Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin

Exploiting the Nucleic Acid Nature of Aptamers for Signal Amplification

Aptamer-based assays and sensors are garnering increasing interest as alternatives to antibodies, particularly due to their increased flexibility for implementation in alternative assay formats, as they can be employed in assays designed for nucleic acids, such as molecular aptamer beacons or aptamer detection combined with amplification. In this work, we took advantage of the inherent nucleic acid nature of aptamers to enhance sensitivity in a rapid and facile assay format. An aptamer selected against the anaphylactic allergen β-conglutin was used to demonstrate the proof of concept. The aptamer was generated by using biotinylated dUTPs, and the affinity of the modified aptamer as compared to the unmodified aptamer was determined by using surface plasmon resonance to calculate the dissociation constant (K_D), and no significant improvement in affinity due to the incorporation of the hydrophobic biotin was observed. The modified aptamer was then applied in a colorimetric competitive enzyme-linked oligonucleotide assay, where β-conglutin was immobilized on the wells of a microtiter plate, competing with β-conglutin free in solution for the binding to the aptamer. The limit of detection achieved was 68 pM, demonstrating an improvement in detection limit of three orders of magnitude as compared with the aptamer simply modified with a terminal biotin label. The concept was then exploited by using electrochemical detection and screen-printed electrodes where detection limits of 326 fM and 7.89 fM were obtained with carbon and gold electrodes, respectively. The assay format is generic in nature and can be applied to all aptamers, facilitating an easy and cost-effective means to achieve lower detection limits.

Preparation of Labeled DNA, RNA, and Oligonucleotide Probes

Labeled nucleic acids and oligonucleotides are typically generated by enzymatic methods such as end-labeling, random priming, nick translation, in vitro transcription, and variations of the polymerase chain reaction (PCR). Some of these methods place the label in specific locations within the nucleic acid (e.g., at the 5' or 3' terminus); others generate molecules that are labeled internally at multiple sites. Some methods yield labeled single-stranded products, whereas others generate double-stranded nucleic acids. Finally, some generate probes of defined length, whereas others yield a heterogeneous population of labeled molecules. Options available for generating and detecting labeled nucleic acids, as well as advice on designing oligonucleotides for use as probes, is included here.

Biotin

Biotin is a water-soluble vitamin that can be attached to a variety of proteins and nucleic acids, often without altering their properties. Its use in molecular biology is introduced here.

Aptamers as the powerhouse of dot blot assays

Dot blot assays have always been associated with antibodies as the main molecular recognition element, which are widely employed in a myriad of diagnostic applications. With the rising of aptamers as the equivalent molecular recognition elements of antibodies, dot blot assays are also one of the diagnostic avenues that should be scrutinized for their amenability with aptamers as the potential surrogates of antibodies. In this review, the stepwise procedures of an aptamer-based dot blot assays are underscored before reviewing the existing aptamer-based dot blot assays developed so far. Most of the applications center on monitoring the progress of SELEX and as the validatory assays to assess the potency of aptamer candidates. For the purpose of diagnostics, the current effort is still languid and as such possible suggestions to galvanize the move to spur the aptamer-based dot blot assays to a point-of-care arena are discussed.

Antiviral Action of Native and Methylated Lactoferrin and β-Lactoglobulin against Potato Virus Y (PVY) Infected into Potato Plants Grown in an Open Field

Potato plants are liable to PVY infection without efficient control. Therefore, they were cultivated under greenhouse and open field conditions, artificially infected with PVY and then treated after 15 days of infection with native lactoferrin (LF) and native β-lactoglobulin (BL) and their esterified forms, MLF (methylated lactoferrin) and BLM (methylated β-lactoglobulin) to test the efficiency of this approach. Viral replication was inhibited by the applied substances, particularly the methylated forms, in a concentration-dependent manner, where the concentration of 500 μg·mL^-1 was sufficient for plant protection against the PVY infection. An open field experiment showed that one single application of the antiviral substance was enough for maximum inhibitory action against PVY. The modified milk proteins induced higher inhibitory action on PVY virus replication in the plants, compared to their native forms, which was reflected by potato growth and yield. Using the dot blot hybridization and RT-PCR techniques to detect PVY in the experimental plants showed the supremacy of native and esterified LF in inhibiting the targeted virus. The generally observed scanning electronic microscopy (SEM) structural deformations and irregular appearance in PVY particles when treated with MLF and BLM revealed their direct action. BLM, MLF and LF are efficient antiviral agents against PVY. They can not only abolish the observed PVY-induced reduction in potato growth and tuber yield, but also further increase them to higher levels than negative control.

