Fluorescent scaffold

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. 

Thus far, only several fluorescent scaffolds have been studied by the diversity-oriented approach and broader chemical space could be achieved for introducing higher diversity. Even more, there are other fluorescent dye scaffolds remain untouched yet. As more fluorescent compounds are synthesized systematically, richer information for structure-photophysical property relationships should be available, which in turn could help for the designing of target-specific fluorescence sensors. 

DNA Y-junctions have been used as fluorescent scaffolds for EcoRII methyltransferase-thioredoxin (M EcoRII-Trx) fusion proteins and covalent links were formed between the DNA scaffold and the methyltransferase at preselected sites on the scaffold containing 5FdC [8]. The resulting... 

Catch-and-release strategies can also be accommodated to the derivatization of fluorescent scaffolds. Mason and Balasubramanian reported a catch-and-release approach... 

Fluorescently modified fibrils are a useful probe. Furthermore, MacPhee and Dobson have shown that it may be possible to bind other non-peptidic functional groups, provided they can be covalently linked during synthesis. They also demonstrate that utilizing intrinsic fibril structural features might be one approach to the production of peptide scaffolds with well-defined ligand spacings. 

Benzimidazolium is one of the typical scaffolds of the hemicyanine group, and cationic hemicyanine derivatives can be assumed as potential fluorescent sensors due to their electrostatic interactions. Based on this assumption, Chang and... 

Rosania GR, Lee JW, Ding L, Yoon HS, Chang YT (2003) Combinatorial approach to organelle-targeted fluorescent library based on the styryl scaffold. J Am Chem Soc 125 1130-1131... 

The same group reported the simultaneous radiolabeling (with DOTA-anchored 4Cu) and fluorescence studies, coupled with biodistribution in vivo and in vitro (92). It is believed that appropriately functionalized SWNTs can efficiently reach tumor tissues in mice with no apparent toxicity (159). Furthermore, water-solubilised carbon nanotubes are nontoxic when taken up by cells even in high concentration (92). These studies have been complemented by the recent PET imaging of water-soluble 86Y labelled carbon nanotubes in vivo (mice) (160,161), to explore the potential usefulness of carbon nanocarriers as scaffolds for drug delivery. The tissue biodistribution and pharmacokinetics of model DOTA functionalized nanotubes have been explored in vivo (mouse model). MicroPET images indicated accumulation of activity mainly in the kidney, liver, spleen, and to a much less... 

Synthesis of Fluorescent Silver Clusters in Various Scaffolds... 

In this chapter, we discuss first how the silver clusters relate to silver atoms and silver nanoparticles. Then we overview the formation of fluorescent silver clusters in aqueous solution, using silver salts as precursors and various scaffolds as stabilizers. Finally we discuss applications of silver clusters in fluorescent labeling of biological tissues, and their use as fluorescent probes for sensing of molecules. 

Fig. 2 (a) Schematic of the formation of silver clusters using DNA oligonucleotide as scaffold. After complexation of DNA with silver cations, the mixture is reduced with NaBtL, and the fluorescent cluster is formed, (b) Absorption spectra of silver clusters acquired every 30 min using [5 -AGGTCGCCGCCC-3 ] = 10 uM. [Ag+] = 60 uM. and [BfLj-] = 60 pM. The foremost spectrum was acquired 9 min after adding the BH4, and it has at 426 nm. The inset spectrum shows the last spectmm in the series (692 min), with peaks at 424 and 520 nm. (c) Induced circular dichroism spectra. The cell path length was 5 cm. The spectra were collected 2 min (A, dashed-dotted line), 20 min (B, dotted line), 40 min (C,fine dashed line), 60 min (D, coarse dotted line), and 150 min (E, solid line) after adding the BH [32]... 

Fig. 14 Use of two different DNA duplexes with inserted cytosine loops working as synthetic scaffolds to generate fluorescent silver clusters for the identification of the sickle cell anemia gene mutation (black dots represent hydrogen bonds formed in base pairing and black dashed lines the sugar-phosphate backbone) [74]...

In contrast to dendrimers built up from aliphatic chains, polyphenylene dendrimer micelles possess shape and size persistent cavities due to their rigid scaffold which strongly depends on the type of dendrimer. In this case a selective incorporation of guest molecules, e.g., fluorescent dyes, should be possible, dependent on the size of the guest molecule and the cavity of the host. The non-covalent uptake of dyes with an appropriate size thus allows the investigation of their interactions within the dendritic micelle. In our case we made the second-generation polyphenylene dendrimer 48, which bears 16 carboxy-functions at the periphery, by starting from a tetrahedral core and an appropriately... 

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