An electron microscopic method for studying nucleic acid-protein complexes. Visualization of RNA polymerase bound to the DNA of bacteriophages T7 and T3

TrpY regulation of trpB2 transcription in Methanothermobacter thermautotrophicus

TrpY binds specifically to TRP box sequences upstream of trpB2, but the repression of trpB2 transcription requires additional TrpY assembly that is stimulated by but not dependent on the presence of tryptophan. Inhibitory complex formation is prevented by insertions within the regulatory region and by a G149R substitution in TrpY, even though TrpY(G149R) retains both TRP box DNA- and tryptophan-binding abilities.

Electron microscopy of DNA-protein complexes and chromatin

This article focused on a number of aspects of the preparation of chromatin and other DNA-protein complexes for conventional transmission EM that are critical for success but may not have been addressed in a single chapter before. These include the importance of optimizing fixation, the generation of active supporting supports, and the use of negative staining as a means of obtaining higher resolution detail than can be garnered from shadow casting methods.

A long purine-pyrimidine homopolymer acts as a transcriptional diode

Polypurine-polypyrimidine (R.Y) sequences have the unusual ability to form DNA triple helices. Such tracts are overrepresented upstream of eukaryotic genes, although a function there has not been clear. We report that transcription in vitro into one such upstream R.Y tract in the direction that makes a predominantly purine RNA is effectively blocked by formation of an intramolecular triple helix. The triplex is triggered by transcription and stabilized by the binding of nascent purine RNA to the template. Transcription in the opposite direction is not restricted. Polypurine-polypyrimidine DNA may provide a dynamic and selective block to transcription without the aid of accessory proteins.

Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope

Reproducible images of uncoated DNA in the atomic force microscope (AFM) have been obtained by imaging plasmid DNA on mica in n-propanol. Specially sharpened AFM tips give images with reproducible features several nanometers in size along the DNA. Plasmids can be dissected in propanol by increasing the force applied by the AFM tip at selected locations.

Changes in the rat liver mitochondrial DNA upon aging

During experiments on the molecular basis of morphological and functional changes observed in rat liver mitochondria upon aging, we found that the buoyant density profile of mitochondrial DNA (mtDNA) shows a wide distribution pattern especially in the lighter region than that of young rat liver mtDNA. The heterogeneous pattern may be partly recovered to become similar to that of young rat liver mtDNA by treatment with proteinase K. Therefore, it is quite likely that mtDNA of old rat liver contains firmly bound protein(s) or peptides. During the morphological observation of mtDNA by electron microscopy, we found that mtDNA of old rat had a novel property, that is, the ability to attach to negatively charged mica in the absence of magnesium ions, although their morphological features showing circular 5 microns contour length form did not change. Further, mtDNA gained resistance against EcoRI digestion during aging. This property was not shared by the DNA from young animal, and might be due to the binding protein(s).

Protocol for 3-D visualization of molecules on mica via the quick-freeze, deep-etch technique

Molecular imaging by freeze-drying of molecules adsorbed to a mica substrate often provides better images of molecules than those attainable with other methods; the images are easier to interpret than those obtained with frozen thin film or negative staining, and the 3-dimensional information content is greater. The complete procedure for the production and examination of platinum-carbon replicas of molecules is described. Topics include production of a mica flake suspension, chemical pretreatment of the flakes to enhance adsorption, quick-freezing of the samples on mica, optimal operation of the freeze-fracture equipment, and orientation of replica topography. The production of stereo micrographs is analyzed in detail, with emphasis on the photographic procedures necessary for interpretation and on the identification of correct micrograph orientation. Guidelines are provided for the extrapolation from observed molecular size in platinum replicas to expected molecular weight.

DNA-protein complexes of the nuclear matrix: visualization and partial characterization of the protein component

Complexes composed of DNA attached to the nuclear matrix and of proteins most tightly bound to DNA are visualized as globular particles 25-35 nm in diameter. Their morphology depends greatly on the isolation conditions: a Cs salts/urea combination permits the isolation while CsCl/sarcosyl destroys the particles. The preparation is shown to have the same protein content regardless of the treatment employed. The proteins of the complex are resistant to SDS and pronase treatment and to phenol/chloroform extraction while being associated with DNA.

Interaction of the bacteriophage phi 29 protein p6 with double-stranded DNA

The Bacillus subtilis bacteriophage phi 29 protein p6 binds to double-stranded DNA, but not to single-stranded DNA, as determined by a gel retardation assay. The nature of the interaction was further studied by DNase I "footprinting" experiments. Protein p6 binds to fragments containing the right or left terminal sequences of phi 29 DNA, producing a characteristic pattern of hypersensitive bands spaced about 24 nucleotides apart along most of the fragment, flanking protected regions. Binding of protein p6 to an internal phi 29 DNA fragment was also observed, but the footprint pattern was more salt sensitive than that obtained with the terminal phi 29 DNA fragments. By electron microscopy, protein p6 was shown to cover the DNA, totally or partially, from one end. In addition, binding of protein p6 to relaxed circular DNA induced positive supercoiling, indicating that a topological change in the DNA occurred.

