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6 Carboxyfluorescein

The Experts below are selected from a list of 264 Experts worldwide ranked by ideXlab platform

Frank W Schaefer – 1st expert on this subject based on the ideXlab platform

  • fluorescent in situ detection of encephalitozoon hellem spores with a 6 Carboxyfluorescein labeled ribosomal rna targeted oligonucleotide probe
    Journal of Eukaryotic Microbiology, 2000
    Co-Authors: Jeff D Hester, H Alan D Lindquist, Albert M Bobst, Frank W Schaefer

    Abstract:

    Abstract A fluorescent in situ hybridization assay has been developed for the detection of the human-pathogenic microsporidian, Encephalitozoon hellem in water samples using epifluorescence microscopy. The assay employs a 19-nucleotide species-specific 6Carboxyfluorescein-labeled oligonucleotide probe, HEL878F, designed to be complementary to the nucleic acid sequence 878–896, a highly variable segment of the 16S ribosomal RNA of E. hellem spores. The specificity of this probe for its ribosomal RNA target site was confirmed using RNA degradation, ribosomal RNA target site competition, and nucleotide base mismatch control probe assays. Furthermore, the specificity of the HEL878F oligonucleotide probe for E. hellem spores was established when it was evaluated on spores from all three species of the genus Encephalitozoon that had been seeded in reagent water and environmental water concentrates. The specificity of the HEL878F oligonucleotide probe was further corroborated when tested on algae, bacteria, and…

  • Fluorescent in situ Detection of Encephalitozoon hellem Spores with a 6Carboxyfluorescein‐Labeled Ribosomal RNA‐Targeted Oligonucleotide Probe
    Journal of Eukaryotic Microbiology, 2000
    Co-Authors: Jeff D Hester, Albert M Bobst, H. D. Alan Lindquist, Frank W Schaefer

    Abstract:

    Abstract A fluorescent in situ hybridization assay has been developed for the detection of the human-pathogenic microsporidian, Encephalitozoon hellem in water samples using epifluorescence microscopy. The assay employs a 19-nucleotide species-specific 6Carboxyfluorescein-labeled oligonucleotide probe, HEL878F, designed to be complementary to the nucleic acid sequence 878–896, a highly variable segment of the 16S ribosomal RNA of E. hellem spores. The specificity of this probe for its ribosomal RNA target site was confirmed using RNA degradation, ribosomal RNA target site competition, and nucleotide base mismatch control probe assays. Furthermore, the specificity of the HEL878F oligonucleotide probe for E. hellem spores was established when it was evaluated on spores from all three species of the genus Encephalitozoon that had been seeded in reagent water and environmental water concentrates. The specificity of the HEL878F oligonucleotide probe was further corroborated when tested on algae, bacteria, and…

Jeff D Hester – 2nd expert on this subject based on the ideXlab platform

  • fluorescent in situ detection of encephalitozoon hellem spores with a 6 Carboxyfluorescein labeled ribosomal rna targeted oligonucleotide probe
    Journal of Eukaryotic Microbiology, 2000
    Co-Authors: Jeff D Hester, H Alan D Lindquist, Albert M Bobst, Frank W Schaefer

    Abstract:

    Abstract A fluorescent in situ hybridization assay has been developed for the detection of the human-pathogenic microsporidian, Encephalitozoon hellem in water samples using epifluorescence microscopy. The assay employs a 19-nucleotide species-specific 6Carboxyfluorescein-labeled oligonucleotide probe, HEL878F, designed to be complementary to the nucleic acid sequence 878–896, a highly variable segment of the 16S ribosomal RNA of E. hellem spores. The specificity of this probe for its ribosomal RNA target site was confirmed using RNA degradation, ribosomal RNA target site competition, and nucleotide base mismatch control probe assays. Furthermore, the specificity of the HEL878F oligonucleotide probe for E. hellem spores was established when it was evaluated on spores from all three species of the genus Encephalitozoon that had been seeded in reagent water and environmental water concentrates. The specificity of the HEL878F oligonucleotide probe was further corroborated when tested on algae, bacteria, and…

  • Fluorescent in situ Detection of Encephalitozoon hellem Spores with a 6Carboxyfluorescein‐Labeled Ribosomal RNA‐Targeted Oligonucleotide Probe
    Journal of Eukaryotic Microbiology, 2000
    Co-Authors: Jeff D Hester, Albert M Bobst, H. D. Alan Lindquist, Frank W Schaefer

    Abstract:

