Molecular Weight Ladder Research Articles

A 96-Well Polyacrylamide Gel for Electrophoresis and Western Blotting.

Western blotting is a stalwart technique for analyzing specific proteins and/or their post-translational modifications. However, it remains challenging to accommodate more than ~10 samples per experiment without substantial departure from trusted, established protocols involving accessible instrumentation. Here, we describe a 96-sample western blot that conforms to standard 96-well plate dimensional constraints and has little operational deviation from standard western blotting. The main differences are that (i) submerged polyacrylamide gel electrophoresis is operated horizontally (similar to agarose gels) as opposed to vertically, and (ii) a 6 mm thick gel is used, with 2 mm most relevant for membrane transfer (vs ~1 mm typical). Results demonstrate both wet and semi-dry transfer are compatible with this gel thickness. The major tradeoff is reduced molecular weight resolution, due primarily to less available migration distance per sample. We demonstrate proof-of-principle using gels loaded with molecular weight ladder, recombinant protein, and cell lysates. We expect the 96-well western blot will increase reproducibility, efficiency (cost and time ~8-fold), and capacity for biological characterization relative to established western blots.

Efficient Escorting Strategy for Aggregation-Prone Notch EGF Repeats with Sparcl1.

Epidermal growth factor (EGF) repeats are present in various proteins and form well-defined structures with three disulfide bonds. One representative protein is the Notch receptor. Each EGF repeat contains unique atypical O-linked glycans, such as O-linked N-acetylglucosamine (O-GlcNAc). To generate a monoclonal antibody against the O-GlcNAc moiety in mouse Notch1, we expressed the recombinant C-terminal His6-tagged Notch1 EGF14-15 protein in HEK293T cells to prepare the immunogen. Most of the proteins were not secreted and showed higher molecular weight ladders in the cell lysate, suggesting protein aggregation. To overcome this issue, we fused Sparcl1 as an extracellular escorting tag to the N-terminus of Notch1 EGF14-15. The fusion protein was efficiently secreted extracellularly without protein aggregates in the lysates. Following PreScission protease treatment, Notch1 EGF14-15 was efficiently released from the escorting tag. Notch1 EGF14-15 prepared using this method was indeed O-GlcNAcylated. The optimal length of the escorting tag was determined by generating deletion mutants to improve the extracellular secretion of EGF14-15. Hence, a large amount of EGF14-15 was successfully prepared from the culture supernatant of HEK293T cells, which were otherwise prone to aggregation.

The study of mutations of CDK4 and TP53 genes in selected breast lesions

Lesions are abnormal changes in tissue. The theories behind tumorigenesis can be genetic epigenetic, immune surveillance and monoclonal hypothesis, which led to genetic changes. The genetic change can be the inactivation of tumor suppressor genes or the activation of oncogenes in the cell cycle. This study investigated the presence of gene mutation in CDK4 and TP53 genes in breast lesions. Ten (10) formalin fixed paraffin embedded tissue block, which includes 5 cases of fibroadenoma and 5 cases of invasive ductal carcinoma from the pathological archives were used. The nuclei amplification technique was carried out on the formalin fixed paraffin embedded tissue blocks. DNA extraction involves lysing the cells and solubilizing DNA, which is followed by chemical or enzymatic methods to remove macromolecules, lipids, RNA or proteins. Thereafter, the DNA is amplified using reagents and heated (denaturing) and cooling (annealing) steps. PCR requires free nucleotide (dNTPs), template DNA to amplify and unique single-stranded DNA primers that bind upstream (5') and downstream (3') of the DNA region of the tissue blocks. The integrity of the DNA is assessed by loading approximately 100 ng per sample on a 1.5% agarose gel and the sizes of PCR products were estimated by comparison with the mobility of a 100bp molecular weight ladder that was run alongside the samples in the gel. However, the amplified fragment was purified to remove PCR reagents and thereafter it was sequenced. The sequence of single nucleotide polymorphism of each gene was analyzed, and the results were reported. In mutation was more in both genes compared to the sequence of FA and IDC. From this study, both genes showed segments of mutation which were either SNPs or functional mutation. It showed that both genes were modified from a proto-oncogene to an oncogene and the protein it produces is an oncoprotein and as such it favours the alteration of both genes led to cell proliferation. The data generated from this research has highlighted the importance of carrying out further studies in assessing both genes to understand their involvement in the etiology of carcinogenesis which will help in clinical information about breast cancer. In line with the findings, there is an urgent need to understand carcinogenesis which may serve in early diagnosis and understanding of breast conditions and further help prevent or delay the onset of chronic complications and reduce morbidity and mortality rates to improve and assure the health of individuals.