Multiple cytosolic DNA sensors bind plasmid DNA after transfection

Mammalian cells express a variety of nucleic acid sensors as one of the first lines of defense against infection. Despite extensive progress in the study of sensor signaling pathways during the last decade, the detailed mechanisms remain unclear. In our previous studies, we reported increased type I interferon expression and the upregulation of several proposed cytosolic DNA sensors after transfection of several tumor cell types with plasmid DNA (pDNA). In the present study, we sought to reveal the early events in the cytosolic sensing of this nucleic acid in a myoblast cell line. We demonstrated that DNA-dependent activator of interferon regulatory factors/Z-DNA binding protein 1 (DAI/ZBP1) bound plasmid DNA in the cytosol within 15 minutes of transfection and at consistent levels for 4 h. Interferon activated gene 204 protein (p204) and DEAH box helicase 9 (DHX9) also bound pDNA, peaking 15 and 30 min respectively. Plasmid DNA was not detectably bound by DEAD box helicase 60 (DDX60) protein, despite a similar level of mRNA upregulation to DAI/ZBP1, or by cyclic GMP-AMP synthase (cGAS), despite its presence in the cell cytosol. Taken together, these results indicate several DNA sensors may participate and cooperate in the complex process of cytosolic DNA sensing.

Selective Single Molecule Nanopore Sensing of microRNA Using PNA Functionalized Magnetic Core-Shell Fe3O4-Au Nanoparticles

Solid-state nanopores have been employed as useful tools for single molecule analysis due to their advantages of easy fabrication and controllable diameter, but selectivity is always a big concern for complicated samples. In this work, functionalized magnetic core-shell Fe₃O₄-Au nanoparticles, which acted as a molecular carrier, were introduced into nanopore electrochemical system for microRNA sensing in complicated samples with high sensitivity, selectivity and signal-to-noise ratio (SNR). This strategy is based on the specific affinity between neutral peptide nucleic acids (PNA)-modified Fe₃O₄-Au nanoparticles and negative miRNA, and the formation of negative Fe₃O₄-Au-PNA-miRNA complex, which can pass through the nanopore by application of a positive potential and eliminate neutral Fe₃O₄-Au-PNA complex. To detect miRNA in complicated samples, a magnet has been used to separate Fe₃O₄-Au-PNA-miRNA complex with good selectivity. We think this is a facile and effective method for the detection of different targets at single molecular level, including nucleic acids, proteins, and other small molecules, which will open up a new approach in the nanopore sensing field.

Dendrimer-encapsulated copper as a novel oligonucleotides label for sensitive electrochemical stripping detection of DNA hybridization

This paper describes the synthesis and characterization of a novel electrochemical label for sensitive electrochemical stripping detection of DNA hybridization based on dendrimer-encapsulated copper. The generation 4.5 (G 4.5) carboxyl-terminated poly(amidoamine) dendrimer with a trimesyl core was used as a template for synthesis of Cu²⁺/dendrimer nanocomposites (Cu-DNCs). Ratios of Cu²⁺/dendrimer were optimized in order to obtain stable nanocomposites with maximal copper loading in the interior of a polymeric shell. Cu-DNCs labeled DNA probe was employed for determining a target ssDNA immobilized on multi-walled carbon nanotubes-modified glassy carbon electrode (GCE) based on a specific hybridization reaction. The hybridization events were monitored by electrochemical detection of Cu anchored on the hybrids after the release in a diluted nitric acid by anodic stripping differential pulse voltammetry (ASDPV). The results showed that only a complementary sequence could form a dsDNA with the Cu-DNCs DNA probe and give an obvious electrochemical signal. The non-complementary sequence exhibited negligible signal change compared with the blank measurement (means: the electrode containing no target DNA incubating in hybridization buffer solution containing Cu-DNCs DNA probe for a certain time). The use of Cu encapsulated-dendrimer as tags and ASDPV for the detection of the released Cu ions could enhance the hybridization signal, and result in the increase of the sensitivity for the target DNA. Under the conditions employed here, the detection limit for measuring the full complementary sequence is down to pM level.

Protein biotinylation

Since its discovery in the first half of the twentieth century, the high-affinity, noncovalent interaction between biotin (vitamin H) and the avian protein avidin (and its bacterial homologs) has been exploited for many diverse biotechnology applications. This unit provides several basic protocols for labeling various protein reactive groups with biotin. These protocols can be applied not only to labeling in vitro or in tissue culture, but also to in vivo labeling of whole laboratory animals or to ex vivo labeling of surgically resected organs.

Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov

Resequencing of the 16S rRNA gene of the type strain of Herbaspirillum putei Ding and Yokota 2004 revealed 99.9 % sequence similarity to that of the type strain of Herbaspirillum huttiense (Leifson 1962) Ding and Yokota 2004. This high phylogenetic relatedness of H. putei and H. huttiense was confirmed by the results of DNA-DNA hybridization between H. huttiense DSM 10281(T) and H. putei ATCC BAA-806(T) (reassociation value 96 %). Therefore, it is proposed to reclassify the type strain of H. putei as a strain of H. huttiense. However, the genome of the type strain of H. putei is about 0.9 Mb larger than that of the H. huttiense type strain. This results in a decrease in the reassociation value in the reciprocal DNA-DNA hybridization to 72 %, a level slightly above the threshold for delineating bacterial species. These data and distinctive phenotypic characteristics indicate that the name Herbaspirillum putei is a later heterotypic synonym of Herbaspirillum huttiense and permit the description of two novel subspecies, Herbaspirillum huttiense subsp. huttiense subsp. nov. (type strain ATCC 14670(T) =JCM 21423(T) =DSM 10281(T)) and Herbaspirillum huttiense subsp. putei subsp. nov., comb. nov. (type strain 7-2(T) =JCM 21495(T) =ATCC BAA-806(T)). Three bacterial strains, IEH 4430(T), IEH 4515 and IEH 8757, isolated from water were found to be the closest relatives of these strains. Strain IEH 8757 was classified as a strain of H. huttiense subsp. putei. Studies of genotypic and phenotypic features of strains IEH 4430(T) and IEH 4515 showed that the strains represent a novel species, which is most closely related to H. huttiense and for which the name Herbaspirillum aquaticum sp. nov. is proposed (type strain IEH 4430(T) =DSM 21191(T) =ATCC BAA-1628(T)).

PAMAM dendrimer-enhanced DNA biosensors based on electrochemical impedance spectroscopy

A novel, simple and sensitive DNA biosensor based on DNA-poly(amidoamine) (PAMAM) dendrimer nanoconjugates was developed by using the electrochemical impedance spectroscopy (EIS) technique. In this context, the assay relies on the hybridization of the single-stranded DNA (ssDNA) probe covalently conjugated on a mercaptoacetic acid self-assembled monolayer on gold electrodes, with the generation 4.5 (G-4.5) PAMAM-target DNA complex in solution. Once the double-stranded DNA (dsDNA) formed on the gold electrodes, G-4.5 PAMAM bearing carboxyls on the periphery was anchored on the hybrids; the changes of interfacial electron-transfer resistance (R(et)) of the electrodes were measured using an Fe(CN)(6)(3-/4-) redox probe by electrochemical impedance spectroscopy. The results showed that only a complementary sequence could form a dsDNA-PAMAM with the DNA-PAMAM probe and give an obviously enlarged R(et) value. The non-complementary and three-base mismatched sequence exhibited negligible impedance change compared with the blank measurement (the blank measurement means: ssDNA probe-modified gold electrode was directly measured by EIS). The unique spherical structure combining with more negative charges on the G-4.5 PAMAM periphery anchored on the hybrids could significantly amplify the hybridization signal (R(et) value), and the detection limit for measuring the full complementary sequence is down to pM level.

Strategies for undertaking expressed sequence tag (EST) projects

Complementary DNA (cDNA) sequencing can be used to sample an organism's transcriptome, and the generated EST sequences can be used for a variety of purposes. They are especially important for enhancing the utility of a genome sequence or for providing a gene catalog for a genome that has not or will not be sequenced. In planning and executing a cDNA project, several criteria must be considered. One should clearly define the project purpose, including organism tissue(s) choice, whether those tissues should be pooled, ability to acquire adequate amounts of clean and well-preserved tissue, choice of type(s) of library, and construction of a library (or libraries) that is compatible with project goals. In addition, one must possess the skills to construct the library (or libraries), keeping in mind the number of clones that will be necessary to meet the project requirements. If one is inexperienced in cDNA library construction, it might be wise to outsource the library production and/or sequence and analysis to a sequencing center or to a company that specializes in those activities. One should also be aware that new sequencing platforms are being marketed that may offer simpler protocols that can produce cDNA data in a more rapid and economical manner. Of course, the bioinformatics tools will have to be in place to de-convolute and aid in data analysis for these newer technologies. Possible funding sources for these projects include well-justified grant proposals, private funding, and/or collaborators with available funds.

