Fluorescence detection of proteins in sodium dodecyl sulfate-polyacrylamide gels using environmentally benign, nonfixative, saline solution

SYPRO Tangerine stain is an environmentally benign alternative to conventional protein stains that does not require solvents such as methanol or acetic acid for effective protein visualization. Instead, proteins can be stained in a wide range of buffers, including phosphate-buffered saline or simply 150 mM NaCl using an easy, one-step procedure that does not require destaining. Stained proteins can be excited by ultraviolet light of about 300 nm or with visible light of about 490 nm. The fluorescence emission maximum of the dye is approximately 640 nm. Noncovalent binding of SYPRO Tangerine dye is mediated by sodium dodecyl sulfate (SDS) and to a lesser extent by hydrophobic amino acid residues in proteins. This is in stark contrast to acidic silver nitrate staining, which interacts predominantly with lysine residues or Coomassie Blue R, which in turn interacts primarily with arginine and lysine residues. The sensitivity of SYPRO Tangerine stain is similar to that of the SYPRO Red and SYPRO Orange stains - about 4-10 ng per protein band. This detection sensitivity is comparable to colloidal Coomassie blue staining and rapid silver staining procedures. Since proteins stained with SYPRO Tangerine dye are not fixed, they can easily be eluted from gels or utilized in zymographic assays, provided that SDS does not inactivate the protein of interest. This is demonstrated with in-gel detection of rabbit liver esterase activity using alpha-naphthyl acetate and Fast Blue BB dye as well as Escherichia coli beta-glucuronidase activity using ELF-97 beta-D-glucuronide. The dye is also suitable for staining proteins in gels prior to their transfer to membranes by electroblotting. Gentle staining conditions are expected to improve protein recovery after electroelution and to reduce the potential for artifactual protein modifications such as the alkylation of lysine and esterification of glutamate residues, which complicate interpretation of peptide fragment profiles generated by mass spectrometry.     

Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex

SYPRO Ruby dye is a permanent stain comprised of ruthenium as part of an organic complex that interacts noncovalently with proteins. SYPRO Ruby Protein Gel Stain provides a sensitive, gentle, fluorescence-based method for detecting proteins in one-dimensional and two-dimensional sodium dodecyl sulfate-polyacrylamide gels. Proteins are fixed, stained from 3h to overnight and then rinsed in deionized water or dilute methanol/acetic acid solution for 30 min. The stain can be visualized using a wide range of excitation sources commonly used in image analysis systems including a 302 nm UV-B transilluminator, 473 nm second harmonic generation (SHG) laser, 488 nm argon-ion laser, 532 nm yttrium-aluminum-garnet (YAG) laser, xenon arc lamp, blue fluorescent light bulb or blue light-emitting diode (LED). The sensitivity of SYPRO Ruby Protein Gel Stain is superior to colloidal Coomassie Brilliant Blue (CBB) stain or monobromobimane labeling and comparable with the highest sensitivity silver or zinc-imidazole staining procedures available. The linear dynamic range of SYPRO Ruby Protein Gel stain extends over three orders of magnitude, which is vastly superior to silver, zinc-imidazole, monobromobimane and CBB stain. The fluorescent stain does not contain superfluous chemicals (formaldehyde, glutaraldehyde, Tween-20) that frequently interfere with peptide identification in mass spectrometry. While peptide mass profiles are severely altered in protein samples prelabeled with monobromobimane, successful identification of proteins by peptide mass profiling using matrix-assisted laser desorption/ionization mass spectrometry was easily performed after protein detection with SYPRO Ruby Protein Gel stain.     