Proposal of a laboratory course dedicated to the generation of protein molecular weight standards for sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Protein molecular weight standards are routinely employed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to estimate the apparent sizes of unknown proteins within a sample. For training students, a laboratory course based on the production of marker proteins is proposed. Following fractionation by column chromatography, a series of purified proteins and mixtures of proteins were combined to generate various sets of unstained, prestained and fluorescently labeled molecular weight ladders for SDS-PAGE. The produced material can be used in successive laboratory practices as an alternative to commercial protein markers.

The pPSU Plasmids for Generating DNA Molecular Weight Markers

Visualizing nucleic acids by gel electrophoresis is one of the most common techniques in molecular biology, and reference molecular weight markers or ladders are commonly used for size estimation. We have created the pPSU1 & pPSU2 pair of molecular weight marker plasmids which produce both 100 bp and 1 kb DNA ladders when digested with two common restriction enzymes. The 100 bp ladder fragments have been optimized to migrate appropriately on both agarose and native polyacrylamide, unlike many currently available DNA ladders. Sufficient plasmid DNA can be isolated from 100 ml E. coli cultures for the two plasmids to produce 100 bp or 1 kb ladders for 1000 gels. As such, the pPSU1 and pPSU2 plasmids provide reference fragments from 50 to 10000 bp at a fraction of the cost of commercial DNA ladders. The pPSU1 and pPSU2 plasmids are available without licensing restrictions to nonprofit academic users, affording freely available high-quality, low-cost molecular weight standards for molecular biology applications.

Does the Sauerbrey equation hold true for binding of peptides and globular proteins to a QCM?: A systematic study of mass dependence of peptide and protein binding with a piezoelectric sensor.

The term ‘microbalance’ arose after Sauerbrey showed a mass per unit area dependence on sensor frequency change for thin, solid films on a QCM. Others have extrapolated this relationship to interactions with biological ‘soft’ matter using acoustic wave devices. We rigorously examined the relationship between QCM frequency change and the molecular weight of protein and peptide analytes on a RAP♦id 4™ system using more than 120 individual assays. A series of amino acid, peptides and proteins with molecular weight from 372 to 150,000Da constituting a molecular weight ladder were biotinylated with a target biotin/protein ratio close to one to minimize avidity effects. Analyte concentration and contact time were chosen so as to attain near saturation of an anti-biotin antibody surface. The series resistance and resonant frequency changes (dF and dR) arising from a 5-parameter fit of the imaginary component of the impedance signal were analysed, giving a linear relationship (R2=0.98) between frequency response and analyte molecular weight, even down to level of a single amino-acid. As predicted by theory, there was also a linear relationship between the changes in density and viscosity of the liquid in contact with the sensor and both dF and dR. The resistance and resonance frequency changes recorded for mixtures of deuterium oxide and glycerol were the sum of changes induced by each individual liquid. Hence the Sauerbrey equation for mass per unit area dependence of QCM signal does hold true for peptides and proteins in a liquid.

Approach to molecular characterization of different strains of Fasciola hepatica using random amplified polymorphic DNA polymerase chain reaction.

The aim of the present study was to genetically characterize Fasciola hepatica strains from diverse ecogeographical regions (America and Europe), susceptible and resistant to Triclabendazole, using the random amplified polymorphic DNA fragments (RAPDs-PCR) technique to elucidate genetic variability between the different isolates. Ten different oligonucleotide primers of 10 bases with GC content varying from 50-70% were used. A polymerase chain reaction (PCR) was carried out in 25 μl of total volume. Duplicate PCR reactions on each individual template DNA were performed to test the reproducibility of the individual DNA bands. The size of the RAPD-PCR fragments was determined by the reciprocal plot between the delay factors (Rf) versus the logarithm of molecular weight ladder. The phenogram obtained showed three main clusters, the major of which contained European Strains (Cullompton and Sligo) showing a genetic distance of 27.2 between them. The American strains (Cedive and Cajamarca) on the other hand formed each their distinctive group but clearly maintaining a closer genetic relationship among them than that to their European counterparts, with which showed a distance of 33.8 and 37.8, respectively. This polymorphism would give this species enhanced adaptability against the host, as well as the environment. The existence of genetically different populations of F. hepatica could allow, against any selection pressure, natural or artificial (for use fasciolicides products and/or control measures), one or more populations of F. hepatica to be able to survive and create resistance or adaptability to such selective pressure.

