In situ hybridization at the electron microscope level: hybrid detection by autoradiography and colloidal gold

Ultrastructural visualization of cytoskeletal mRNAs and their associated proteins using double-label in situ hybridization

We have been able to visualize cytoskeletal messenger RNA molecules at high resolution using nonisotopic in situ hybridization followed by whole-mount electron microscopy. Biotinated cDNA probes for actin, tubulin, or vimentin mRNAs were hybridized to Triton-extracted chicken embryo fibroblasts and myoblasts. The cells were then exposed to antibodies against biotin followed by colloidal gold-conjugated antibodies and then critical-point dried. Identification of mRNA was possible using a probe fragmented to small sizes such that hybridization of several probe fragments along the mRNA was detected as a string of colloidal gold particles qualitatively and quantitatively distinguishable from nonspecific background. Extensive analysis showed that when eight gold particles were seen in this iterated array, the signal to noise ratio was greater than 30:1. Furthermore, these gold particles were colinear, often spiral, or circular suggesting detection of a single nucleic acid molecule. Antibodies against actin, vimentin, or tubulin proteins were used after in situ hybridization, allowing simultaneous detection of the protein and its cognate message on the same sample. This revealed that cytoskeletal mRNAs are likely to be extremely close to actin protein (5 nm or less) and unlikely to be within 20 nm of vimentin or tubulin filaments. Actin mRNA was found to be more predominant in lamellipodia of motile cells, confirming previous results. These results indicate that this high resolution in situ hybridization approach is a powerful tool by which to investigate the association of mRNA with the cytoskeleton.

An alternative nonradioactive method for labeling DNA using biotin

An alternative nonradioactive labeling method and a highly sensitive technique for detecting specific DNA sequences are described. The labeling method requires the "Klenow" fragment of DNA polymerase I and random hexanucleotides (synthesized or naturally extracted) as a primer for the production of highly sensitive DNA probes. The system has three main steps: (i) labeling of DNA with biotinylated 11-dUTP; (ii) detection of biotinylated DNA by a one-step procedure with streptavidin-alkaline phosphatase complex; (iii) blocking of background with Tween 20. Twenty attograms (2 X 10(-17) g) of pBR322 plasmid DNA was detected by dot-blot hybridization. Upon Southern blot hybridization, 7.4 fg (7.4 X 10(-15) g) of pBR322 HindIII DNA was detected using the biotinylated pBR322 plasmid DNA probe; 40.8 ag and 7.4 fg of lambda HindIII DNA were detected with the biotinylated whole lambda DNA probe by dot and Southern blot hybridization, respectively. Specific bands were also detected with the biotinylated argininosuccinolyase probe upon Northern blotting of mouse poly(A+) RNA. Further applications for in situ hybridization are also described.

In situ hybridization of biotinylated DNA probes to cotton meiotic chromosomes

A modified procedure for in situ hybridization of biotinylated probes to meiotic chromosomes of cotton has been developed with high retention of squashed cells on slides, preservation of acid-fixed chromosome morphology, exceptionally low levels of background precipitate at nonspecific hybridization sites and improved photomicrographic recording. Salient features of the techniques include pretreatment of slides before squashing, cold storage of squash preparations, and use of interference filters for distinguishing precipitate from chromatin. A cloned 18S/28S ribosomal DNA fragment from soybean was biotinylated via nick-translation and hybridized to microsporocyte meiotic chromosomes of cotton (Gossypium hirsutum L. and G. hirsutum L. X G. barbadense L.). Enzymatically formed precipitate from streptavidin-bound peroxidase marked the in situ hybridization. In situ hybridization of biotinylated probes to cotton meiotic chromosomes adds the specificity and resoltion of in situ hybridization to the chromosomal and genomic perspectives provided by meiotic cytogenetic analyses. Molecular cytogenetic analyses of meiotic cells offer certain inherent analytical advantages over analyses of somatic cells, e.g., in terms of mapping, and for studying fundamental biological and genetic problems, particularly for organisms that are not amenable to somatic karyotypic analysis.