Enhanced stability and bioconjugation of photo-cross-linked polystyrene-shell, Au-core nanoparticles

Encapsulating Au nanoparticles within a shell of photo-cross-linked block copolymer surfactant dramatically improves the physical and chemical stability of the nanoparticles, particularly when they are applied as bioconjugates. Photo-cross-linkable block copolymer amphiphiles [polystyrene-co-poly(4-vinyl benzophenone)]-block-poly(acrylic acid) [(PS-co-PVBP)-b-PAA] and [poly(styrene)-co-poly(4-vinyl benzophenone)]-block-poly(ethylene oxide) [(PS-co-PVBP)-b-PEO] were assembled around Au nanoparticles ranging from 12 to 108 nm in diameter. UV irradiation cross-linked the PVBP groups on the polymer to yield particles that withstood extremes of temperature, ionic strength, and chemical etching. Streptavidin was attached to [PS-co-PVBP]-b-PAA-coated particles using the same noncovalent and covalent conjugation protocols used to bind biomolecules to divinylbenzene-cross-linked PS microspheres. We expect that these particles will be useful as plasmonic, highly light-scattering and light-absorbing analogs to fluorescently labeled PS nanospheres.

Nondisruptive, sequence-specific coupling of fluorochromes to plasmid DNA

A method to attach a fluorochrome sequence-specifically to supercoiled plasmid DNA (pDNA) without perturbing transgene expression would provide an invaluable aid in a variety of applications requiring probes for the intracellular tracking of transfected pDNA. Here we report a method to couple commercially available fluorochromes covalently and sequence-specifically to pDNA using a peptide nucleic acid (PNA) as a linker molecule. The terminal cysteine thiol group on the PNA peptide backbone is reacted with a maleimide moiety on the fluorochrome to produce a fluorescent conjugate which is in turn hybridized to a plasmid expression vector containing an 11-bp target sequence. Spectroscopic evaluation and an electrophoretic mobility shift assay showed that the pDNA hybridized to one PNA-fluorochrome conjugate molecule. The fluorescence signal comigrated with pDNA on acrylamide gels, confirming the stable attachment of the fluorescent conjugate to the pDNA. The utility of one of the conjugates, PNA-Oregon green 488/pCMVbeta-DTS, to probe pDNA transport across the nuclear envelope, a significant barrier to gene transfer, was undertaken using a digitonin-permeabilized HeLa cell assay. The PNA-Oregon green 488/pCMVbeta-DTS conjugate is able to efficiently traverse the nuclear membrane of the permeabilized cells, accumulating in the nuclei within 30 min and reaching maximal levels by 1h. When transfected into HeLa cells, the PNA-Oregon green 488/pCMVbeta-DTS conjugate retained 55% of the native plasmid's biological activity, as determined by a beta-galactosidase assay. Thus, this method allows for the sequence-specific coupling of commercially available fluorochromes to DNA expression vectors while retaining biological function.

Postmitotic nuclear retention of episomal plasmids is altered by DNA labeling and detection methods

One often overlooked aspect of nonviral gene therapy is the maintenance and localization of plasmids within a transfected cell. In this study we have quantified the nuclear retention of plasmids within microinjected cells after a single round of cell division. We employed several commercially available reagents to label plasmids with fluorophores for our microinjection tracking experiments. Interestingly, plasmids labeled with different techniques produced drastically different results. Naked plasmids microinjected directly into nuclei and later detected by in situ hybridization were found almost exclusively within the nuclei of the daughter cells after mitosis and were partitioned between the daughter nuclei with a normal, Gaussian distribution. Identical results were obtained with plasmids labeled with a fluorescent peptide nucleic acid. However, when plasmids were labeled with several commercially available fluorescent DNA labeling kits that randomly attach fluorophores to the entire plasmid and injected into HeLa cell nuclei, the modified plasmids were excluded from daughter nuclei after cell division. Taken together, these results suggest that naked, unmodified plasmids are retained in the nucleus following cell division and likely continue to express in the daughter cells. Our results demonstrate the significant alterations in episome localization that the labeling technique itself can have on plasmid trafficking.

Role of viral load in the pathogenesis of chicken anemia virus

The pathogenesis of strain 3711 of the chicken anemia virus (CAV), propagated in chickens, and two preparations of strain 3711 that had been adapted to grow to high titre in cells of the MDCC-MSB1 line were studied in chicken embryos and/or chickens. Highest viral loads in infected chickens, as measured by a microplate DNA-hybridization assay, were detected in the thymus, clotted blood and pancreas, and the lowest in the duodenum. The CAV DNA copy number in the organs of chicken embryos was significantly lower than in chickens. Route of infection was an important determinant of the course of disease in chickens, with clinical signs appearing earlier in birds infected by the intramuscular than those infected by the oral route; there was a direct relationship between viral load in particular organs and the extent of clinical signs. No reduction in the pathogenicity for chickens was noted for strain 3711 after 65 or 129 passages in the MDCC-MSB1 cell line.

