Usefulness of visible dyes for the staining of protein or DNA in electrophoresis

Li, Jin; Choi, Jung Kap

doi:10.1002/elps.200305995

Cited by 21 publications

(19 citation statements)

References 47 publications

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“…As expected, these two anionic complexes successfully marked proteins separated by SDS-PAGE due to disulfonate groups (Fiorini et al, 2018). Although the presence of the disulfonate groups has been widely used to achieve the (dye-SO 3 − / + NH 3 -protein) interaction, as stated above, other strategies can also be used (Jin and Choi, 2004). Cationic dyes can also interact with proteins, presumably by electrostatic interactions with negatively charged residues (e.g., the presence of -COO − in aspartate and glutamate) (Jin and Choi, 2004).…”

Section: Introductionsupporting

confidence: 53%

New Cationic fac-[Re(CO)3(deeb)B2]+ Complex, Where B2 Is a Benzimidazole Derivative, as a Potential New Luminescent Dye for Proteins Separated by SDS-PAGE

et al. 2021

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Sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) can be used to separate proteins based mainly on their size such as in denaturing gels. Different staining methods have been reported to observe proteins in the gel matrix, where the most used dyes are generally anionic. Anionic dyes allow for interactions with protonated amino acids, retaining the dye in the proteins. Fluorescent staining is an alternative technique considered to be sensitive, safe, and versatile. Some anionic complexes based on d6 transition metals have been used for this purpose, where cationic dyes have been less explored in this context. In this work, we synthesized and characterized a new monocationic rhenium complex fac-[Re(CO)3(deeb)B2]+ (where deeb is 4,4′-bis(ethoxycarbonyl)-2,2′-bpy and B2 is 2,4-di-tert-butyl-6-(3H-imidazo[4,5-c]pyridine-2-yl)phenol). We carried out a structural characterization of this complex by MS+, FTIR, 1H NMR, D2O exchange, and HHCOSY. Moreover, we carried out UV-Vis, luminescence, and cyclic voltammetry experiments to understand the effect of ligands on the complex’s electronic structure. We also performed relativistic theoretical calculations using the B3LYP/TZ2P level of theory and R-TDDFT within a dielectric continuum model (COSMO) to better understand electronic transitions and optical properties. We finally assessed the potential of fac-[Re(CO)3(deeb)B2]+ (as well as the precursor fac-Re(CO)3(deeb)Br and the free ligand B2) to stain proteins separated by SDS-PAGE. We found that only fac-[Re(CO)3(deeb)B2]+ proved viable to be directly used as a luminescent dye for proteins, presumably due to its interaction with negatively charged residues in proteins and by weak interactions provided by B2. In addition, fac-[Re(CO)3(deeb)B2]+ seems to interact preferentially with proteins and not with the gel matrix despite the presence of sodium dodecyl sulfate (SDS). In future applications, these alternative cationic complexes might be used alone or in combination with more traditional anionic compounds to generate counterion dye stains to improve the process.

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Section: Introductionsupporting

confidence: 53%

New Cationic fac-[Re(CO)3(deeb)B2]+ Complex, Where B2 Is a Benzimidazole Derivative, as a Potential New Luminescent Dye for Proteins Separated by SDS-PAGE

et al. 2021

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“…Fluorescence sensors are highly desirable because of their high sensitivity to fluorescence spectroscopy and light‐up probes, whose emission intensity increases when associated with biomolecules, and are useful markers in genomics and proteomics since binding events to the host molecule can result in the appearance of an intense fluorescence emission of the probes . Light‐up probes are mainly used for quantification of biomacromolecules and as stains in gel electrophoresis such as 1‐anilino‐8‐naphthalene sulfonate (1,8‐ANS), Nile Red and the SYPRO dye family . Nevertheless, studies aimed at better understanding the origin of fluorescence properties of a given probe and in particular, their dependence on the environment, are scarce.…”

Section: Introductionmentioning

confidence: 99%

A novel amphiphilic thiosemicarbazone derivative for binding and selective sensing of human serum albumin

2013

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The interaction of ligands and drug molecules with protein is of major interest in drug pharmacokinetics and pharmacodynamics. In this study, we synthesized a novel thiosemicarbazone-based amphiphilic molecule for selective binding and detection of human serum albumin (HSA) with significant increase in fluorescence intensity. The compound 5-(octyloxy) naphthalene substituted salicylaldehyde thiosemicarbazone was designed to interact with site I of HSA. The weak fluorescence of the probes in aqueous solution showed a dramatic increase in fluorescence intensity upon binding with HSA, while the responses to various other proteins and enzymes were negligible under similar experimental conditions. Changes in fluorescence intensity and formation of a new emission maximum of the compound in the presence of HSA as well as an increase in steady-state anisotropy values reflected well the nature of binding and location of the probe inside the protein environment.

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“…DNA staining using counterion-dye can resolve this problem. As mentioned earlier, there are several counterion-dyestaining methods which use visible dyes to visualize protein and DNA following electrophoresis [12][13][14][15]. IB/MO staining, which uses two oppositely charged dyes, a cationic dye and an anionic dye, can form hydrophobic ion pair complexes during staining.…”

Section: Resultsmentioning

confidence: 99%

Counterion‐dye staining for DNA in electrophoresed gels using indoine blue and methyl orange

et al. 2006

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In this study, we describe a sensitive staining method for DNA in agarose and polyacrylamide gels using organic visible dyes, indoine blue (IB) and methyl orange (MO). The counterion-dye staining method uses two oppositely charged dyes to form a hydrophobic ion pair complex in the staining solution. A decrease in the number of free forms of dyes in staining solution can enhance the selectivity of binding between the dye and DNA, and can reduce nonspecific background staining. As a result, the sensitivity of counterion-dye staining was significantly improved compared with other dye-based staining. This method uses a staining solution consisting of 0.008% IB, 0.002% MO, 10% ethanol and 0.2 M sodium acetate at pH 4.7, and can detect 5 ng of lambda DNA/HindIII within 60 min in agarose gels and 10 ng of PhiX174 DNA/HaeIII within 20 min in polyacrylamide gels.

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Usefulness of visible dyes for the staining of protein or DNA in electrophoresis

Cited by 21 publications

References 47 publications

New Cationic fac-[Re(CO)3(deeb)B2]+ Complex, Where B2 Is a Benzimidazole Derivative, as a Potential New Luminescent Dye for Proteins Separated by SDS-PAGE

New Cationic fac-[Re(CO)3(deeb)B2]+ Complex, Where B2 Is a Benzimidazole Derivative, as a Potential New Luminescent Dye for Proteins Separated by SDS-PAGE

A novel amphiphilic thiosemicarbazone derivative for binding and selective sensing of human serum albumin

Counterion‐dye staining for DNA in electrophoresed gels using indoine blue and methyl orange

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