The Hippo Tumor Pathway Promotes TAZ Degradation by Phosphorylating a Phosphodegron and Recruiting the SCFβ-TrCP E3 Ligase

The TAZ transcription co-activator promotes cell proliferation and epithelial-mesenchymal transition. TAZ is inhibited by the Hippo tumor suppressor pathway, which promotes TAZ cytoplasmic localization by phosphorylation. We report here that TAZ protein stability is controlled by a phosphodegron recognized by the F-box protein β-TrCP and ubiquitylated by the SCF/CRL1(β-TrCP) E3 ligase. The interaction between TAZ and β-TrCP is regulated by the Hippo pathway. Phosphorylation of a phosphodegron in TAZ by LATS primes it for further phosphorylation by CK1ε and subsequent binding by β-TrCP. Therefore, the Hippo pathway negatively regulates TAZ function by both limiting its nuclear accumulation and promoting its degradation. The phosphodegron-mediated TAZ degradation plays an important role in negatively regulating TAZ biological functions.

Linear High Molecular Weight Ladder Polymers by Optimized Polycondensation of Tetrahydroxytetramethylspirobisindane and 1,4-Dicyanotetrafluorobenzene

A study on the optimization of conditions for polycondensation of 3,3,3′,3′-tetramethyl-1,1′-spirobisindane-5,5′,6,6′-tetrol, TTSBI, with 1,4-dicyanotetrafluorobenzene (DCTB) in dimethylformamide (DMF) at 50−70 °C is reported. A linear PIM-1 polymer (PIM = polymer with intrinsic microporosity) with high molecular weight was obtained by optimized reaction conditions. Of the solvents tested, DMF was the preferred solvent for this reaction. The optimized molar ratio TTSBI/DCTB/K2CO3 was 1/1/2.04. The mechanism of PIM-1 cross-linking during polymerization was studied, and gel-free, high molecular weight PIM-1 polymer was prepared. The physical properties of anhydrous K2CO3 significantly affected the reaction rate. Flexible tough polymer films were cast from PIM-1 solution in chloroform, and pure permeability data are reported for several gases.

Linear High Molecular Weight Ladder Polymer via Fast Polycondensation of 5,5′,6,6′‐Tetrahydroxy‐3,3,3′,3′‐tetramethylspirobisindane with 1,4‐Dicyanotetrafluorobenzene

AbstractA high molecular weight ladder polymer based on 5,5′,6,6′‐tetrahydroxy‐3,3,3′,3′‐tetramethylspirobisindane and 1,4‐dicyanotetraflurobenzene has been synthesized by polycondensation under high‐intensity mixing conditions at about 155 °C and cyclic‐free products were obtained in high yield with low molecular weight distribution (1.7–2.3). The reaction could be completed within a few minutes. The polymer properties were characterized by GPC, 1H NMR, 13C NMR, F NMR, FT‐IR, and MALDI‐TOF MS. In addition, the mechanical properties, apparent surface areas and gas permeability are also reported. This procedure can also be used for the synthesis of other ladder polymers by irreversible polycondensations of tetraphenols with activated tetrafluoro aromatics.magnified image

Sgt1p Is a Unique Co-chaperone That Acts as a Client Adaptor to Link Hsp90 to Skp1p