CTAB precipitation of cestode DNA

DNA probes are proving extremely valuable in the characterization o f cestodes - as well as other parasites. In this article, Kok Wei Yap and Andrew Thompson discuss some of the problems of DNA isolation, stressing the need for a gentle and economical procedure such as CTAB precipitation.

Specific 3′-Terminal Modification of DNA with a Novel Nucleoside Analogue that Allows a Covalent Linkage of a Nuclear Localization Signal and Enhancement of DNA Stability

We report a straightforward method for the site-specific modification of long double-stranded DNA by using a maleimide adduct of deoxycytidine. This novel nucleoside analogue was efficiently incorporated at the 3'-termini of DNA by terminal deoxynucleotidyl transferase (TdT). Thiol-containing compounds can be covalently linked to the maleimide moieties. We added a nuclear localization signal peptide to the 3'-terminal of a 350 bp-long DNA that encoded short-hairpin RNA, and these modifications resulted in the enhancement of silencing activity by RNA interference. This enhancement is mainly attributed to increased stability of the template DNA.

Glial and neuronal regulation of the lipid carrier R-FABP

Neuroembryogenesis critically depends on signaling molecules that modulate cell proliferation, differentiation, and the formation of neural networks. In an attempt to identify potential morphogenetic active components that are distributed in a graded fashion in the developing nervous system, we generated substraction libraries of the embryonic nasal and temporal chick retina. Selected clones were analyzed by sequencing, Northern and Western blotting, in situ hybridization, and immunocytochemistry. Retinal fatty acid-binding protein (R-FABP) mRNA displayed the most pronounced topographic gradient. R-FABP was most strongly expressed in nasal retina, though topographic differences were not evident on the protein level. R-FABP expression was subject to a pronounced spatio-temporal regulation. Peak expression was at the period of cell generation/migration and differentiation. To identify the cell types involved in R-FAPB synthesis, ganglion cells as the only retinal projection neurons were enriched by enzymatic delayering. Cell somata, axons, and growth cones were R-FABP immunoreactive. Most interestingly, R-FABP immunoreactivity was critically dependent on the growth substratum. It was abrogated when axons grew on isolated glial endfeet. Radial glia purified by complement-mediated cytolysis also expressed R-FABP at moderate levels. The expression level was significantly increased during mitosis and dropped down again in postmitotic cells. Further on, transient loss of cell-cell and substratum contact induced a subcellular redistribution of R-FABP. In conjunction with the morphogen-binding activity of other FABP family members and their impact on cell migration and tissue differentiation, R-FABP characteristics suggest a regulatory function during retinal histogenesis but not during topographic map formation.

Fluorescence in situ hybridization (FISH) on human chromosomes using photoprobe biotin-labeled probes

Fluorescence in situ hybridization (FISH) on human chromosomes in meta- and interphase is a well-established technique in clinical and tumor cytogenetics and for studies of evolution and interphase architecture. Many different protocols for labeling the DNA probes used for FISH have been published. Here we describe for the first time the successful use of Photoprobe biotin-labeled DNA probes in FISH experiments. Yeast artificial chromosome (YAC) and whole chromosome painting (wcp) probes were tested.

Distribution of Tyrosine Hydroxylase mRNA in the Rat Central Nervous System Visualized by Alkaline Phosphatase in situ Hybridization Histochemistry

The expression of tyrosine hydroxylase mRNA in the rat brain was examined using a novel alkaline phosphatase labelled antisense oligodeoxynucleotide probe. The alkaline phosphatase labelled probe revealed the presence of tyrosine hydroxylase mRNA in all the major cell groups and cell bodies previously described as containing catecholamine fluorescence or known to contain tyrosine hydroxylase immunoreactivity. Using standardized development protocols qualitative comparisons between the amount of mRNA signal in different adrenergic, noradrenergic or dopaminergic cell groups could be made. These studies showed that of the three known catecholaminergic cell types the level of tyrosine hydroxylase mRNA signal was high in the noradrenergic and dopaminergic cells, but much lower in the adrenergic cell groups. The sensitivity of this nonradioactive method of in situ hybridization is excellent and has considerable potential for studies of coexistence or coexpression of two mRNA signals for the localization of mRNA signals at the electron-microscope level.