Strategies for ultrastructural visualization of biotinated probes hybridized to messenger RNA in situ

A progressive development of the application of in situ methodology to ultrastructural procedures has resulted in the ability to detect individual molecules of mRNA with high probability. Beginning with whole-mount cells and then developing myotubes, both in culture and detergent extracted before fixation, we were able to progress to methods which allow detection of mRNA in tissue sections. Initial results confirm that the detection of mRNA in thin-sectioned tissue is very similar to observations on the extracted, cultured cells, and that the same methods of data analysis apply. Current work is devoted to the application of the methodology to other cellular structures, such as the nucleus, and to other tissue-probe systems, such as brain. Acknowledgements. The authors appreciate the skilled help from John McNeil and Shirwin Pockwinse in the laborious and time-consuming preparations of material and photography. FS was on sabbatical leave from the Department of Pathology at Southwestern Medical Center.

Comparative evaluation of non-radioactive in situ hybridization techniques for pathologic diagnosis of viral infection

We have compared the efficiency of biotinylated DNA probes and various visualization techniques with 35S-labeled DNA probes in routine paraffin sections from the pathology service; both autopsy and biopsy tissue were investigated. Probes included DNA genomic fragments from cytomegalovirus (CMV), Epstein-Barr-Virus (EBV) and human immunodeficiency virus (HIV). Methods of detection by Pathogene II kit (ENZO) and Blue Gene kit (BRL) with visualization by AEC, NBT/BCIP, Immunogold (Janssen) and autoradiography were used. The study shows most satisfactory results by applying the Blue Gene-NBT/BCIP combination followed by the Immunogold technique. Data obtained by these techniques compare well to those of using radioactive DNA probes and autoradiography.

Plaque-lift testing of expression vector lambda gt11 with gold-labeled immunoglobulins

Colloidal gold particles were coated with affinity-purified antibodies against the human plasma protein, C1 inhibitor, and used to probe for fusion proteins of C1 inhibitor with beta-galactosidase encoded by recombinant bacteriophage lambda gt11 DNA. Plaque-lift tests were done with recombinant proteins immobilized on nitrocellulose applying anti-C1 inhibitor gold particles followed by the silver enhancement treatment. This procedure resulted in a sensitive and specific staining of the recombinant proteins and allowed the selective detection of relevant clones in a complex cDNA expression library. Under optimized conditions, plaque-lift testing was completed within 2.5 h after removal of nitrocellulose filters from the plate. Hence, the immunogold detection method provides an alternative to conventional enzyme- or radionuclide-based screening procedures for cDNA expression libraries.

Detection of proopiomelanocortin mRNA by in situ hybridization, using a biotinylated oligodeoxynucleotide probe and avidin-alkaline phosphatase histochemistry

A synthetic 24-mer oligodeoxynucleotide complementary to the region of proopiomelanocortin (POMC) mRNA that codes for the MSH core sequence (alpha MSH/ACTH[4-11]), was synthesized and labelled in the 3'-end by use of terminal transferase. Probes tailed with either [3H]- or biotin-labelled nucleotides could be used for in situ hybridization studies. Biotinylated probes, hybridized to mouse and rat pituitary sections, were detected by avidin-alkaline phosphatase or streptavidin-alkaline phosphatase procedures and development in 5-bromo-4-chloro-3-indolyl phosphate (BCIP)-nitroblue tetrazolium (NBT). Proteinase K pretreatment of sections produced a drastic enhancement of the signal obtained, particularly in strongly fixed, paraffin-embedded material. The non-radioactive in situ hybridization technique compared favourably to radioactive in situ hybridization in terms of rapidity and precision of the localization. Controls involved deletion of the probe to prove that other components of the reaction sequence did not yield stain, digestion with RNase to prove that tissue RNA was necessary to bind the probe, prehybridization (blocking) with unlabelled probe to prove that the biotinylated probe reacted with its anti-sense region and not its tail and Northern blotting to show that the probe reacted with only one species of pituitary RNA, having the size of mouse pituitary POMC mRNA. In addition, adrenalectomy, known to increase anterior lobe POMC levels, resulted in both increased numbers and increased intensity of positive corticotroph-like cells. Synthetic oligodeoxynucleotides labelled with biotin appear to constitute attractive reagents for in situ hybridization studies when supported by appropriate control procedures.