Disintegration of nucleoskeletal elements by metrizamide/2 M salt isopyknic centrifugation

Supramolecular structures that remain bound to chromosomal DNA under high salt conditions are believed to anchor DNA in the interphase nuclear skeleton. In order to identify these anchorage structures, the non-DNA materials that remain firmly bound to chromosomal DNA under conditions that disintegrate the high salt-stable architecture of nuclei were investigated. Nuclei of Ehrlich ascites cells were histone-depleted by treatment with 2 M salt. The residual halo structures were gently sheared and subjected to metrizamide isopyknic centrifugation in the presence of 2 M salt. By this combined treatment the high salt stable nuclear skeleton becomes disintegrated and three main fractions are resolved. A light fraction comprises the DNA which appears to be essentially depleted of other nuclear components. The only non-DNA material that could be identified in the DNA band is a fraction of (nascent) RNP. No other materials which could reflect nucleoskeletal elements (e.g. lamina proteins) were found together with DNA. A peak of intermediate density comprises RNA/RNP dissociated from DNA. The heavy fraction contains the proteins that become dissociated from DNA by high-salt and/or centrifugal forces, e.g. histones and the major nuclear lamina proteins. The results indicate that nascent RNP is more tightly bound to chromosomal DNA than other components that may be involved in nuclear skeletons. This suggest that transcription complexes represent at least one type of anchorage structure of DNA, which is consistent with results indicating that nascent RNA and actively transcribed DNA sequences are preferentially retained in high-salt-treated nuclei.

Interaction of the bacteriophage phi 29 connector protein with the viral DNA

The protein that forms the connector of phage phi 29, p10, binds to DNA. Apparently, p10 binding is not sequence specific. Nevertheless, the presence of the terminal protein (p3) covalently attached to the ends of phi 29 DNA produces a significant increase of p10 molecules bound to the DNA ends, thus suggesting a terminal protein-mediated recognition of DNA ends by the phage connector. As the p3-DNA complex is the substrate for phage phi 29 DNA packaging, these results may reflect a direct implication of the phage connector in the packaging process.

Visualization of RNA polymerase bound to R-loop molecules improves electron microscopic analysis of in vitro transcription

An electron microscope method is described which allows improved analysis of in vitro transcription. Transcription complexes are fixed with glutaraldehyde, subjected to R-loop conditions which allow the nascent RNA chains to hybridize to the DNA templates, and mounted for electron microscopy by a protein-free preparation method. An RNA polymerase molecule (or parts of it) associated with only one end of the R-loop identifies the polarity of the transcript, thus determining the origin and direction of transcription. The method was evaluated using known in vitro promoters on the bacteriophage P1 genome and was used for mapping of additional promoters in their vicinity.

Sputter shadowing

A device has been constructed which allows specimens to be shadowed in a conventional sputter water. This process of sputter shadowing lends to specimens a contrast suitable for imaging in the transmission electron microscope (TEM). The process has the practical advantages over metal evaporation shadowing of lower instrumentation costs, less user training, and less time expenditure per shadowing operation. It provides on a single grid a spectrum of shadowing contrasts from which optimal imaging for a particular specimen can be chosen. The process minimizes radiant and metal deposition heating of the specimen and, thereby, may better preserve its structure during the contrasting procedure. The grain resulting from sputter shadowing differs significantly from that obtained by metal evaporation shadowing and the possibility for using this difference to improve resolution in shadowed preparations is discussed.

Sputter shadowing improved by using a tungsten target

This work builds upon a previous paper (W. Colquhoun, 1984, J. Ultrastruct. Res. 87, 97) in which a sputter shadowing device was briefly described. The device allowed TEM specimens to be shadowed in a conventional sputter coater. Images obtained by sputter shadowing with a standard Au/Pd target were of good quality but were slightly inferior to the best that could be obtained by e--beam evaporation of tungsten. Here we show that construction and use of a tungsten target greatly improves the quality of the sputter shadowed deposit. Images of DNA and ribosomal subunits contrasted by sputter shadowing with tungsten are shown. The DNA images indicate that sputter shadowing with tungsten is a gentle contrasting technique. The sputter shadowed images of the 30 S ribosomal subunits show the major features of the particle revealed by evaporation shadowing using the most sophisticated of methods in that technology. Advantages of sputter shadowing are discussed and a rationale for the improved grain obtained by sputtering tungsten is suggested.