Intracellular processing and stability of DNA complexed with histidylated polylysine conjugates

BACKGROUND

Glycosylated polylysines and histidylated polylysines complexed with plasmid DNA (pDNA) were proposed to develop polymer-based gene delivery systems. The present work has been undertaken in two steps to study the uptake and the intracellular processing of pDNA, which are still poorly understood in the polyfection pathway.

METHODS AND RESULTS

The kinetics of the uptake and the intracellular processing of pDNA complexed with lactosylated polylysine, histidylated polylysine or histidylated polylysine bearing lactosyl residues (polyplexes) into a CF human airway epithelial cell line were assessed by flow cytometry and confocal microscopy. Complexes formed from histidylated polylysine, even though they were less taken up by cells, show better transfection efficiency with compared with lactosylated complexes. Lactosylated polymers segregated more rapidly when compared with non-lactosylated polymers into compartments different from those containing pDNA on internalization. Intracellular location and pH measurements indicated that polymers ended up in compartments of pH approximately 6.2 while pDNA reached less acidic compartments of pH approximately 6.6. These compartments did not contain the LAMP-1 lysosomal marker.

CONCLUSIONS

The present study exhibits that, upon internalization, pDNA and polylysine conjugates underwent segregation with a rate depending on the polylysine substitution and polymer degradation. The better transfection efficiency of polyplexes with histidylated polylysine can be ascribed to their prolonged stability inside the endocytic vesicles that likely favored the pDNA escape in the cytosol.

Covalent DNA immobilization on polymer-shielded silver-coated quartz crystal microbalance using photobiotin-based UV irradiation

The use of a commercial, silver-coated quartz crystal microbalance (QCM) as a disposable, low-cost, and reliable DNA sensor is presented. This is an incorporation of polymer-based silver electrode shielding and photochemistry-based surface modification for covalent DNA immobilization. To prevent undesired oxidation, the silver electrodes are coated with thin polystyrene films. The polymer surfaces are then modified by a photoreactive biotin derivative (photobiotin) under UV irradiation. The resulting biotin residues on the polymer-shielded surface react with a tetrameric avidin. Consequently a biotin-labeled DNA probe can be immobilized through a biotin-avidin-biotin bridge. A 14-mer single-stranded biotin-DNA probe and a 70-mer single-stranded DNA fragment containing complementary or noncomplementary sequences are used as a model system for DNA hybridization assay on the proposed sensors. The shielding ability of the polystyrene coatings after photo irradiation is investigated. The DNA probe binding capacity, hybridization efficiency, and kinetics are also investigated.

Subtractive hybridization of biotinylated DNA in phenol emulsion

A method of subtractive hybridization using biotinylated DNA and phenol emulsion reassociation technique (PERT) has been proposed. A possibility of combining these techniques has been shown for the first time. The effect of biotinylation degree on the formation of water-insoluble Bio-DNA aggregates was studied. The conditions when Bio-DNA aggregation is actually absent were revealed. A possible use of the above method in hybridization experiments in a wide range of DNA concentrations has been shown. The time of hybridization was 0.5-1 h. The method was approved on a model system, and its possible application for the enrichment of rare mRNA was shown. No less than 300-fold enrichment is achieved for a rare transcript (IL-2) in three cycles of subtractive hybridization.

Genes identified by an expression screen of the vector mosquito Anopheles gambiae display differential molecular immune response to malaria parasites and bacteria

We performed a gene expression screen of the entire transcriptome of the major African malaria vector Anopheles gambiae for immune response genes in adult female mosquitoes, which is the developmental stage infected by malaria parasites. Mosquitoes were immune-stimulated for subtractive cloning by treatment with bacterial lipopolysaccharide, a potent and general elicitor of the innate immune response, and by injury. The screen yielded a highly enriched cDNA library in which more than half of the clones were immune responsive. In this paper, we describe 23 immune-regulated genes, including putative protease inhibitors, serine proteases, regulatory molecules, and a number of genes without known relatives. A molecule related to the protease inhibitor alpha-2-macroglobulin responded strongly to malaria parasite infection, but displayed little or no response to bacteria, whereas other genes exhibited the inverse pattern. These results indicate that the insect immune system discriminates between molecular signals specific to infection with bacteria and malaria parasites.