Multiple peptide production and presence of general neuroendocrine markers detected in 12 cases of human phaeochromocytoma and in mammalian adrenal glands

In this study, antibodies to a range of markers of neuroendocrine differentiation were evaluated for their use in the histopathological assessment and characterisation of phaeochromocytomas. Routinely processed wax blocks from eleven adrenal phaeochromocytomas (10 benign and 1 malignant) and one benign phaeochromocytoma of the urinary bladder were investigated. In addition to these tumours, normal human, cat and piglet adrenal glands were examined. In the phaeochromocytomas, immunostaining was obtained with 21 of the 25 antisera used. Of the general neuroendocrine markers, neuron-specific enolase was found in all tumours, and chromogranin and protein gene-product 9.5 in most of the cases. A range of regulatory peptide immunoreactivities could be demonstrated, such as enkephalin, neuropeptide tyrosine (NPY), 7B2, galanin and vasoactive intestinal polypeptide (VIP). In addition, two peptides were found which have not been reported previously in these tumours, peptide histidine methionine (PHM) and the cryptic fragment of the precursor encoding VIP. Co-localisation studies revealed that peptides derived from the same precursor or peptide family were found in the same tumour cells (e.g. VIP and PHM, NPY and its C-flanking peptide CPON). In the normal adrenal medulla, all the peptides previously reported to be present could be demonstrated immunocytochemically. Galanin was present in a subpopulation of cells also immunoreactive for enkephalin. Neuropeptide tyrosine and CPON were demonstrated in another subpopulation. Occasionally, cells were found to contain all four antigen immunoreactivities. Using antisera to enzymes involved in catecholamine synthesis, galanin was found to be present in noradrenaline-containing cells. The study demonstrates the presence of various antigens in chromaffin tissue of the adrenal gland. A range of substances can also be identified immunocytochemically in phaeochromocytoma tissue, using routinely-processed material.

Non-radioactive in situ hybridization. A comparison of several immunocytochemical detection systems using reflection-contrast and electron microscopy

A number of immunocytochemical detection systems for determining the chromosomal localization of specific nucleic acid sequences by non-radioactive in situ hybridization have been compared. The procedures were: 1. the peroxidase/diaminobenzidine (PO/DAB) combination, either or not gold/silver intensificated; 2. alkaline phosphatase marking using the nitro-blue tetrazolium plus bromochloro-indolyl phosphate substrate combination (AP/NBT + BCIP); and 3. immunogold with or without silver enhancement. The procedures were first tested and optimized in dot blot experiments and then applied to in situ hybridization. As hybridization probes, both a middle-repetitive and a unique sequence (modified with 2-acetylaminofluorene (AAF] were used. The advantages and disadvantages of the various methods for reflection contrast (RC) or transmission electron microscopic (TEM) visualization of hybrids are discussed.

Hybridization histochemistry

The location of gene expression by hybridization histochemistry is being applied in many areas of research and diagnosis. The aim of this technique is to detect specific mRNA in cells and tissues by hybridization with a complementary DNA or RNA probe. Requirements for optimal specificity, sensitivity, resolution and speed of detection may not all be encompassed in one simple technique suitable for all applications, thus appropriate procedures should be selected for specific objectives. With reference to published procedures and our own extensive experience, we have evaluated fixatives, probes, labels and other aspects of the technique critical to the preservation and hybridization in situ of mRNA and detection and quantitation of hybrids.

Molecular diagnosis of infectious diseases by nucleic acid hybridization

Diagnostic microbiology has traditionally relied on the cultivation of an infecting agent in an in vitro system. However, the limitations of these methods have led to the development of alternative, molecular techniques which can detect specific microbial proteins or nucleic acids directly in body fluids. One such method, nucleic acid hybridization, has many attractive features including the potential for high sensitivity and specificity, the detection of a chemically stable analyte and the use of uniform reagents. Nucleic acid hybridization reactions have been used to detect a variety of microbial pathogens in assay formats using extracted nucleic acids or tissue sections. However, wider application of these techniques is limited by the fact that current methods employ radioisotopically labelled probes and cumbersome assay procedures. Solutions to these problems have been sought by the development of non-radioactive hybridization techniques which utilize enzymatic detection methods and by the development of rapid hybridization assays performed in solution. Further improvements in labelling techniques, assay formats and enzymatic detection methods should allow for the wider application of nucleic acid hybridization reactions in diagnostic microbiology.