RNA-polymerase binding sites within the tra region of the F factor of Escherichia coli K-12

Chimeric plasmids containing the tra operon of the Escherichia coli K-12 F factor were used to map by electron microscopy the RNA polymerase binding sites within the contiguous F EcoRI restriction fragments f6, f16, f1, f17, f19 and f2. [These fragments have been previously cloned in the EcoRI site of pSC101 to give the chimeric plasmids pRS27 (f6, f15), pRS29 (f15, f1) and pRS31 (f17, f19 and f2)]. The results may reflect the presence of a number of previously unrecognized promoters within the traY----Z operon.

DNA of the Streptomyces phage SH10: binding sites for Escherichia coli RNA polymerase and denaturation map

Escherichia coli RNA polymerase bound to Streptomyces phage SH10 DNA was visualized by electron microscopy. Six specific binding sites were observed at map units 53, 85, 93, 97, 98, and 99 on the physical map of the 48 kb long genome. Electron microscopy of partially denatured SH10 DNA revealed a characteristic melting pattern of A + T-rich regions around map units 1, 3, 48, 52, and 99. A comparison of the denaturation map with the RNA polymerase binding sites indicates that three binding sites are located in the most A + T-rich regions, two in other early melting regions and one in a segment of higher DNA helix stability.

[Electron microscopy studies of DNA complexes with restriction endonuclease SalGI]

The binding properties of the type II restriction endonuclease SalGI to the plasmid DNA pGW 10 has been investigated by electron microscopic studies. Samples were spread by the BAC technique. In the presence of magnesium, SalGI binds as dimers and tetramers to the specific recognition site 5'-G-T-C-G-A-C-3' and with lower rate to the sequence 5'-G-T-C-A-A-C-3', which represents the recognition site of the restriction endonucleases Hind II and Hinc II.

Purified glucocorticoid receptor-hormone complex from rat liver cytosol binds specifically to cloned mouse mammary tumor virus long terminal repeats in vitro

Purified glucocorticoid hormone-receptor complex (HRC) from rat liver binds to specific DNA sequences contained in cloned mouse mammary tumor virus (MMTV)DNA. The binding site of the hormone-receptor complex is located in the long terminal repeat (LTR) of MMTV DNA as shown by filter binding studies with labeled restriction fragments and by visualization of DNA-receptor complexes with the electron microscope. The DNAs from cloned MMTV lacking the LTR sequences were neither retained on nitrocellulose filters nor bound specifically to HRCs examined in the electron microscope. The HRC also failed to bind to restriction fragments from pBR322 and phage lambda. Specific binding of the HRC to LTR sequences is dependent upon occupancy of the receptor by a glucocorticoid. Previous work has demonstrated that the MMTV transcription is initiated within the LTR; additionally, MMTV transcription is known to be regulated by glucocorticoids. Our present results therefore support the hypothesis that HRC regulates hormone-induced transcription by binding to specific DNA sequences near the MMTV transcription start site.

A comparison of the phage T4 gene 32 protein and Escherichia coli RNA polymerase binding sites on hamster papovavirus DNA

Phage T4 gene 32 protein and Escherichia coli RNA polymerase were bound to hamster papovavirus DNA. The binding regions were identified by electron microscopy employing a protein-free spreading technique. After gene 32 protein treatment four denaturation regions could be mapped, at 0.04-0.12, 0.30-0.36, 0.50-0.60 and 0.75-0.90 DNA map units, respectively, using the unique BamHI cleavage site as zero point. Eight RNA polymerase binding sites can be found which are localized at positions 0.05; 0.11; 0.18; 0.31; 0.57; 0.66; 0.76 and 0.82. A comparison of the RNA polymerase binding sites with the gene 32 protein denaturation pattern reveals a correspondence of six of eight polymerase binding sites with (A+T)-rich regions within the hamster papovavirus genome.

Knotted DNA from bacteriophage capsids

The majority of the DNA prepared from tailless capsids of bacteriophage P2 by the phenol extraction procedure consists of monomeric rings that have their cohesive ends joined. Electron microscopic and ultracentrifugal studies indicate that these molecules have a complex structure that is topologically knotted; they have a more compact appearance and a higher sedimentation coefficient when compared with regular nicked P2 DNA rings. Linearization of these rings by thermal dissociation or repair of the cohesive ends by DNA polymerase I in the presence of all four deoxynucleoside triphosphates gives molecules that are indistinguishable from normal P2 DNA that has been similarly treated. The knotted nature of the majority of P2 head DNA is further supported by analyzing the products when these molecules are treated with ligase and the ligase-treated molecules are subsequently nicked randomly with DNase I. The data are consistent with the notion that, if such a molecule is first converted to a form that contains only one single-chain scission per molecule, strand separation gives a linear strand and a highly knotted single-stranded ring. The results suggest that the DNA packaged in tailless P2 capsids is arranged in a way that leads to the formation of a complex knot when the ends join. In an intact phage particle, the anchoring of one terminus of the DNA to the head-proximal end of the tail [Chattoraj, D. K. & Inman, R. B. (1974) J. Mol. Biol. 87, 11-22] presumably diminishes or prevents this kind of joining. The novel knotted DNA can be used to assay type II DNA topoisomerases that break and rejoin DNA in a double-stranded fashion.