In vivo gene delivery to tumor cells by transferrin-streptavidin-DNA conjugate

To target disseminated tumors in vivo, transgenes [beta-galactosidase gene, green fluorescence protein (GFP) gene, herpes simplex virus thymidine kinase (HSV-TK)] were conjugated to transferrin (Tf) by a biotin-streptavidin bridging, which is stoichiometrically controllable, and Tf receptor (Tf-R) affinity chromatography, which selects Tf conjugates with intact receptor bindings sites from reacting with the linker. Tf-beta-galactosidase plasmid conjugate thus constructed was specifically transfected to human erythroleukemia cells (K562) via Tf-R without the aid of any lysosomotropic agents. The transfection efficiency of the conjugate was superior to those of lipofection (1% staining) and retroviral vector (5%) and slightly lower than that of adenovirus (70%). The high level of expression with our conjugate was confirmed using other tumor cells (M7609, TMK-1) whereas in normal diploid cells (HEL), which express low levels of Tf-R, expression was negligible. When GFP gene conjugates were systemically administered through the tail vein to nude mice subcutaneously inoculated with tumor, expression of GFP mRNA was found almost exclusively in tumors and to a much lesser extent in muscles, whereas GFP revealed by fluorescence microscopy was detected only in the former. To exploit a therapeutic applicability of this method, suicide gene therapy using Tf-HSV-TK gene conjugate for massively metastasized k562 tumors in severe combined immune-deficient mice was conducted, and a marked prolongation of survival and significant reduction of tumor burden were confirmed. Thus, this method could also be used for gene therapy to disseminated tumors.

Segregation of micrometer-dimension biosensor elements on a variety of substrate surfaces

With the rapid development of micro total analysis systems and sensitive biosensing technologies, it is often desirable to immobilize biomolecules to small areas of surfaces other than silicon. To this end, photolithographic techniques were used to derivatize micrometer-sized, spatially segregated biosensing elements on several different substrate surfaces. Both an interference pattern and a dynamic confocal patterning apparatus were used to control the dimensions and positions of immobilized regions. In both of these methods, a UV laser was used to initiate attachment of a photoactive biotin molecule to the substrate surfaces. Once biotin was attached to a substrate, biotin/avidin/biotin chemistry was used to attach fluorescently labeled or nonlabeled avidin and biotinylated sensing elements such as biotinylated antibodies. Dimensions of 2-10 microm were achievable with these methods. A wide variety of materials, including glassy carbon, quartz, acrylic, polystyrene, acetonitrile-butadiene-styrene, polycarbonate, and poly(dimethylsiloxane), were used as substrates. Nitrene- and carbene-generating photolinkers were investigated to achieve the most homogeneous films. These techniques were applied to create a prototype microfluidic sensor device that was used to separate fluorescently labeled secondary antibodies.

Ultrastructural cytochemical, immunocytochemical and in situ hybridization methods with polyuridine probes detect mRNA in human mast cell granules

Mature human mast cells are classical secretory cells that are filled with secretory-storage granules but are poorly endowed with visible free or membrane-bound cytoplasmic ribosomes. We recently reported close associations of ribosomes and various components essential to RNA metabolism in and close to human mast cell granules using multiple ultrastructural imaging methods. In view of these findings and an increased awareness of RNA sorting and localization to specific subcellular sites and organelles, we used human mast cells purified from non-tumour portions of lung samples resected at surgery for carcinoma and ultrastructural methods to investigate this further. Poly(U) probes were used to detect direct en grid binding, and radiolabelled as well as non-radiolabelled poly(U) probes were used in in situ hybridization protocols to detect poly(A)-positive pre-mRNA and mRNA in nuclear, cytoplasmic and granular compartments of mature human mast cells. Negative controls verified specificity of label; expected nuclear and cytoplasmic locations of poly(A)-positive RNA served as positive controls for each sample. These findings lend support to the hypothesis that site-specific synthesis in secretory-storage granules may occur in secretory cells.

High-density hapten labeling and HRP conjugation of oligonucleotides for use as in situ hybridization probes to detect mRNA targets in cells and tissues

Oligonucleotides that carry a detectable label can be used to probe for mRNA targets in in situ hybridization experiments. Oligonucleotide probes (OPs) have several advantages over cDNA probes and riboprobes. These include the easy synthesis of large quantities of probe, superior penetration of probe into cells and tissues, and the ability to design gene- or allele-specific probes. One significant disadvantage of OPs is poor sensitivity, in part due to the constraints of adding and subsequently detecting multiple labels per oligonucleotide. In this study, we compared OPs labeled with multiple detectable haptens (such as biotin, digoxigenin, or fluorescein) to those directly conjugated with horseradish peroxidase (HRP). We used branching phosphoramidites to add from two to 64 haptens per OP and show that in cells, 16-32 haptens per OP give the best detection sensitivity for mRNA targets. OPs were also made by directly conjugating the same oligonucleotide sequences to HRP. In general, the HRP-conjugated OPs were more sensitive than the multihapten versions of the same sequence. Both probe designs work well both on cells and on formaldehyde-fixed, paraffin-embedded tissues. We also show that a cocktail of OPs further increases sensitivity and that OPs can be designed to detect specific members of a gene family. This work demonstrates that multihapten-labeled and HRP-conjugated OPs are sensitive and specific and can make superior in situ hybridization probes for both research and diagnostic applications.

