Fluorescent labels for proteomics and genomics

Waggoner, Alan S.

doi:10.1016/j.cbpa.2006.01.005

Cited by 201 publications

(84 citation statements)

References 12 publications

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“…[3] While this practice continues to the present day, organic dyes have more recently made significant contributions to 21st century technologies, such as fluorescence bioimaging [4] and semiconductor materials for organic electronics. Organic electronics is a closely related new technology that promises to deliver cheaper, flexible, large-scale manufactured electronic devices that rely on organic small-molecule or polymer semiconductors.…”

Section: Introductionmentioning

confidence: 99%

Thiophene‐Containing Pechmann Dyes and Related Compounds: Synthesis, and Experimental and DFT Characterisation

Kantchev

Norsten

Tan

et al. 2011

Chemistry A European J

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Attaching 2-thienyl residues to the Pechmann dye core chromophore (5,5-exo-dilactone situated around a C-C double bond) results in a novel magenta-coloured compound (UV/Vis spectroscopy λ(max) =570 nm in CHCl(3)), which can be rearranged to a yellow 6,6-endo-dilactone (λ(max) =462 nm in CHCl(3)). Single and double amidation results in pronounced redshift in the 5,5-exo series (violet, λ(max) =570 nm and blue, λ(max) =606 nm in CHCl(3), respectively) but pronounced blueshift in the 6,6-endo series (yellow, λ(max) =424 nm and pale yellow bordering on colourless, λ(max) =395 nm in CHCl(3), respectively). Incorporation of a 3-alkyl substituent on the thiophene ring allows for sharp increase of solubility in organic solvents concomitant with fine-tuning of the colour: a redshift in 5,5-exo-dilactones but a blueshift in 5,5-exo-dilactams. DFT computations demonstrate that both lactone classes are planar regardless of the presence of a 3-alkyl group. The lactam derivatives are non-planar: the thiophene-core chromophore dihedral angles increase on going from 5,5-exo to 6,6-endo and from thiophene to 3-alkyl thiophene. Depending on the core heteroatom (O vs. N-alkyl), ring junction (5,5-exo vs. 6,6-endo) and 3-thiophene substituent (H vs. alkyl), two, three, four or six conformers are possible. All of these conformers were characterised by DFT and were found to be very close in energy at both IEFPCM/B3LYP/DGDZVP and SMD/M06/DGDZVP levels of theory. Within each conformer set, the HOMO and LUMO energies were within 0.05 eV and the predicted λ(max) values (TD-DFT) within 10 nm, and this implies low sensitivity of the optical and electronic properties to conformation. Cyclic voltammetry measurements of selected compounds demonstrated good matching to the HOMO and LUMO energies from IEFPCM/B3LYP/DGDZVP computations. M06-2X was the best DFT functional for TD-DFT, giving predicted λ(max) values within about 20 nm.

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Section: Introductionmentioning

confidence: 99%

Thiophene‐Containing Pechmann Dyes and Related Compounds: Synthesis, and Experimental and DFT Characterisation

Kantchev

Norsten

Tan

et al. 2011

Chemistry A European J

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“…Artificial covalent modification of proteins is an arduous but fruitful task of major interest for the biophysics and biochemistry communities that normally pursue as goals the detection or purification of the protein itself in order to have a more thorough understanding of molecular mechanisms and the expansion of the applicability of such biomolecules. Despite the intrinsic difficulties associated to perform those chemical modifications of proteins, the attachment of analytical or engineered probes for protein tracking (labelling) (Giepmans et al, 2006;Waggoner, 2006;Wu & Goody, 2010) or protein profiling (chemical proteomics) (Evans & Cravatt, 2006;Cravatt et al, 2008), the introduction of affinity tags for separation-isolation of proteins (affinity chromatography) (Azarkan et al, 2007;Fang & Zhang, 2008) or for mass spectroscopy-based protein identification and characterization (chemical tagging) (Leitner & Lindner, 2006), the immobilization onto solid supports (microarray technologies) (Wong et al, 2009) and the conjugation with other biomolecules (post-translational modifications) (Gamblin et al, 2008b;Walsh, 2009;Heal & Tate, 2010) are among some of the most useful and frontier techniques and methodologies used in Proteomics. For the chemical modification of proteins, a large number of strategies are nowadays available (Hermanson, 2008).…”

Section: Introductionmentioning

confidence: 99%

Vinyl Sulfone: A Multi-Purpose Function in Proteomics

Lopéz-Jaramillo¹,

Hernández-Matéo²,

Santoyo‐González³

2012

Integrative Proteomics

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“…The low-molecular mass BPLPs can be made to be water-insoluble or -soluble maximizing their potential applications in biological labeling and imaging. The water soluble low-molecular-weight BPLPs may potentially be used for single molecule labeling such as protein and DNA labeling in proteomics and genomics research, where quantum dots may not be ideal because of their size (7,8). The BPLP family may also be suitable for use in fluorescence resonance energy transfer (FRET) (5), 2-photon excited fluorescence microscopy (6), multimodal compositions (combined with magnetic or radionuclear agents) (31), and biosensors (32).…”

Section: Cytotoxicity Evaluation and Bioimaging Study In Vitro And Inmentioning

confidence: 99%

Development of aliphatic biodegradable photoluminescent polymers

Yang

Zhang

Gautam

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

222

271

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Fig. 1. Labeling of the liposome. (A)Outline of the method. Cells were rapidly frozen, freeze-fractured, and evaporated with carbon (C) and platinum/carbon (Pt/C) in vacuum. The replica of the split membrane was digested with SDS to remove noncast molecules and labeled by GST-PH. Both the cytoplasmic and exoplasmic halves of the membrane were examined. (B) Labeling of small unilamellar liposome replicas. Freeze-fracture replicas of liposomes containing 95 mol % of phosphatidylcholine (PC) and 5 mol % of phosphatidylinositol or a phosphoinositide were labeled. Only liposomes containing PI(4,5)P 2 were labeled intensely by GST-PH. A PH mutant, GST-PH (K30N, K32N), which does not bind PI(4,5)P 2, showed little labeling in the PI(4,5)P 2-containing liposome. (C) Quantification of the GST-PH labeling in the liposomes. The number of gold particles per 1 m 2 of the liposome surface is shown (blue). The labeling on the convex (green) and concave (yellow) surfaces showed equivalent results.

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Fluorescent labels for proteomics and genomics

Cited by 201 publications

References 12 publications

Thiophene‐Containing Pechmann Dyes and Related Compounds: Synthesis, and Experimental and DFT Characterisation

Thiophene‐Containing Pechmann Dyes and Related Compounds: Synthesis, and Experimental and DFT Characterisation

Vinyl Sulfone: A Multi-Purpose Function in Proteomics

Development of aliphatic biodegradable photoluminescent polymers

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