Mouse satellite DNA, centromere structure, and sister chromatid pairing

The experiments described were directed toward understanding relationships between mouse satellite DNA, sister chromatid pairing, and centromere function. Electron microscopy of a large mouse L929 marker chromosome shows that each of its multiple constrictions is coincident with a site of sister chromatid contact and the presence of mouse satellite DNA. However, only one of these sites, the central one, possesses kinetochores. This observation suggests either that satellite DNA alone is not sufficient for kinetochore formation or that when one kinetochore forms, other potential sites are suppressed. In the second set of experiments, we show that highly extended chromosomes from Hoechst 33258-treated cells (Hilwig, I., and A. Gropp, 1973, Exp. Cell Res., 81:474-477) lack kinetochores. Kinetochores are not seen in Miller spreads of these chromosomes, and at least one kinetochore antigen is not associated with these chromosomes when they were subjected to immunofluorescent analysis using anti-kinetochore scleroderma serum. These data suggest that kinetochore formation at centromeric heterochromatin may require a higher order chromatin structure which is altered by Hoechst binding. Finally, when metaphase chromosomes are subjected to digestion by restriction enzymes that degrade the bulk of mouse satellite DNA, contact between sister chromatids appears to be disrupted. Electron microscopy of digested chromosomes shows that there is a significant loss of heterochromatin between the sister chromatids at paired sites. In addition, fluorescence microscopy using anti-kinetochore serum reveals a greater inter-kinetochore distance than in controls or chromosomes digested with enzymes that spare satellite. We conclude that the presence of mouse satellite DNA in these regions is necessary for maintenance of contact between the sister chromatids of mouse mitotic chromosomes.

Chinese hamster cells with a minichromosome containing the centromere region of human chromosome 1

We describe a series of primary and secondary hamster-human hybrids which have selectively retained a small amount of human DNA. The hybrid XJM12.1.3 contains an estimated 4000-8000 kb of human DNA, and for a secondary hybrid derived from it, XEW8.2.3, our estimate is 1000-2000 kb. The hybridization of Southern blots of DNA from these hybrids with a variety of human satellite DNA probes reveals that these lines include centromere sequences of human chromosome 1. The identifiable human DNA is in the form of a minichromosome, as detected by in situ hybridization in the light microscope and in the electron microscope. At mitosis, the minichromosome can be observed to have kinetochores and to be associated with microtubules. Therefore, it can segregate in a stable fashion. It may be significant that in the selection of the hybrids we had selected for a human gene which has been mapped on human chromosome 1.

In situ hybridization at the electron microscope level: localization of transcripts on ultrathin sections of Lowicryl K4M-embedded tissue using biotinylated probes and protein A-gold complexes

A technique has been developed for localizing hybrids formed in situ on semi-thin and ultrathin sections of Lowicryl K4M-embedded tissue. Biotinylated dUTP (Bio-11-dUTP and/or Bio-16-dUTP) was incorporated into mitochondrial rDNA and small nuclear U1 probes by nick-translation. The probes were hybridized to sections of Drosophila ovaries and subsequently detected with an anti-biotin antibody and protein A-gold complex. On semi-thin sections, probe detection was achieved by amplification steps with anti-protein A antibody and protein A-gold with subsequent silver enhancement. At the electron microscope level, specific labeling was obtained over structures known to be the site of expression of the appropriate genes (i.e., either over mitochondria or over nuclei). The labeling pattern at the light microscope level (semi-thin sections) was consistent with that obtained at the electron microscope level. The described nonradioactive procedures for hybrid detection on Lowicryl K4M-embedded tissue sections offer several advantages: rapid signal detection: superior morphological preservation and spatial resolution; and signal-to-noise ratios equivalent to radiolabeling.