Ultrasensitive fluorescence protein detection in isoelectric focusing gels using a ruthenium metal chelate stain

SYPRO Ruby IEF Protein Gel Stain is an ultrasensitive, luminescent stain optimized for the analysis of protein in isoelectric focusing gels. Proteins are stained in a ruthenium-containing metal complex overnight and then rinsed in distilled water for 2 h. Stained proteins can be excited by ultraviolet light of about 302 nm (UV-B transilluminator) or with visible light of about 470 nm. Fluorescence emission of the dye is maximal at approximately 610 nm. The sensitivity of the SYPRO Ruby IEF protein gel stain is superior to colloidal Coomassie blue stain and the highest sensitivity silver staining procedures available. The SYPRO Ruby IEF protein gel stain is suitable for staining proteins in nondenaturing or denaturing carrier ampholyte isoelectric focusing and immobilized pH gradient gel electrophoresis. The stain is compatible with N,N'-methylenebisacrylamide or piperazine diacylamide cross-linked polyacrylamide gels as well as with agarose gels and high tensile strength Duracryl gels. The stain does not contain extraneous chemicals (formaldehyde, glutaraldehyde, Tween-20) that frequently interfere with peptide identification in mass spectrometry. Successful identification of stained proteins by peptide mass profiling is demonstrated.     

Fluorescent staining of protein in SDS polyacrylamide gels by salicylaldehyde azine

As a noncovalent fluorescence probe, in this study, salicylaldehyde azine (SA) was introduced as a sensitive fluorescence‐based dye for detecting proteins both in 1D and 2D polyacrylamide electrophoresis gels. Down to 0.2 ng of single protein band could be detected within 1 h, which is similar to that of glutaraldehyde‐silver stain, but approximately four times higher than that of SYPRO Ruby fluorescent stain. Furthermore, comparative analysis of the MS compatibility of SA stain with SYPRO Ruby stain indicated that SA stain is compatible with the downstream of protein identification by LC‐MS/MS. Additionally, the probable mechanism of the SA stain was investigated by molecular docking. The results demonstrated that the interaction between SA and protein was mainly contributed by hydrogen bonding and hydrophobic forces.     

Sensitive silver staining of protein in sodium dodecyl sulfate-polyacrylamide gels using an azo dye, calconcarboxylic acid, as a silver-ion sensitizer

A highly sensitive silver staining method for detecting proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was developed. It is based on the silver nitrate staining method but also employs an azo dye, calconcarboxylic acid (NN), as a silver-ion sensitizer. It increases silver binding on protein bands or spots by the formation of a silver-dye complex and also increases the reducing power of silver ions to metallic silver by NN itself with formaldehyde. After a 2 h gel fixing step, the protocol including sensitization, silver-ion impregnation, and reduction steps can be completed in 1 h. The sensitivity is superior to that of silver stain with glutardialdehyde as a silver-ion sensitizer. The detection limit of NN-silver stain is 0.05-0.2 ng protein. Considering the high sensitivity without using glutardialdehyde, the NN-silver stain would be useful for routine silver staining of proteins.     

A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling

Proteomic projects are often focused on the discovery of differentially expressed proteins between control and experimental samples. Most laboratories choose the approach of running two-dimensional (2-D) gels, analyzing them and identifying the differentially expressed proteins by in-gel digestion and mass spectrometry. To date, the available stains for visualizing proteins on 2-D gels have been less than ideal for these projects because of poor detection sensitivity (Coomassie blue stain) or poor peptide recovery from in-gel digests and mass spectrometry (silver stain), unless extra destaining and washing steps are included in the protocol. In addition, the limited dynamic range of these stains has made it difficult to rigorously and reliably determine subtle differences in protein quantities. SYPRO Ruby Protein Gel Stain is a novel, ruthenium-based fluorescent dye for the detection of proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels that has properties making it well suited to high-throughput proteomics projects. The advantages of SYPRO Ruby Protein Gel Stain relative to silver stain demonstrated in this study include a broad linear dynamic range and enhanced recovery of peptides from in-gel digests for matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry.     