Sgt1p is a conserved, essential protein required for kinetochore assembly in both yeast and animal cells. Sgt1p has homology to both TPR and p23 domains, sequences often found in proteins that interact with and regulate the molecular chaperone, Hsp90. The presence of these domains and the recent findings that Sgt1p interacts with Hsp90 has led to the speculation that Sgt1p and Hsp90 form a co-chaperone complex. To test this possibility, we have used purified recombinant proteins to characterize the in vitro interactions between yeast Sgt1p and Hsp82p (an Hsp90 homologue in yeast). We show that Sgt1p interacts directly with Hsp82p via its p23 homology region in a nucleotide-dependent manner. However, Sgt1p binding does not alter the enzymatic activity of Hsp82p, suggesting that it is distinct from other co-chaperones. We find that Sgt1p can form a ternary chaperone complex with Hsp82p and Sti1p, a well characterized Hsp90 co-chaperone. Sgt1p interacts with its binding partner Skp1p through its TPR domains and links Skp1p to the core Hsp82p-Sti1p co-chaperone complex. The multidomain nature of Sgt1p and its ability to bridge the interaction between Skp1p and Hsp82p argue that Sgt1p acts as a "client adaptor" recruiting specific clients to Hsp82p co-chaperone complexes.

The Tyrosine Kinase c-Abl Protects c-Jun from Ubiquitination-mediated Degradation in T Cells

The cross-talk of ubiquitination with other types of posttranscriptional modifications, such as phosphorylation, regulates the stability of many proteins. We have previously demonstrated that c-Jun is a substrate of Itch, a HECT-type E3 ubiquitin ligase. c-Jun is also a substrate of the tyrosine kinase c-Abl. Here we report that genetic ablation of c-Abl accelerated c-Jun degradation. Phosphorylation of the tyrosine within the PPXY motif by c-Abl inhibited c-Jun ubiquitination and its binding by Itch. The nuclear localization of c-Abl, triggered by T-cell activation signals, was essential for its activity in regulating c-Jun transcription activity. These findings define a potential molecular mechanism for the immunodeficiency in mice lacking the c-abl gene.

A Novel Tool to Characterize Paracellular Transport: The APTS–Dextran Ladder

The aim of this work was to develop an easy, manageable, and precise analytic tool to describe the tightness of cell layers by a molecular weight ladder. Dextrans were labeled by reductive amination with fluorescent 8-aminopyrene-1,3,6-trisulfonate (APTS). This mixture, including the internal standard diazepam, was used for transport studies in Transwell models using Caco-2, ECV304, and PBMEC/C1-2 cell lines. Samples were analyzed by fluorimetry, capillary electrophoresis, and reverse-phase high-performance liquid chromatography. Following this approach, a logarithm correlation of R2 = 0.8958 between transepithelial electrical resistance (TEER) and APTS-dextran permeability was shown. In addition, a TEER-dependent permeability pattern could be observed including each single fraction from free APTS, APTS-glucose up to APTS-dextran consisting of 35 glucose units. The TEER-independent permeability coefficients of diazepam and confocal laser scanning microscopy images confirmed the paracellular transport of APTS-dextran. All in all, the developed APTS-dextran ladder is a useful tool to characterize cell layer tightness and especially to describe paracellular transport ways and the extent of leakiness of cell layers (for blood-brain barrier or intestinal studies) over time--applying a wide array from smaller to larger molecules at the same time to refine TEER, sucrose, or Evans blue measurements.

Luteal phase serum cell-free DNA as a marker of failed pregnancy after assisted reproductive technology

DNA-damaging factors have been reported in patients that failed to achieve pregnancy after assisted reproductive technologies (ART). The hypothesis was that increased circulating cell-free DNA released by damaged cells could predict unfavorable conditions leading to failed ART treatment. The objective was to compare the relative concentrations of cell-free DNA in the luteal phase sera of nonpregnant versus pregnant patients. Frozen-thawed sera (30 IVF cases) were obtained 1 week after embryo transfer. There were 16 pregnant and 14 nonpregnant cases and controls consisting of male sera (n = 8 cases). Modified isocratic capillary electrophoresis was performed and the images analyzed for cell-free DNA. Circulating cell-free DNA were identified in the sera of all patients. The serum concentrations of high (12 kb) and low (1 kb) molecular weight cell-free DNA were similar for both nonpregnant and pregnant patients. Male control sera had higher cell-free DNA concentrations compared with females. Evaluation of sera from a control case showed no fluctuations in cell-free DNA concentrations throughout specific days of the menstrual cycle. The results do not support the use of the luteal phase cell-free DNA concentration as a marker for failed pregnancies. The equal concentrations of high and low molecular weight cell-free DNA and ladder band-like gel patterns suggested cell apoptosis as the source of DNA.