Gene mapping on human metaphase chromosomes by in situ hybridization with 3H, 35S, and 32P labeled probes and transmission electron microscopy

A method based on in situ hybridization, autoradiography and transmission electron microscopy for mapping genes on human metaphase chromosomes is presented. Successful mapping of the tandemly repeated rDNA genes and of two nucleic acid probes, N-myc and probe 3 (Kanda et al. 1983), that are amplified in a homogeneously staining region (HSR) of the neuroblastoma cell line, IMR-32 is described. By using sufficiently thin AgBr emulsions, it is possible to obtain observable grains and good resolution with probes radiolabeled with 3H, 35S, or 32P, but the former gives the best results. We observe that neither of the two probes, N-myc and probe 3, has a uniform spatial distribution along the HSR and that the distributions of the two probes differ from each other. These observations support previous studies which indicated that the formation of an HSR is a more complex process than uniform amplification of a single DNA segment to form an n-fold set of perfect tandem repeats. The present study shows that the electron microscopic method is useful for extending the results of light microscopic studies for problems where higher resolution mapping is needed.

Controlled growth of colloidal gold particles and implications for labelling efficiency

A new method is reported for the preparation of colloidal gold particles with diameters ranging between 5 and 12 nm. The initial gold particle population, with an average diameter of 5.6 +/- 0.9 nm, is prepared by reduction of chloroauric acid with white phosphorous. An increase in particle diameter by growth is obtained by reduction of chloroauric acid with white phosphorous in the presence of colloidal gold particles. The labelling efficiency of these gold particles, conjugated with protein A, in indirect immunolabelling experiments is investigated by labelling of beta-galactosidase on ultrathin cryosections of Escherichia coli cells. We demonstrate that the labelling efficiency is at least dependent on particle diameter, probe concentration and preparation method. In addition it is shown, that with this new method, gold particle populations can be prepared with minor overlap in diameter spreading. Therefore these gold probes are suitable for qualitative double labelling experiments. The quantitative aspect of immunolabelling is discussed.

The use of submicroscopic gold particles combined with video contrast enhancement as a simple molecular probe for the living cell

We describe a new approach to probe the molecular biology of the living cell that uses small colloidal gold particles coupled to specific ligands. They are visualized in cells by bright-field, video enhanced contrast microscopy. We describe the basic aspects of the technique and provide examples of applications to intracellular motility, cell membrane dynamics, receptor translocation, internalization, and intracellular routing. We also provide examples of the use of this approach in immunospecific labelling of cells and tissue sections.

Detection of sub-picogram quantities of specific DNA sequences on blot hybridization with biotinylated probes

A sensitive method for detecting biotinylated DNA probes on dot and Southern blots is described which is based on the principle outlined by Leary et al (1). This system has two main components: detection of biotinylated DNA by a two-step procedure with streptavidin and poly(alkaline phosphatase); and blocking background with Tween 20. 32fg and 80fg of lambda phage DNA was detected on dot and Southern blot hybridizations respectively. 150fg of beta-globin was detected on Southern blots of genomic DNA. This method is fast, reproducible and can detect single copy genes in 0.25 micrograms genomic DNA on Southern blots.

Detection of species specific chromosomes in somatic cell hybrids

We describe an in situ hybridization technique which allows rapid identification of species-specific chromosomes in somatic cell hybrid lines. Chromosome preparations from rodent-human hybrid lines are hybridized to biotinylated total human DNA which is subsequently detected by a series of immunocytochemical reactions which culminate in a peroxidase reaction visible by light microscopy. This technique not only allows identification of intact human chromosomes but also fragmented and rearranged human chromosomal segments. We have detected as little as 1 X 10(7) bp of human DNA inserted into a mouse chromosome using this procedure and estimate that the sensitivity of the technique would allow detection of sequences 5- to 10-fold smaller. The usefulness of the technique for screening hybrid cell gene mapping panels is discussed.

High resolution mapping of in situ hybridized biotinylated DNA to surface-spread Drosophila polytene chromosomes

We describe a method of mapping genes or transcripts on polytene chromosomes by transmission electron microscopy. We present several applications which illustrate that, in favorable cases, the method has a resolution of ca. 10 kg, and that high resolution mapping of hybridization sites relative to bands and puffs can be achieved. We mapped sites of transcription for poly-(A) RNA and present evidence which shows that these sites are localized in some bands and puffs, but are also found in interbands.