Prediction of low-sensitivity reactive dye recipe in exhaust dyeing influenced by material to liquor ratio and nature of salt

Reactive dyeings were carried out by exhaust method on 100% cotton knits. A trichromatic combination was chosen with only change in blue component. Colorimetric data were produced under controlled dyeing conditions by comparing the color difference between the target shade and resulting shades. Giving a change in liquor ratio and nature of salt the colorimetric data were regenerated again produced the shades. The data will be helpful to predict the low-sensitivity reactive dye recipe, which lead to the concept of right-first-time dyeing. The aim of this research is to help a dyer to select the right recipe. A set of the dye recipes was applied by dyeing with reactive dyes on cotton. Sodium chloride shows best results in terms of dye sensitivity as compared to Glauber's salt at low liquor ratio that is 1:10. Blue BRF in combination with yellow and red shows best result as compared to navy blue BF.     

Red–Green–Blue Trichromophoric Nanoparticles with Dual Fluorescence Resonance Energy Transfer: Highly Sensitive Fluorogenic Response Toward Polyanions

A red–green–blue (RGB) trichromophoric fluorescent organic nanoparticle exhibiting multi‐colour emission was constructed; the blue‐emitting cationic oligofluorene nanoparticle acted as an energy‐donor scaffold to undergo fluorescence resonance energy transfer (FRET) to a red‐emitting dye embedded in the nanoparticle (interior FRET) and to a green‐emitting dye adsorbed on the surface through electrostatic interactions (exterior FRET). Each FRET event occurs independently and is free from sequential FRET, thus the resultant dual‐FRET system exhibits multi‐colour emission, including white, in aqueous solution and film state. A characteristic white‐emissive nanoparticle showed visible responses upon perturbation of the exterior FRET efficiency by acceptor displacement, leading to highly sensitive responses toward polyanions in a ratiometric manner. Specifically, our system exhibits high sensitivity toward heparin with an extremely low detection limit.     

Fast visible dye staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels compatible with matrix assisted laser desorption/ionization-mass spectrometry

A fast and matrix assisted laser desorption/ionization-mass spectrometry (MALDI-MS) compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (1- and 2-D SDS-PAGE) is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, zincon (ZC) and ethyl violet (EV) to form an ion-pair complex. The protocol, including fixing, staining and quick washing steps, can be completed in 1-1.5 h depending upon gel thickness. It has a sensitivity of 4-8 ng, comparable to that of colloidal Coomassie Brilliant Blue G (CBBG) staining with phosphoric acid in the staining solution. The counterion dye stain does not induce protein modifications that complicate interpretation of peptide mapping data from MS. Considering the speed, sensitivity and compatibility with MS, the counterion dye stain may be more practical than any other dye-based protein stains for routine proteomic researches.     

Stain efficiency and MALDI-TOF MS compatibility of seven visible staining procedures

Visible stain is still the most popular protein staining method used in proteomic approaches. However, most published data have been derived from comparisons between visible dyes and fluorescent dyes. In this work, we have focused on seven widely used visible staining procedures—Neuhoff CCB, blue silver, and five silver stains (LKB SN, He SN, Yan SN, Vorum SN, and Blum SN)—and studied their stain efficiencies and MALDI-TOF MS compatibilities on 1-D and 2-D PAGE. It was concluded that blue silver is slightly better in terms of stain efficiency than Neuhoff CCB, but it presented worse MS compatibility. Neuhoff CCB presented better MS compatibility and superior linearity but worse sensitivity than silver stains. Among the five silvering procedures, He SN showed the best MS compatibility and a reasonable staining efficiency; Yan SN lowered the chances of obtaining the protein identity by PMF but gave the best stain efficiency; Vorum SN gave a very clear background and a great contrast, while Blum SN was the worst in this respect. The implications of these results for the selection of a convenient stain are discussed according to specific objectives as well as practical aspects.     

