A Nucleic Acid Nanostructure Built through On-Electrode Ligation for Electrochemical Detection of a Broad Range of Analytes.

For an assay to be most effective in point-of-care clinical analysis, it needs to be economical, simple, generalizable, and free from tedious workflows. While electrochemistry-based DNA sensors reduce instrumental costs and eliminate complicated procedures, there remains a need to address probe costs and generalizability, as numerous probes with multiple conjugations are needed to quantify a wide range of biomarkers. In this work, we have opened a route to circumvent complicated multiconjugation schemes using enzyme-catalyzed probe construction directly on the surface of the electrode. With this, we have created a versatile DNA nanostructure probe and validated its effectiveness by quantification of proteins (streptavidin, anti-digoxigenin, anti-tacrolimus) and small molecules (biotin, digoxigenin, tacrolimus) using the same platform. Tacrolimus, a widely prescribed immunosuppressant drug for organ transplant patients, was directly quantified with electrochemistry for the first time, with the assay range matching the therapeutic index range. Finally, the stability and sensitivity of the probe was confirmed in a background of minimally diluted human serum.

Engineered Biosensors from Dimeric Ligand-Binding Domains.

Biosensors are important components of many synthetic biology and metabolic engineering applications. Here, we report a second generation of Saccharomyces cerevisiae digoxigenin and progesterone biosensors based on destabilized dimeric ligand-binding domains that undergo ligand-induced stabilization. The biosensors, comprising one ligand-binding domain monomer fused to a DNA-binding domain and another fused to a transcriptional activation domain, activate reporter gene expression in response to steroid binding and receptor dimerization. The introduction of a destabilizing mutation to the dimer interface increased biosensor dynamic range by an order of magnitude. Computational redesign of the dimer interface and functional selections were used to create heterodimeric pairs with further improved dynamic range. A heterodimeric biosensor built from the digoxigenin and progesterone ligand-binding domains functioned as a synthetic "AND"-gate, with 20-fold stronger response to the two ligands in combination than to either one alone. We also identified mutations that increase the sensitivity or selectivity of the biosensors to chemically similar ligands. These dimerizing biosensors provide additional flexibility for the construction of logic gates and other applications.

Quantifying Nanomolar Protein Concentrations Using Designed DNA Carriers and Solid-State Nanopores.

Designed "DNA carriers" have been proposed as a new method for nanopore based specific protein detection. In this system, target protein molecules bind to a long DNA strand at a defined position creating a second level transient current drop against the background DNA translocation. Here, we demonstrate the ability of this system to quantify protein concentrations in the nanomolar range. After incubation with target protein at different concentrations, the fraction of DNA translocations showing a secondary current spike allows for the quantification of the corresponding protein concentration. For our proof-of-principle experiments we use two standard binding systems, biotin-streptavidin and digoxigenin-antidigoxigenin, that allow for measurements of the concentration down to the low nanomolar range. The results demonstrate the potential for a novel quantitative and specific protein detection scheme using the DNA carrier method.

Whole-mount in situ hybridization using DIG-labeled probes in planarian.

In recent years freshwater flatworms (planarian) have become a powerful model for studies of regeneration and stem cell biology. Whole-mount in situ hybridization (WISH) and fluorescent in situ hybridization (FISH) are key and most commonly used techniques to determine and visualize gene expression patterns in planaria. Here, we present the established version of whole-mount in situ hybridization (WISH) and whole-mount fluorescence in situ hybridization (WFISH) protocol optimized over the last years by several labs from the rapidly growing planaria field and give an overview of recently introduced modifications which can be critical in the study of low abundant transcripts.

Whole-mount fluorescence in situ hybridization and antibody staining of Drosophila embryos.