Hybridization histochemistry

In this review we have used our own recent work as a flagship to illustrate the recent renaissance of interest in hybridization histochemistry. A trickle of papers followed the initial key excursion into the in situ labeling of tissue sections (48-50). Our own entry into this field started in 1978 and since then a confluence of important questions and technical advances has served to make hybridization histochemistry much more attractive as a research tool. Hybridization histochemistry is able to solve some problems for which there is no other suitable technique at this time. Hybridization histochemistry provides the location of anatomical sites of gene expression, and viral replication, with uniquely high specificity. We have taken 32P-labeled probes to what appears to be their limit of resolution, which is single cells in thin sections. While 32P has clear disadvantages, exposure time is relatively short and the use of fast-X-ray film to preview the results and estimate exposure time for emulsion has been turned to advantage. Our introduction (27) of the use of whole-mouse sections in hybridization histochemistry has great potential in hormonal, enzymatic, and growth factor gene expression and will no doubt prove of great use in developmental studies and examination of viral infection. The use of synthetic DNA (synthetic oligonucleotides) unshackles the technique from the need for an associated molecular biology laboratory and at once widens the horizon of application of the technique. Although hybridization histochemistry is a valuable research tool which will soon find a niche in many fields, in a short time it should become a key diagnostic aid. It may well become the method of preference for detection of the expression of oncogenes and other cancer-related genes and for viruses which for other reasons are difficult to detect.

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

A photo-activatable analogue of biotin, N-(4-azido-2-nitrophenyl)-N'-(N-d-biotinyl-3-aminopropyl)-N'-methyl-1,3- propanediamine (photobiotin), has been synthesized and used for the rapid and reliable preparation of large amounts of stable, non-radioactive, biotin-labelled DNA and RNA hybridization probes. Upon brief irradiation with visible light, photobiotin formed stable linkages with single- and double-stranded nucleic acids yielding probes which were purified from excess reagent by 2-butanol extraction and ethanol precipitation. Using single-stranded phage M13 DNA probes chemically labelled with one biotin per 100-400 residues and dot-blot hybridization reactions on nitrocellulose, as little as 0.5 pg (6 X 10(-18) mol) of target DNA was detected colorimetrically by avidin or streptavidin complexes with acid or alkaline phosphatase from three commercial sources. The sensitivity of detection of target RNA in dot-blots and Northern blots was equivalent to that obtained with 32p-labelled DNA probes. Photobiotin was also used for the labelling of proteins with biotin.

Ultrastructural features of minute chromosomes in a methotrexate-resistant mouse 3T3 cell line

The Miller spreading procedure was applied to mouse metaphase spreads of methotrexate-resistant 3T3 cells that contain large numbers of minute chromosomes and dihydrofolate reductase genes. There is substantial variation in both size and numbers of minutes in individual cells, the smallest of which (estimated as 5 X 10(3) kilobase pairs) would be undetected by standard light microscopic analyses. Minute chromosomes are composed of nucleosomal chromatin, which is organized into typical higher order fibers that are folded to form rosette-like structures characteristic of normal chromosome organization. There is no evidence that the DNA in minutes is linear. Minutes exist singly and in pairs, and members of a pair are connected by higher order chromatin fibers, suggesting that they are topologically interlocked. They are often closely apposed to chromosomal telomeres or arms, a configuration that may be involved in their distribution at mitosis. In addition to typical minutes, which do not possess kinetochores, a small marker chromosome possessing all of the features of a centromere region is present in parental and resistant cells. An unusual feature of this cell line is the retention of resistance, minute chromosomes, and amplified dihydrofolate reductase genes; most methotrexate-resistant mouse cell lines with minute chromosomes lose these properties when grown in the absence of methotrexate.

