Suitable labels are at the core of Luminescence and fluorescence imaging and sensing. One of the most exciting, yet also controversial, advances in label technology is the emerging development of quantum dots (QDs)--inorganic nanocrystals with unique optical and chemical properties but complicated surface chemistry--as in vitro and in vivo fluorophores. Here we compare and evaluate the differences in physicochemical properties of common fluorescent labels, focusing on traditional organic dyes and QDs. Our aim is to provide a better understanding of the advantages and limitations of both classes of chromophores, to facilitate label choice and to address future challenges in the rational design and manipulation of QD labels.

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Quantum dots versus organic dyes as fluorescent labels

"United we stand, divided we fall."--Aesop. Aggregation-induced emission (AIE) refers to a photophysical phenomenon shown by a group of luminogenic materials that are non-emissive when they are dissolved in good solvents as molecules but become highly luminescent when they are clustered in poor solvents or solid state as aggregates. In this Review we summarize the recent progresses made in the area of AIE research. We conduct mechanistic analyses of the AIE processes, unify the restriction of intramolecular motions (RIM) as the main cause for the AIE effects, and derive RIM-based molecular engineering strategies for the design of new AIE luminogens (AIEgens). Typical examples of the newly developed AIEgens and their high-tech applications as optoelectronic materials, chemical sensors and biomedical probes are presented and discussed.

Aggregation-Induced Emission: The Whole Is More Brilliant than the Parts

5. Cyanine-Based pHi Indicators 2717 5.1. Design of pH-Sensitive Cyanine Dyes 2717 5.2. Near-Neutral Cyanine-Based pH Indicators 2718 5.3. Acidic Cyanine-Based pH Indicators 2719 6. Miscellaneous Small Molecule pHi Indicators 2719 6.1. Various Indicators for Near-Neutral pH Values 2719 6.1.1. Europium Complex 2719 6.1.2. Fluorene Derivative 2719 6.1.3. 1,4-Dihydroxyphthalonitrile (1,4-DHPN) 2720 6.1.4. 8-Hydroxypyrene-1,3,6-trisulfonic acid (HPTS) 2720

Fluorescent indicators for intracellular pH.

Cyanines during the 1990s: A Review

Specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. Genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. Intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. Here we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. Inspired by molecular modeling, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. This addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. The novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the UV and visible range.

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A general method to improve fluorophores for live-cell and single-molecule microscopy

Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters

A novel fluorescence ratiometric method confirms the low solvent viscosity of the cytoplasm.

A series of new fluorescent labeling reagents based on sulfoindocyanine dyes has been developed. We describe the synthesis and properties of these reagents. They contain succinimidyl ester reactive groups and can be readily conjugated to antibodies, avidin, DNA, lipids, polymers, and other amino-group-containing materials. The labeling reagents are water soluble, pH insensitive, and show much reduced dye aggregation under labeling conditions. One of the reagents, Cy3, can be excited with the 488-, 514- and 532-nm laser lines and is optimally excited with the 546-nm mercury arc line. Another, Cy5, can be excited with the 633-nm HeNe and 647-nm Kr laser lines available with many flow cytometers and confocal laser-scanning microscopes. New laser diodes emitting near 650 nm should also be excellent excitation sources for Cy5.

Swati R. Mujumdar

Papers

Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters

A novel fluorescence ratiometric method confirms the low solvent viscosity of the cytoplasm.

Cyanine Dye Labeling Reagents: Sulfoindocyanine Succinimidyl Esters.