Whole-mount RNA in situ hybridizations with digoxigenin-conjugated probes and alkaline phosphatase biochemistry have been used widely for many years to map expression pattern domains in the Drosophila embryo. To capitalize on the number of molecular markers in the central nervous system (CNS) and to enable expression analysis at the single-cell level, fluorescence in situ hybridization procedures are becoming standard. This protocol describes methods for the simultaneous detection of RNA and protein using fluorescence in Drosophila embryos. It uses the tyramide signal amplication (TSA) system from PerkinElmer to amplify a horseradish peroxidase (HRP) signal. By combining this technology with an HRP-conjugated antidigoxigenin antibody, we can detect standard antidigoxigenin RNA probes fluorescently.

Determination of gene expression patterns using in situ hybridization to Drosophila testes.

We describe a whole-mount RNA in situ hybridization (ISH) method optimized for detection of the cellular and subcellular distributions of specific mRNA within Drosophila testes and male genital tract. Digoxygenin (dig)-labeled antisense RNA probes are in vitro transcribed from a template synthesized by (RT)-PCR; the probe length is reduced by hydrolysis. Testes and male genital tracts are dissected from adult flies, fixed and processed for hybridization. Both probe and fixed testes can be stored before use. Extensive post-hybridization washing reduces the background. Detection is through alkaline phosphatase-conjugated anti-dig antibodies followed by a color reaction. This protocol is suitable for low-medium throughput applications with parallel processing of 2-48 samples, and takes 4-5 d to complete. We have used this protocol, which is similar to other RNA ISH protocols, but optimized for whole-mount Drosophila testes, to document the expression of about 1,000 genes in Drosophila melanogaster male genital tract.

Competitive homogeneous digoxigenin immunoassay based on fluorescence quenching by gold nanoparticles.

We report on a competitive, homogeneous immunoassay for the detection of the hapten digoxigenin. The assay is based on competitive fluorescence quenching by gold nanoparticles. Digoxigenin is indirectly labeled with the fluorophore Cy3B through bovine serum albumin and used as a marker. Gold nanoparticles functionalized with anti-digoxigenin antibodies serve as fluorescence quenchers. Free digoxigenin molecules in the analyte solution compete with the labeled markers for antibodies on the gold nanoparticles. The fluorescence signal depends linearly on the free digoxigenin concentration within a range of concentration from 0.5 to 3 ng mL(-1). The limit of detection is estimated as 0.2 ng mL(-1) and the limit of quantitation is estimated as 0.6 ng mL(-1). The method can be used to detect digoxin, a drug used to cure cardiac arrhythmia.

One-way PCR-based mapping of a replication initiation point (RIP).

The lamin B2 locus is the only mammalian origin whose replication initiation points (RIPs) have been mapped. Although this paper was published 8 years ago, no further mammalian RIP-mapping studies have been reported, largely due to technical difficulties of ligation-mediated (LM)-PCR used by the authors. Here, we report the development of a simple, one-way PCR-based protocol that allows one to accurately determine RIPs at mammalian origins. The procedure can be completed within 48 h from the time of cell lysis in the agarose gel. Nascent DNA is then isolated from the same gel after DNA is separated by alkaline gel electrophoresis. Subsequently, RIPs are determined by one-way PCR-based primer extension using labeled primers. Using this protocol, we have successfully mapped RIPs in the human DBF4 locus. As one-way PCR is routinely used by many scientists, this protocol will provide a powerful new tool for studying DNA replication in many organisms including mammalian cells.

Development of a receptor-based microplate assay for the detection of beta-lactam antibiotics in different food matrices.