多尺度结构Ag/PA6纳米纤维膜的制备及其催化性能

随着工业的进步,废水处理特别是印染废水的处理成为亟待解决的问题.银纳米粒子因其特殊的物理化学性能而表现出催化活性,但银纳米粒子的团聚限制了其使用,所以出现了一系列新的载体材料,如微球、薄膜和纤维等.其中电纺纳米纤维由于具有高比表面积,作为载体材料具有非常大的优势,而将常规电纺纳米纤维作为载体也已有报道.但是,将具有更高比表面积的电纺纳米纤维作为载体,特别是一种类似于树枝状结构的多尺度纳米纤维作为载体还鲜有报道.本文制备了一种多尺度结构的PA6纳米纤维膜,该纳米纤维膜由直径为50?120 nm的主纤维和10?50 nm的分支纤维构成;由于分支纤维的出现,多尺度结构纳米纤维膜的比表面积得到了提高,可以为银纳米粒子的负载提供更多附着位点.制备的多尺度结构纳米纤维膜通过银胶溶液浸渍成功地负载银纳米粒子,对制备的纳米纤维膜的形态、化学结构以及对亚甲基蓝的催化性能进行了探讨.SEM,EDS和TEM结果表明,银纳米粒子成功地负载在多尺度结构纳米纤维的表面,并且银纳米粒子的粒径以及负载量可以通过变换银胶溶液的浓度合理调控.此外,与常规PA6纳米纤维膜相比,多尺度结构纳米纤维膜更有利于银纳米粒子的分散,同样通过银胶溶液A浸渍,负载在多尺度结构纳米纤维上银纳米粒子粒径为8.6 nm,而负载在普通PA6纳米纤维上银纳米粒子粒径为11.2 nm.XPS分析表明,银纳米粒子成功地负载到多尺度结构纳米纤维上,并且经不同银胶溶液处理,纳米纤维膜的载银量不同.通过O的高能XPS分析发现,银纳米粒子与PA6分子间形成了配位键,这在一定程度上有利于Ag纳米粒子的固定,阻止了Ag纳米粒子的团聚.Ag/PA6纳米纤维膜以及多尺度结构Ag/PA6纳米纤维膜催化降解实验表明,多尺度结构Ag/PA6纳米纤维膜具有较高的催化活性,反应2 h后对10 mg/L亚甲基蓝的降解率达到98.13%,并且降解过程符合伪一级动力学.不同浸渍液浓度处理纳米纤维膜催化实验表明,Ag纳米粒子的大小以及含量都会影响纳米纤维的催化活性,纳米粒子粒径越小,其催化活性越高;不同NaBH4加入量催化体系催化实验表明,随着NaBH4加入量的增大,催化体系的降解率增高,其对催化体系的催化性能起着至关重要的作用;其他条件一定,随着染料初始浓度的增大,催化体系的催化性能下降;循环实验表明,经5次循环之后,其降解率仍高达83.5%,该纳米纤维膜具有一定的循环使用性能.     

Improved conditions for fluorescent staining of proteins with 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid in SDS‐PAGE

A simple and sensitive fluorescent staining method for the detection of proteins in SDS‐PAGE, namely IB (improved 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid) stain, is described. Non‐covalent hydrophobic probe 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid was applied as a fluorescent dye, which can bind to hydrophobic sites in proteins non‐specifically. As low as 1 ng of protein band can be detected briefly by 30 min washing followed by 15 min staining without the aiding of stop or destaining step. The sensitivity of the new presented protocol is similar to that of SYPRO Ruby, which has been widely accepted in proteomic research. Comparative analysis of the MS compatibility of IB stain and SYPRO Ruby stain allowed us to address that IB stain is compatible with the downstream of protein identification by PMF.     