Micrometer dimension derivatization of biosensor surfaces using confocal dynamic patterning

Using laser scanning confocal optics in conjunction with avidin/biotin technology, micrometer-sized patterns of biomolecules were fabricated on glassy-carbon and fused-silica surfaces. Photoactive biotin was immobilized using the 325-nm line of a Helium-Cadmium laser, which was focused through a 25x or 100x quartz microscope objective. A three-dimensional piezoelectric micromanipulator was used to position the sample surface in the focal plane of the microscope objective and to create patterns on the focused surface. Biotin patterns with line widths of 5-20 microns were produced by varying the scan speed of the micromanipulator while exposing the surface to the laser. The integrity of the immobilized biotin was confirmed by subsequent derivatization with fluorescently labeled avidin. Fluorescence microscopy with a cooled charge coupled device (CCD) imaging system was used to visualize the distribution of biotin and fluorescent avidin within the patterns created by the laser.

Binding of the protein disulfide isomerase isoform ERp60 to the nuclear matrix-associated regions of DNA

Protein ERp60, previously found in the internal nuclear matrix in chicken liver nuclei, is a member of the protein disulfide isomerase family. It binds DNA and double helical polynucleotides in vitro with a preferential recognition toward the matrix-associated regions of DNA and poly(dA) x poly(dT), and its binding is inhibited by distamycin. ERp60 can be cross-linked chemically to DNA in the intact nuclei, suggesting that its association with DNA is present in vivo. As a whole, these results indicate that ERp60 is a component of the subset of nuclear matrix proteins that are responsible for the attachment of DNA to the nuclear matrix and for the formation of DNA loops. A distinctive feature of this protein, which has two thioredoxin-like sites, is that its affinity to poly(dA) x poly(dT) is strongly dependent on its redox state. Only its oxidized form, in fact, does it bind poly(dA) x poly(dT). The hypothesis can be made that through the intervention of ERp60, the redox state of the nucleus influences the formation or the stability of some selected nuclear matrix-DNA interactions.

Monitoring impurities in biopharmaceuticals produced by recombinant technology

The unique nature of recombinant technology and the biotherapeutic production process means that regulatory agencies around the world not only require extensive characterization of the product, but they have also provided 'guidelines' to control and monitor product- and process-derived impurities and contaminants. Not only might these impurities and contaminants have a profound effect on product quality and efficacy, but they might also introduce unwanted and unknown side effects, even in trace amounts. The authors present a comprehensive understanding of the nature of possible product- and process-related impurities, and also describe current and future methodologies to control and monitor these impurities.

Quantitative aspects of an in situ hybridization procedure for detecting mRNAs in cells using 96-well microplates

The universal quantitation of the DNA hybridization reaction has been a goal sought by many researchers. Part of this search has been the need to develop a rapid, sensitive, easy-to-perform, and quantitative method to measure the abundance of specific mRNAs directly within cells. Conventionally mRNA detection can be done by advanced quantitative in situ hybridization (ISH) using either image analysis or fluorescence in situ hybridization (FISH), or indirectly by extraction of mRNA from cells or tissue and using Northern blot or quantitative polymerase chain reaction (PCR). We examined the quantitative nature of probe binding to intracellular mRNA in a sensitive and easy-to-use nonisotopic method of ISH previously developed in our laboratories. The method is applicable to isolated primary cells or cells in culture. The procedural details are very simple, with cells being centrifuged into 96-well microplates, fixed with formalin, and pretreated with Triton X-100 and Nonidet P-40 before photobiotin-labeled cDNA probes are applied. Biotin from the hybridization of probe to target is detected using multiple applications of streptavidin and biotinylated alkaline phosphatase and visualized by the p-nitrophenyl phosphate conversion method. The quantitative parameters of the ISH procedure were determined by measuring the levels of expression of erythropoietin (EPO) mRNA and its translated protein in transfected COS-7 cells. There is a log-linear relationship between the levels of signal obtained in the ISH reaction in 96-well microplates and the EPO protein levels measured by enzyme-linked immunosorbent assay (ELISA). This demonstrated relationship is important in the standardization and use of these procedures to measure quantitatively mRNAs within cells.