The penicillin-binding protein PBP 2x* from Streptococcus pneumoniae has been utilised to develop a novel microplate assay for the detection and determination of penicillins and cephalosporins with intact beta-lactam structure in milk, bovine and porcine muscle juice, honey and egg. In the assay, the receptor protein is immobilised to a microplate in the first step. To each sample a bifunctional reagent is added, with ampicillin and digoxigenin as functional groups (DIG-AMPI). The amount of bifunctional reagent, which is bound via its ampicillin part to the receptor protein, decreases with increasing beta-lactam concentration in the sample. The detection step uses anti-digoxigenin F(ab) fragments marked with horseradish peroxidase. The more bifunctional reagent is bound to the receptor protein, the more antibody fragments are bound via the digoxigenin part of the reagent. A maximum colour development with tetramethylbenzidine as chromogen for the peroxidase reaction is achieved, when no beta-lactam residues are present. A fractional factorial design was applied to detect chemometrically effects and interactions of the assay parameters. For optimisation of the significant parameters a Box-Behnken design was used. The assay has been developed for various food matrices as screening test with the option for a quantitative assay, when the identity of the residual beta-lactam is known (e.g. elimination studies). Cefoperazon, cefquinome, cefazolin, cloxacillin, ampicillin and benzylpenicillin could be detected at levels corresponding to 1/2 EU maximum residue limit (MRL) in milk, meat juice from muscle tissue of different species, egg and honey (where applicable) without needing lengthy and elaborate sample pre-treatment. Matrix calibration curves are presented, which show that quantitative analyses are possible.

Whole-mount in situ hybridization and detection of RNAs in vertebrate embryos and isolated organs.

Nonisotopic in situ hybridization using intact embryos or organs is an important method for determining the spatial distribution of RNAs. Because it allows the analysis of large numbers of samples, it is amenable to temporal expression studies and comparison between different genotypes. It offers sensitivity and reproducibility. In addition, histological details are not lost during the staining process. The protocols in this unit can be used for whole-mount in situ hybridization in Xenopus, mouse, and chicken embryos, as well as dissected organs from mouse and chicken. Preparation of digoxigenin-labeled riboprobes is also described.

On-line continuous-flow, multi-protein biochemical assays for the characterization of bioaffinity compounds using electrospray quadrupole time-of-flight mass spectrometry.

The applicability of a homogeneous on-line continuous-flow, multi-protein biochemical assay was demonstrated for the interaction between fluorescein-biotin and streptavidin and for digoxin and anti-digoxigenin using electrospray quadrupole time-of-flight mass spectrometry (Q-TOF MS). In the on-line continuous-flow biochemical MS-based system several receptors (e.g., streptavidin and anti-digoxigenin, respectively) were allowed to react with corresponding reporter ligands (e.g.,fluorescein-biotin and digoxin, respectively). The methodology presented allows the simultaneous measurement of affinity and molecular mass of an active compound. By using automated MS and MS-MS switching functions of the Q-TOF, structure information is obtained allowing the characterization of bioactive compounds. No cross-reactivities were observed between the two model systems fluorescein-biotin/streptavidin and digoxin/anti-digoxigenin.

[HER2 gene amplification assay: is CISH an alternative to FISH?]. / Recherche de l'amplification du gène HER2: la CISH est-elle une alternative à la technique FISH?

The HER2 proto-oncogene encodes a transmembrane protein, which is considered to function as a growth factor receptor. Overexpression of this protein found by immunohistochemistry in about 20% of infiltrating breast carcinomas, has a predictive value of response to treatment by trastuzumab, an anti-HER2 humanized monoclonal antibody. Search for HER2 gene amplification is necessary to adapt the immunohistochemical technique quality and also in the cases of delicate analysis or weak overexpression. It is usually carried out by Fluorescence In Situ Hybridization (FISH). A more recent hybridization technique, named CISH because of its chromogenic revelation is an alternative method, which gives highly correlated results with FISH. We present details of this technique, which may be more familiar for the pathologists than FISH, because reading analysis is similar to that of immunohistochemical staining.

Quantification of Escherichia coli genomic DNA contamination in recombinant protein preparations by polymerase chain reaction and affinity-based collection.