对一种蓝色染料影象的象质评价

本文对黑白胶片经过特殊的蓝色成象工艺加工后形成的影象的质量进行了客观评价。结果表明,用蓝色成象工艺,感光度、特性曲线直线部分的斜率γ、最大密度及调制传递函数在低空间频率的响应等,均较黑白影象有不同程度的改善和提高;分辨率基本相同;粒度有些增高;调制传递函数的高频响应变坏。这种成象工艺用于对空间频率上限要求不高的一些成象体系,如X射线照象是有利的。这与临床诊断的主观评价的结果一致。     

Silver‐Doped TiO2‐Coated Cotton Fabric as an Effective Photocatalytic System for Dye Decolorization in UV and Visible Light

In this study, titanium tetra‐isopropoxide was used as a precursor of TiO₂ for in situ coating on cotton fabric by sol–gel method. Subsequently, silver nitrate was used as doping agent to prepare silver‐doped TiO₂‐coated cotton fabric during hydrothermal treatment. The treated samples were characterized through field‐emission scanning electron microscopy, energy‐dispersive X‐ray analysis, inductively coupled plasma‐mass spectroscopy and UV–visible absorption spectroscopy to study morphology, composition of deposited elements and light absorption behavior of treated samples. X‐ray photoelectron spectroscopy was carried out to analyze the electronic state of silver in TiO₂‐coated fabric after hydrothermal treatment. Doping of silver on TiO₂‐coated fabric and subsequent hydrothermal treatment was found to enhance dye decolorization rate of rhodamine B dye solution in both UV and visible light radiations with respect to undoped TiO₂. The study shows that an optimal level of silver‐doped TiO₂‐coated fabric can be used repeatedly for dye decolorization without significant loss in its photocatalytic activity. The self‐cleaning properties of samples were also studied using methylene blue as a staining agent. It was observed that the presence of 1.8% silver on the weight of titanium in doped samples provides almost 82% of stain degradation.     

Supramolecular Gels Derived from the Salts of Variously Substituted Phenylacetic Acid and Dicyclohexylamine: Design,Synthesis, Structures,and Dye Adsorption

A well‐studied supramolecular synthon, namely, secondary ammonium monocarboxylate (SAM), was exploited to generate a new series of organic salts derived from variously substituted phenylacetic acid and dicyclohexylamine as potential low‐molecular‐weight gelators. As much as 25 % of the SAM salts under study were gelators. The gels were characterized by rheology, and the morphology of the gel networks was studied by high‐resolution electron microscopy. Single‐crystal and powder XRD data were employed to study structure–property (gelation) correlations. One of the gels could adsorb a hydrophobic dye (Nile Red) more efficiently than that of a hydrophilic dye (Calcein) from dimethyl sulfoxide; this might provide useful clues towards the development of stain‐removing gels.     

偶氮氯膦—DBC光度法测定银合金中镨

研究提出镨 ( ) - DBC-偶氮氯膦 -磷酸 - EDTA新体系光度法测定贵金属合金中微量镨。反应体系生成 α型蓝色配合物的 λmax=650 nm,灵敏度高 ,摩尔吸光系数 ε=0 .93× 1 0 5L·mol-1·cm-1,镨浓度在 0～ 50 μg/2 5ml范围内符合比耳定律 ,方法选择性强 ,有较好的适用性 ,用于分析银合金中镨 ,标准偏差 S≤ 0 .0 1 1 ,相对标准偏差 RSD≤ 1 .97%。     

Preferential Partition of Nanowires in Thin Films of Immiscible Polymer Blends

Summary: The preferential partition of silver nanowires in thin films of polystyrene/poly(vinyl pyrrolidone) (PS/PVP, with a 30/70 weight ratio) blends, that induces drastic blend morphology variation, is reported. The silver nanowires are fabricated with the anodic aluminum oxide templating method, and have a diameter of 300 nm and length of 10 µm. At a higher nanowire loading of 10 wt.‐%, the silver nanowires are entangled and selectively concentrate within the continuous PVP domain. If surface modified by thiols carrying hydrophobic tails, the silver nanowires become hydrophobic and prefer to stay within the discrete hydrophobic PS domains. At a lower nanowire loading of 5 wt.‐%, the nanowires are non‐entangled and concentrate at regions near the interfaces of the PS and PVP phases, which induces the formation of interconnected PS domains.