Chemical and enzymatic biotin-labeling of oligodeoxyribonucleotides

Biotin has been converted to 2-(biotinylamido)ethanol and condensed to phosphorylated oligonucleotides in a solid phase synthesis. The 5'-biotinylated oligonucleotides were enzymatically coupled to other DNA fragments by T4 DNA ligase or T4 RNA ligase. The hybridization properties of such biotin-labeled oligonucleotide probes were studied.

Chromosomal location of a major tRNA gene cluster of Xenopus laevis

In Xenopus laevis, genes encoding tRNAPhe, tRNATyr, tRNAMet1, tRNAAsn, tRNAAla, tRNALeu, and tRNALys are clustered within a 3.18-kb (kilobase) fragment of DNA. This fragment is tandemly repeated some 150 times in the haploid genome and its components are found outside the repeat only to a limited extent. The fragment hybridizes in situ to a single site very near the telomere on the long arm of one of the acrocentric chromosomes of the group comprising chromosomes 13-18. All the chromosomes of this group also hybridize with DNA coding for oocyte-specific 5S RNA. The tRNA gene cluster is slightly proximal to the cluster of 5S RNA genes.

2-Acetylaminofluorene-modified probes for the indirect hybridocytochemical detection of specific nucleic acid sequences

A new approach is presented for the indirect hybridocytochemical localization of specific nucleic acid sequences in microscopic preparations. The method is based on the application of probes modified with N-acetoxy-2-acetylaminofluorene. After hybridization, the 2-acetylaminofluorene-labelled probes are recognized by antibodies directed against modified guanosine and visualized immunocytochemically. This procedure has been optimized on two model objects: mouse satellite DNA in interphase nuclei and chromosomes, and kinetoplast DNA in Crithidia fasciculata. A first application that may be of clinical importance is given by the detection of human cytomegalovirus in infected human lung fibroblasts. Other potentials of this procedure are discussed. Its advantages are: (1) the simple, rapid and reproducible labelling procedure; (2) the high stability of both label and modified probes; (3) the feasibility of labelling both double-stranded (ds) and single-stranded (ss) probes (DNA as well as RNA); (4) the rapid and sensitive detection of hybrids.

Different central nervous system cell types display distinct and nonrandom arrangements of satellite DNA sequences

Paraformaldehyde-fixed tissue from mouse cerebellum was hybridized with biotin-labeled satellite DNA for identification of centromeres. By using avidin-peroxidase conjugates, it was possible to define the nuclear position of centromeres at the ultrastructural level. Three-dimensional analysis of well-resolved centromere arrays were aided by computer reconstruction of serial sections. Different cell types displayed distinct, nonrandom centromere locations. In Purkinje neurons, the majority of detected sequences were clustered together around the central nucleolus, whereas in granule neurons, more numerous, dispersed centromere clusters were associated with the nuclear membrane. In Purkinje cells, peroxidase-labeled regions corresponded to dense heterochromatic aggregates were detected in Purkinje cells of several different species. These observations suggest that in these highly differentiated cells, the nuclear position of centromeres is maintained in evolution despite species differences in centromeric DNA sequence. Such defined ordering of centromeres may be integral to specific functional capacities.

U1 small nuclear RNA genes are located on human chromosome 1 and are expressed in mouse-human hybrid cells

The majority, and perhaps all, of the genes for human U1 small nuclear RNA (U1 RNA) were shown to be located on the short arm of human chromosome 1. These genes were mapped by Southern blot analysis of DNA from rodent-human somatic cell hybrids, using the 5' region of a human U1 RNA gene as a human-specific probe. This probe hybridized to DNA fragments present only in digests of total human DNA or to the DNAs of cell lines which contained human chromosome 1. The major families of human U1 RNA genes were identified, but some human genes may have gone undetected. Also, the presence of a few U1 RNA genes on human chromosome 19 could not be ruled out. In spite of the lack of extensive 5'-flanking-region homology between the human and mouse U1 RNA genes, the genes of both species were efficiently transcribed in the hybrid cells, and the U1 RNAs of both species were incorporated into specific ribonucleoprotein particles.