This study describes the development of a novel assay for the quantification of Escherichia coli genomic DNA contamination in recombinant protein samples. The technique is based on PCR amplification and digoxygenin labeling of the genes encoding 5S ribosomal RNA followed by affinity-based collection and detection. Samples containing 1 pg x mL(-1) of extracted E. coli genomic DNA (gDNA) could be measured using this method. Using extracted E. coli gDNA as standards, a 35-cycle PCR reaction exhibited a linear response versus template concentration between 1 pg x mL(-1) and1 ng x mL(-1) genomic DNA even when diluted in a variety of buffering conditions. Comparison of the novel assay with a traditional filter binding and hybridization technique using recombinant protein samples confirmed that the procedure was accurate and sensitive. The assay described in this report is a safer and less expensive alternative to radioactive techniques employed for DNA quantification, utilizing readily available reagents and apparatus.

A new DIG-PCR-EIA method for the detection of Chlamydia pneumoniae DNA in clinical samples.

Chlamydia pneumoniae, a common respiratory pathogen, may also play a role in the pathogenesis of other chronic conditions. For accurate detection of infected persons and verification of results obtained by other PCR methods, a DIG-PCR-EIA method was evaluated. In the DIG-PCR-EIA, a 437 bp DNA sequence was amplified and hybridized with a newly synthesized 229 bp biotin-labeled probe. The end product was detected by an enzyme immunoassay. The sensitivity of DIG-PCR-EIA was compared with Southern blot hybridization and one-step HR/HL PCR, which was the routine method used. DNA was detected to the level of 20 elementary bodies of DIG-EIA-PCR compared to less than 2 by Southern blot, and 200 by HR/HL PCR. Thus a 100-fold increase in sensitivity could be expected by DIG-EIA-PCR compared to the routine method. Throat swabs and adenoid tissue from 22 children with otitis and middle ear secretions from 29 children, as well as throat swabs from 179 blood donors, were analyzed with DIG-EIA-PCR, HL/HR PCR and nested touchdown PCR. 32% of the ear secretions were positive by DIG-EIA-PCR as compared to 5% by the other two methods. Three adenoid tissue samples were positive by all methods applied. Among the child and adult throat samples, 18% and 32%, respectively, were positive by DIG-EIA-PCR and 5% and 10% by HR/HLPCR. The results indicate the suitability of DIG-PCR-EIA for verification of results of HR/HL PCR. DIG-PCR-EIA has a potential for increased sensitivity and adaptation for automation. It should be further evaluated using various types of tissue specimens and DNA extraction methods.

Rapid regulation of cytoskeletal proteins and their mRNAs following afferent deprivation in the avian cochlear nucleus.

During development, removal of neuronal input can lead to profound changes in postsynaptic cells, including atrophy and cell death. In the chicken brainstem cochlear nucleus, the nucleus magnocellularis (NM), deprivation of auditory input via unilateral cochlea removal or silencing the eighth nerve with tetrodotoxin leads to a loss of 25-30% of the neurons and the atrophy of surviving neurons. One intracellular component that may be involved in both cell atrophy and cell death is the cytoskeleton. The degradation of the cytoskeleton following deafferentation could potentially lead to either atrophy or death of NM neurons. However, little is known regarding the role of neuronal input on the cytoskeletal structure of NM neurons and whether changes in the cytoskeleton are responsible for cell death following deafferentation. The present study examined whether changes in the cytoskeleton of NM neurons occurred following cochlea removal. Several components of the cytoskeleton were analyzed following unilateral afferent deprivation. Levels of immunostaining for tubulin, actin, and microtubule-associated protein 2 (MAP-2), and levels of beta-tubulin and beta-actin mRNAs were assessed in NM neurons following cochlea removal. Our results revealed that afferent deprivation results in a rapid decrease in immunostaining for all three cytoskeletal proteins examined. These decreases were observed as early as 3 hours after cochlea removal and persisted for up to 4 days. In addition, these changes occurred in all deafferented NM neurons at the early time points, indicating that both dying and surviving NM neurons undergo a similar change in their cytoskeletons. In contrast to the decreases in immunostaining, levels of beta-tubulin and beta-actin mRNAs were not noticeably altered by deafferentation. Our findings indicate that the cytoskeleton is altered or degraded following deafferentation but that this process is not regulated at the transcriptional level.