    Abstract A fluorescent in situ hybridization assay has been developed for the detection of the human-pathogenic microsporidian, Encephalitozoon hellem in water samples using epifluorescence microscopy. The assay employs a 19-nucleotide species-specific 6Carboxyfluorescein-labeled oligonucleotide probe, HEL878F, designed to be complementary to the nucleic acid sequence 878–896, a highly variable segment of the 16S ribosomal RNA of E. hellem spores. The specificity of this probe for its ribosomal RNA target site was confirmed using RNA degradation, ribosomal RNA target site competition, and nucleotide base mismatch control probe assays. Furthermore, the specificity of the HEL878F oligonucleotide probe for E. hellem spores was established when it was evaluated on spores from all three species of the genus Encephalitozoon that had been seeded in reagent water and environmental water concentrates. The specificity of the HEL878F oligonucleotide probe was further corroborated when tested on algae, bacteria, and…

Vadim V Shmanai – 3rd expert on this subject based on the ideXlab platform

  • 4 5 dichloro 2 7 dimethoxy 5 6 Carboxyfluorescein joe synthesis and spectral properties of oligonucleotide conjugates
    Journal of Organic Chemistry, 2012
    Co-Authors: Dmitry A Tsybulsky, Maksim V Kvach, Irina A Stepanova, Vladimir A Korshun, Vadim V Shmanai

    Abstract:

    A convenient procedure for the preparation of the fluorescent dye 4′,5′-dichloro-2′,7′-dimethoxy-5(6)-Carboxyfluorescein (JOE) is reported; the overall yield achieved starting from isovanillin is 10 times higher (40% vs 4%) compared to the known procedure. Isomers (5- and 6-) are easily chromatographically separable as pentafluorophenyl esters of 3′,6′-O-bis(cyclohexylcarbonyl) derivatives. Four non-nucleoside JOE phosphoramidites based on 5- and 6-isomers and flexible 6-aminohexanol (AH) or rigid 4-trans-aminocyclohexanol (ACH) linkers have been prepared and used for oligonucleotide labeling. Spectral and photophysical properties of 5′-JOE-modified oligonucleotides have been studied. Fluorescence quantum yield of the dye correlates with the nature of the linker (rigid vs flexible) and with the presence of dG nucleosides in close proximity to a JOE residue.

  • 4′,5′-Dichloro-2′,7′-dimethoxy-5(6)-Carboxyfluorescein (JOE): Synthesis and Spectral Properties of Oligonucleotide Conjugates
    Journal of Organic Chemistry, 2011
    Co-Authors: Dmitry A Tsybulsky, Maksim V Kvach, Irina A Stepanova, Vladimir A Korshun, Vadim V Shmanai

    Abstract:

    A convenient procedure for the preparation of the fluorescent dye 4′,5′-dichloro-2′,7′-dimethoxy-5(6)-Carboxyfluorescein (JOE) is reported; the overall yield achieved starting from isovanillin is 10 times higher (40% vs 4%) compared to the known procedure. Isomers (5- and 6-) are easily chromatographically separable as pentafluorophenyl esters of 3′,6′-O-bis(cyclohexylcarbonyl) derivatives. Four non-nucleoside JOE phosphoramidites based on 5- and 6-isomers and flexible 6-aminohexanol (AH) or rigid 4-trans-aminocyclohexanol (ACH) linkers have been prepared and used for oligonucleotide labeling. Spectral and photophysical properties of 5′-JOE-modified oligonucleotides have been studied. Fluorescence quantum yield of the dye correlates with the nature of the linker (rigid vs flexible) and with the presence of dG nucleosides in close proximity to a JOE residue.

  • 5 6 Carboxyfluorescein revisited new protecting group separation of isomers and their spectral properties on oligonucleotides
    Bioconjugate Chemistry, 2007
    Co-Authors: Maksim V Kvach, Dmitry A Tsybulsky, A V Ustinov, Irina A Stepanova, Stanislav L Bondarev, Sergey V Gontarev, Vladimir A Korshun, Vadim V Shmanai

    Abstract:

    Pentafluorophenyl esters of 5- and 6Carboxyfluorescein-3‘,6‘-O-dipivalate can be easily separated in multigram quantities by column chromatography. The individual isomers were converted into stable phosphoramidites suitable for oligonucleotide synthesis. The use of the cyclohexylcarbonyl (Chc) protecting group instead of pivaloyl (Piv) facilitates the separation of isomers. The fluorescence spectra of 5- and 6Carboxyfluoresceins on oligonucleotides were compared.