Bcl-2 Protein Is Required for the Adenine/Uridine-rich Element (ARE)-dependent Degradation of Its Own Messenger

We have shown previously that the decay of human bcl-2 mRNA is mediated by an adenine/uridine-rich element (ARE) located in the 3'-untranslated region. Here, we have utilized a non-radioactive cell-free mRNA decay system to investigate the biochemical and functional mechanisms regulating the ARE-dependent degradation of bcl-2 mRNA. Using RNA substrates, mutants, and competitors, we found that decay is specific and ARE-dependent, although maximized by the ARE-flanking regions. In unfractionated extracts from different cell types and in whole cells, the relative enzymatic activity was related to the amount of Bcl-2 protein expressed by the cells at steady state. The degradation activity was lost upon Bcl-2 depletion and was reconstituted by adding recombinant Bcl-2. Ineffective extracts from cells that constitutively do not express Bcl-2 acquire full degradation activity by adding recombinant Bcl-2 protein. We conclude that Bcl-2 is necessary to activate the degradation complex on the relevant RNA target.

Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins.

Now that it is likely that all yeast nucleoporins are known, one of the ultimate goals is the in vitro assembly of the entire nuclear pore complex from its approximately 30 individual components. Here, we report the reconstitution of seven proteins (Nup133p, Nup145p-C, Nup120p, Nup85p, Nup84p, Seh1p and Sec13p) into a heptameric 0.5 MDa nuclear pore subcomplex. We found that double plasmid transformation combined with bi-cistronic mRNA translation allow the expression and assembly of distinct subcomplexes of up to five nucleoporins in a single Escherichia coli cell. During the sequential reconstitution of the Nup84p complex, smaller assembly intermediates can be isolated, which exhibit modular structures determined by electron microscopy that finally make up the whole Y-shaped Nup84p complex. Importantly, a seventh subunit, Nup133p, was incorporated into the complex through its interaction with Nup84p, thereby elongating one arm of the Y-shaped assembly to an approximately 40 nm long stalk. Taken together, our data document that the Nup84p-Nup133p complex self-assembles in a modular concept from distinct smaller nucleoporin construction sets.

Gelatinase activity in keloids and hypertrophic scars.

Keloids and hypertrophic scars are characterized by excessive deposition of collagen, which may result from insufficient protein degradation. Little is known about the levels of two gelatinases, matrix metalloproteinase-2 (72 kD type IV collagenase) and matrix metalloproteinase-9 (matrix metalloproteinase-9; 92 kD type IV collagenase) in these abnormal scars. The purpose of this study was to determine levels of these proteinases in tissue from hypertrophic scars, keloids, and donor skin. Ten hypertrophic scar samples, 9 keloid samples, and 10 donor skin samples were frozen, pulverized, homogenized, clarified by centrifugation, and analyzed for matrix metalloproteinases by quantitative zymography. Identity of matrix metalloproteinases was determined using a conditioned media reference standard, molecular weight ladders, and Western blotting. Levels of matrix metalloproteinase-9 activity were very low or undetectable in all samples. However, matrix metalloproteinase-2 activity was significantly elevated in keloids and hypertrophic scars vs. donor samples: 2.6 and 3.9-fold increases for latent matrix metalloproteinase-2, 7.8 and 6.9-fold increases for active matrix metalloproteinase-2, respectively. We conclude that little matrix metalloproteinase-9 activity (the gelatinase involved in early tissue repair) is present in keloids and hypertrophic scars, while matrix metalloproteinase-2 activity (the gelatinase involved in prolonged tissue remodeling) is present in donor skin and is significantly increased in hypertrophic scars and keloids.

Apparent pore size of polyacrylamide gels: comparison of gels cast and run in Tris-acetate-EDTA and Tris-borate-EDTA buffers.