Lectin binding sites on CD34+ human haematopoietic stem cells and lymphocytes from peripheral blood: an ultrastructural post-embedding study.

This study was performed to obtain a better insight into the glycosylation pattern of human CD34+ haematopoietic stem cells and lymphocytes from peripheral blood using an ultrastructural post-embedding technique. Lectins applied were derived from Canavalia ensiformis (Con A), Triticum vulgare (WGA), Lycopersicon esculentum (LEA), Limulus polyphemus (LPA), Ulex europaeus-I (UEA-I), Bauhinia purpurea (BPA), Glycine max (SBA), Helix pomatia (HPA), Arachis hypogaea (PNA) and Erythrina cristagalli (ECA). Our results showed almost identical staining patterns with both CD34+ cells and mature lymphocytes from peripheral blood. Con A displayed a prominent reactivity with the nuclear envelope and a weak staining of the plasma membrane. As demonstrated by an elaborate lectin double-labelling technique, WGA revealed an opposite staining pattern. Following neuraminidase treatment of sections, BPA, PNA and SBA exhibited a prominent staining of the plasma membrane in CD34+ cells and lymphocytes as well. Membrane reactivity with HPA was restricted to the majority of lymphocytes, presumably T-lymphocytes. Infrequently occurring dense cytoplasmic (lysosomal) bodies were reactive with a variety of lectins, and a weak diffuse nuclear labelling was observable with LPA, UEA-I, WGA and Con A. It is tempting to speculate that carbohydrate moieties on plasma membranes may be involved in the complex mechanisms characterizing cell-to-cell interactions (adhesion) and particularly in the so-called phenomenon of homing.

Synthesis and mass spectrometric characterization of digoxigenin and biotin labeled ganglioside GM1 and their uptake by and metabolism in cultured cells.

Selective acylation of mono-deacetyl lyso-GM1, i.e. beta-D-galactopyranosyl-(1-->3)-2-acetamido-2-deoxy-beta-D-galactopyr ano syl -(1-->4)-(alpha-D-neuraminyl-(2-->3))-beta-D-galactopyranosyl- (1-->4)-beta-D-glucopyranosyl-(1-->1)-(2S,3R,4E)-2-amino-4-octa decen-1,3-diol, with N-succinimidyl-[1-14C]stearate afforded labeled mono-deacetyl GM1, i.e. beta-D-galactopyranosyl-(1-->3)-2-acetamido-2-deoxy-beta-D-galactopyr ano syl- (1-->4)-(alpha-D-neuraminyl-(2-->3)-beta-D-galactopyranosyl-(1-->4)-beta -D- glucopyranosyl-(1-->1)-(2S,3R,4E)-2-[1-14C]octadecanamido-4- octadecen-1, 3-diol, in good yield. Its condensation with either N-succinimidyl-digoxigenyl-3-O-methyl carbonyl-epsilon-amino caproate or N-succinimidyl-D-biotinyl-epsilon-aminocaproate led to radioactive GM1 derivatives carrying a tag for immuno-electron microscopy at the sialic acid residue. These GM1 derivatives could be hydrolyzed to the corresponding GM3 derivatives by treatment with GM1-beta-galactosidase and beta-hexosaminidases. There was no further degradation by sialidases due to the bulky tag in the sialic acid residue. The uptake of biotin labeled GM1 by human skin fibroblasts, rat neuroblastoma cells B104 and human neuroblastoma cells SHSY5Y was 0.85, 0.58 and 1.62 nmol lipid/mg cellular protein, respectively, after an incubation for 66 h at 37 degrees C and was similar to that of untagged GM1. The uptake of digoxigenin labeled GM1 by these cell types was, however, significantly higher (3.1, 6.8, and 20.0 nmol lipid/mg cellular protein, respectively). Both the biotin and digoxigenin labeled GM1 analogs were catabolized to the corresponding GM2 and GM3 derivatives in lysosomes of cultured cells. This demonstrates that these synthetic analogues are suitable for studying, by immuno-electron microscopy, their endocytosis and distribution in intralysosomal membranes.