U1 small nuclear RNA genes are located on human chromosome 1 and are expressed in mouse-human hybrid cells

The majority, and perhaps all, of the genes for human U1 small nuclear RNA (U1 RNA) were shown to be located on the short arm of human chromosome 1. These genes were mapped by Southern blot analysis of DNA from rodent-human somatic cell hybrids, using the 5' region of a human U1 RNA gene as a human-specific probe. This probe hybridized to DNA fragments present only in digests of total human DNA or to the DNAs of cell lines which contained human chromosome 1. The major families of human U1 RNA genes were identified, but some human genes may have gone undetected. Also, the presence of a few U1 RNA genes on human chromosome 19 could not be ruled out. In spite of the lack of extensive 5'-flanking-region homology between the human and mouse U1 RNA genes, the genes of both species were efficiently transcribed in the hybrid cells, and the U1 RNAs of both species were incorporated into specific ribonucleoprotein particles.

Rapid and sensitive colorimetric method for visualizing biotin-labeled DNA probes hybridized to DNA or RNA immobilized on nitrocellulose: Bio-blots

Biotin-labelled DNA probes, prepared by nick-translation in the presence of biotinylated analogs of TTP, are hybridized to DNA or RNA immobilized on nitrocellulose filters. After removal of residual probe, the filters are incubated for 2--5 min with a preformed complex made with avidin-DH (or streptavidin) and biotinylated polymers of intestinal alkaline phosphatase. The filters are then incubated with a mixture of 5-bromo-4-chloro-3-indolyl phosphate and nitro blue tetrazolium, which results in the deposition of a purple precipitate at the sites of hybridization. This procedure will detect target sequences in the 1- to 10-pg range after enzyme incubation periods of 1 hr or less. The incubation period can be extended up to 24 hr, if required, to increase the color intensity of the hybridization signal. Furthermore, at high probe concentrations (250--7560 ng/ml), biotin-labeled DNA exhibits lower nonspecific binding to nitrocellulose than does radiolabeled DNA, so hybridization times required for the analysis of unique mammalian gene sequences can be decreased to 1--2 hr. This nonradiographic method of probe detection should be of general utility for genetic studies using Southern, RNA, or dot-blot hybridization protocols.

Detection of viral genomes in cultured cells and paraffin-embedded tissue sections using biotin-labeled hybridization probes

A method of in situ cytohybridization is described for the detection of specific viral genomes in infected cell cultures or paraffin-embedded tissue sections without the use of radioisotopes. Biotin-labeled analogs of TTP are incorporated into viral DNA in vitro by nick translation and the resultant DNA probes hybridized to cytologic samples. Cells containing viral genetic material are then revealed by standard immunofluorescence, immunoperoxidase, or affinity cytochemical techniques that are based on the specific interaction between biotin and antibiotin IgG or avidin. Hybridization probes containing nucleotides that have an 11- or 16-atom spacer arm between the biotin molecule and the pyrimidine ring interact with these detector proteins more efficiently than probes containing biotin-nucleotides with a 4-atom spacer arm. The total procedure can be performed fairly rapidly (24 hr or less) and numerous samples can be processed simultaneously. Although the detection methods employed to date are not as sensitive as autoradiographic procedures with high specific activity probes, more sensitive protein detector complexes are currently being constructed. The speed, specificity, and resolving power of this technique should be of general utility in screening for the presence of infectious agents in cell or tissue samples. Here we report the visualization of parvovirus, polyomavirus, herpes simplex virus, adenovirus, and retrovirus genetic material in infected cell cultures and herpes simplex and adenovirus DNA in paraffin-embedded autopsy tissues.

High-resolution mapping of satellite DNA using biotin-labeled DNA probes

We have developed a novel method for high resolution mapping of specific DNA sequences after in situ hybridization. DNA probes, labeled with biotin-nucleotides in conventional nick-translation reactions, are hybridized to cytological preparations and detected with affinity-purified rabbit antibiotin antibodies followed by antibodies to rabbit IgG that are conjugated to fluorescent or enzymatic reagents. Using peroxidase labeled anti-rabbit IgG, we are able to detect and localize specific sequences at both the light and electron microscopic levels. Initial studies were done with repeated DNA sequences previously mapped by light microscope autoradiography to assess the fidelity and resolution of this method. An analysis using biotin-labeled mouse satellite DNA is presented here.