The electrophoretic mobilities of DNA molecules in three different molecular weight ladders were measured in polyacrylamide gels containing different acrylamide concentrations (%T) and cross-linker ratios (%C), cast and run in Trisacetate-EDTA (TAE) buffer. The apparent pore radius of each gel was estimated from Ferguson plots of the relative mobilities of each of the DNA molecules, using the mobility of the monomer fragment in each molecular weight ladder as the reference mobility. The effective size of each of the DNA molecules was estimated from its radius of gyration. The apparent gel pore radii calculated in this manner ranged from 21 nm in gels containing 10.5%T, 5%C to 200 nm in gels with 4.6%T, 2%C, similar to the values observed for polyacrylamide gels cast and run in Tris-borate-EDTA (TBE) buffer (Holmes and Stellwagen, Electrophoresis 1991, 12, 612-619). Hence, the effective pore size of polyacrylamide gels is essentially independent of whether the gels are cast and run in TAE or TBE buffer.

DNA mobility anomalies are determined primarily by polyacrylamide gel concentration, not gel pore size.

The dependence of DNA mobility anomalies on gel pore size has been studied in polyacrylamide gels with a wide variety of compositions, using molecular weight ladders containing multiple copies of normal (12B) and anomalously slowly migrating (12A) 147-base pair restriction fragments from plasmid pBR322 as the migrating probe molecules. If the gel pore size is increased by decreasing the total acrylamide concentration (%T) at constant cross-linker ratio (%C), the usual method of increasing gel pore size, the mobility anomalies decrease with increasing gel pore radius as though the 12A multimers were retarded by a sieving mechanism. However, the decrease in the mobility anomalies is independent of whether the apparent gel pore radius is larger or smaller than the DNA radius of gyration, suggesting that gel pore size is not the controlling variable. If the acrylamide concentration is held constant and the gel pore size is increased by decreasing %C at constant %T, the mobility anomalies of the largest 12A multimers (6 mers and higher) decrease with increasing gel pore radius, because of sieving effects, until the effective gel pore radius becomes approximately equal to the DNA radius of gyration, after which the mobility anomalies level off and become independent of gel pore size. The mobility anomalies exhibited by 5-mers and smaller multimers of fragment 12A are independent of gel pore radius in all gels with constant %T. Similar results are observed with a molecular weight ladder containing phased A-tracts from the kinetoplast bending locus. Since the anomalous electrophoretic mobilities depend primarily on the total acrylamide concentration in the gel, and not on the apparent gel pore radius, increases in the magnitude of the mobility anomalies with increasing gel concentration (and decreasing gel pore radius) cannot be taken as evidence for DNA curvature.

Apoptosis of human ovary and uterine endometrium during the menstrual cycle.

To investigate apoptotic changes in the ovary or uterine endometrium, we studied the cleavage of DNA in these tissues obtained from regularly cycling women by in situ analysis of DNA integrity and quantitative end labeling of DNA gel fractionation. In situ analysis of several sized atretic follicles of ovaries revealed that granulosa cells showed positive staining to some extent, however, these methods do not discriminate between cells undergoing apoptosis and those undergoing necrosis. Total DNA extracted from human corpora lutea (CL) of the early luteal phase contained predominantly high molecular weight DNA, whereas CL of the midluteal phase exhibited the appearance of DNA cleavage into low molecular weight ladders characteristic of apoptosis. Although apoptotic DNA cleavage of human CL increased from the midluteal phase to the late luteal phase, CL of early pregnancy did not exhibit apoptotic DNA fragmentation. Both large and small luteal cells were the primary cell type exhibiting DNA cleavage in human CL of the midluteal and late luteal phases and in regressive CL. Biochemical analysis of human endometrium revealed that the ladder pattern cleavage of DNA was identified at three different phases of the menstrual cycle, namely the early proliferative, late secretory, and menstrual phases. Cells undergoing apoptosis were scattered in the functional layer of the early proliferative endometrium, but not in the late proliferative phase to midsecretory phase: At the beginning of the late secretory phase, apoptosis reappeared in the stromal cells and spread gradually to almost all components of the functional layer. By contrast, cells in the basal layer showed no evidence of apoptosis throughout the menstrual cycle. The present findings suggest that: (1) human luteal regression may be mediated by apoptosis; (2) CL of early pregnancy may be rescued from luteolysis through inhibition of the occurrence of apoptotic luteal cell death, and (3) apoptosis occurs in specific populations of endometrial cells during the human endometrial cycle. In conclusion, apoptosis might play an important role in the regulation of the menstrual cycle in women.