Preferential partition of silver nanowires in thin films of PS/PVP (30/70) blends at a casting temperature of −10 °C.     

An improved, luminescent europium-based stain for detection of electroblotted proteins on nitrocellulose or polyvinylidene difluoride membranes

SYPRO Rose Plus protein blot stain is an improved europium-based metal chelate stain for the detection of proteins on nitrocellulose and poly(vinylidene difluoride) (PVDF) membranes. Staining is achieved without covalently modifying the proteins. The stain may be excited with a 254 nm (UV-C), 302 nm (UV-B), or 365 nm (UV-A) light source and displays a sharp emission maximum at 612 nm. The emission peak has a full width at half-maximum of only 8 nm. The stain exhibits exceptional photostability, allowing long exposure times for maximum sensitivity. Since the dye is composed of a europium complex, it has a long emission lifetime, potentially allowing time-resolved detection, greatly reducing background fluorescence. Proteins immobilized to a nitrocellulose or PVDF membrane by electroblotting, dot-blotting, or vacuum slot-blotting are incubated with SYPRO Rose Plus protein blot stain for 15-30 min. Membranes are rinsed briefly, visualized with UV epi-illumination and the luminescence of the europium dye is measured using a 490 nm long-pass or 625 +/- 15 nm band-pass filter in combination with a conventional photographic or charge-coupled device (CCD) camera system. Alternatively, the dye may be visualized using a xenon-arc illumination source. The stain is readily removed from proteins by incubating membranes at mildly alkaline pH. The reversibility of the protein staining procedure allows for subsequent biochemical analyses, such as immunoblotting and biotin-streptavidin detection using colorimetric, direct fluorescence or fluorogenic visualization methods.     

Mechanism of Coomassie brilliant blue G-250 binding to proteins: a hydrophobic assay for nanogram quantities of proteins

We investigated the mechanism of Coomassie brilliant blue G-250 (CBB) binding to proteins in order to develop a protein assay with the maximum possible sensitivity. We found that the neutral ionic species of CBB binds to proteins by a combination of hydrophobic interactions and heteropolar bonding with basic amino acids. On the basis of these findings, we developed a very sensitive hydrophobic assay for proteins (at the nanogram level) using the hydrophobic reagents ammonium sulfate and trichloroacetic acid under pH conditions that increase neutral species concentration in the assay reagent in order to enhance the binding of more CBB dye molecules per protein molecule than in previous CBB-based assays.     

Proton hopping in phosphoric acid solvated nafion membrane: a molecular simulation study

Molecular simulation studies of the microstructure and of the proton transport properties of phosphoric acid solvated Nafion membrane are carried out. The ab initio calculations show that the phosphoric acid is a good solvent to promote the proton ionization of the sulfonic acid group, and only two phosphoric acid molecules are necessary for the dissociation of one sulfonic acid group. A mechanism of proton hopping between phosphoric acid and protonated phosphoric acid cation in the hydrophilic subphase is also elucidated by ab initio calculations. The molecular dynamics simulations, conducted at a phosphoric acid concentration of 25.4% (wt) which is slightly lower than that of phosphoric acid swollen Nafion, show that the phosphoric acid exists in subphases and that it cannot develop into a continuous subphase. Thus, proton-hopping pathways are interrupted, and the conductivity is expected to be lower than that for pure phosphoric acid. The molecular dynamics simulations, conducted at a phosphoric acid concentration of 45.1% (wt) which corresponds to an unstable state, show that the hydrophobic poly(tetrafluoroethylene) backbones trend to gather together forming hydrophobic clusters and that the phosphoric acid forms a continuous subphase with the sulfonic acid groups located at the hydrophobic/hydrophilic interface. Thus, proton-hopping pathways can develop uninterruptedly like the pure phosphoric acid, and high conductivity is expected. The molecular dynamics study also shows that the hydrogen-bonding characteristics of phosphoric acid and sulfonate anion are similar regardless of the factor that the former can move freely while the latter is attached to Nafion backbone.