Identification of type VI collagen synthesizing cells in human diabetic glomerulosclerosis using renal biopsy sections.

Although the role of extracellular matrices in the development of glomerulosclerosis has been discussed widely, the cellular origin of type VI collagen in diabetic nephropathy (DN) has remained relatively unexplored. This study reports the distribution and cellular origin of type VI collagen in DN. Type VI collagen-specific oligonucleotide probes and monoclonal antibody were used to assess the relative expression of mRNA for alpha 1 (VI) chain and its translated protein in paraffin-embedded renal biopsy sections of DN. By immunohistochemistry, compared to the control, increased deposition of type VI collagen was noted in the diffuse and nodular lesions of diabetic glomeruli. For cellular localization of type VI collagen mRNA, paraffin-embedded renal sections of the control and DN were hybridized in situ with digoxigenin (Dig)-labeled antisense oligo-DNA probe complementary to a part of alpha 1 (VI) mRNA. In comparison to the control kidney sections, increased numbers of intraglomerular cells (both mesangial and epithelial cells) were positive for alpha 1 (VI) mRNA in renal biopsy sections of DN. From the results, we conclude that overexpression of type VI collagen by intraglomerular cells with its increased deposition might significantly contribute to the glomerulosclerosis found in DN.

Detection of phosphatidylinositol glycan class A gene transcripts by RT in situ PCR hybridization. A comparative study using fluorescein, Texas Red, and digoxigenin-11 dUTP for color detection.

Gene-specific probes labeled with fluorescein, Texas Red, and digoxigenin-11 dUTP (DIG) were used for RT in situ PCR hybridization to detect PIG-A gene (phosphatidylinositol glycan class A) transcripts. The PIG-A gene is responsible for biosynthesis of the glycosylphosphatidyl-inositol (GPI) anchor. Lack of GPI anchor expression due to mutations can cause an acquired clonal hematologic disorder called paroxysmal nocturnal hemoglobinuria (PNH). In this RT in situ PCR study, two types of labeling methods, a direct method (using fluorescein and Texas Red) and an indirect method (using DIG-11 dUTP) were compared. Both were successfully applied to detect and localize the PIG-A gene transcripts within single cells of the cell lines AA2, H9, and JY. Furthermore, similar results for sensitivity and reproducibility were obtained. Advantages and disadvantages of the different labeling techniques are discussed. In addition, peripheral blood mononuclear cells from PNH patients were also included in this study.

Design of non-competitive flow injection enzyme immunoassays for determination of haptens: application to digoxigenin.

A theoretical model immunoradiometric assay (IRMA) was adapted to provide a non-competitive flow injection enzyme immunoassay for haptens and used as a guide in studying the effects of different parameters on the sensitivity, precision and dynamic range of the assay. As well as the concentration of the antibody-enzyme conjugate, the affinity constant, the run time through the affinity column, the homogeneity of the antibody population and purity of the antibody-enzyme conjugate were all shown to be important parameters in the optimisation of the assay. The findings were used to design an optimised enzyme flow injection immunoassay for the model compound digoxigenin in standard solutions. A linear calibration curve was established in the range 0.38-7.7 fmol of digoxigenin, resulting in a precision of 14.8% RSD at 1 fmol and 3.7% RSD at 7.7 fmol. Antibody fragments reacting with digoxigenin and labelled with alkaline phosphatase, (Fab-AP) were used to convert 4-methyl umbelliferyl phosphate to a fluorescent product measured downstream. The sample throughput was 15 h-1 and over 60 injections were possible before regenerating the affinity column.