken F, Anderson HL (2001) Enhanced chemical reversibility of redox processes in cyanine dye rotaxanes. Chem Commun 11 1046—1047... 

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