DNA electron microscopy

In recent years DNA electron microscopy has become a tool of increasing interest in the fields of molecular genetics and molecular and cell biology. Together with the development of in vitro recombination and DNA cloning, new electron microscope techniques have been developed with the aim of studying the structural and functional organization of genetic material. The most important methods are based on nucleic acid hybridizations: DNA-DNA hybridization (heteroduplex, D-loop), RNA-DNA hybridization (R-loop), or combinations of both (R-hybrid). They allow both qualitative and quantitative analysis of gene organization, position and extension of homology regions, and characterization of transcription. The reproducibility and resolution of these methods make it possible to map a specific DNA region within 50 to 100 nucleotides. Therefore they have become a prerequisite for determining regions of interest for subsequent nucleotide sequencing. Special methods have been developed also for the analysis of protein-DNA interaction: e.g., direct visualization of specific protein-DNA complexes (enzymes, regulatory proteins), and analysis of structures with higher complexity (chromatin, transcription complexes).

DNA strand specificity in promoter recognition by RNA polymerase

DNA strand and enzyme subunit specificities involved in the interaction between E. coli RNA polymerase and T7 DNA were studied by photo-crosslinking techniques. In non-specific enzyme-DNA complexes, subunits, sigma, beta, and beta' were crosslinked to both strands of the DNA. Under conditions leading to specific enzyme-promoter complexes, however, only sigma and beta subunits were crosslinked. The sigma subunit was crosslinked preferentially to the non-sense strand at promoter sites. No such strand specificity was observed for the beta subunit. These results provide insight into the molecular mechanism of promoter recognition and indicate that the interaction between RNA polymerase and DNA template is different at promoters and at non-specific sites.

RNA-polymerase binding at the promoters of the rRNA genes of Escherichia coli

The promoter region of two bacterial rRNA genes was investigated by electron-microscopic analysis of polymerase binding, transcription initiation and nitrocellulose filtration of RNA-polymerase-DNA complexes, using restriction endonuclease generated fragments of recombinant plasmids and a transducing phage. The following observations have been made: 1. Two transcription initiation sites have been located approximately 200 and 300 base pairs upstream from the beginning of the sequence coding for mature 16 S rRNA. 2. Polymerase binding at these sites can be observed electronmicroscopically and a 360 base-pair fragment containing these sites binds to nitrocellulose in the presence of RNA-polymerase. This complex dissociates even at moderately high (0.1-0.2 M) salt concentrations. Although transcription initiation is reported to be more frequent at the first of these sites, the binding is much stronger at the second site. 3. In the case of the rrnD gene, BamHI cleaves a few base pairs upstream from the first transcription start site. This cleavage destroys polymerase binding at this site but does not influence binding at the second site. 4. At higher polymerase/DNA ratio four weak but distinct and regularly spaced binding sites can be observed preceding the two initiation sites at approximately 1000, 820, 640 and 440 base pairs before the mature 16 S rRNA sequence. 5. An extremely strong binding site is located about 1300 base pairs upstream from the beginning of the 16 S rRNA sequence. Very little (if any) initiation occurs at this site. The possibility is discussed that the noninitiating binding sites preceding the two transcription start points might functionally belong to the promoter region.

Structure of replicating DNA molecules of Bacillus subtilis bacteriophage phi 29

We isolated phi 29 DNA replicative intermediates from extracts of phage-infected Bacillus subtilis, pulsed-labeled with [3H]thymidine, by velocity sedimentation in neutral sucrose followed by CsCl equilibrium density gradient centrifugation. During a chase, the DNA with a higher sedimentation coefficient in neutral sucrose and a lower sedimentation rate in alkaline sucrose than that of viral phi 29 DNA was converted into mature DNA. The material with a density higher than that of mature phi 29 DNA consisted of replicative intermediates, as analyzed with an electron microscope. We found two major types of molecules. One consisted of unit-length duplex DNA with one single-stranded branch at a random position. The length of the single-stranded branches was similar to that of one of the double-stranded regions. The other type of molecules was unit-length DNA with one double-stranded region and one single-stranded region extending a variable distance from one end. Partial denaturation of the latter molecules showed that replication was initiated with a similar frequency from either DNA end. These findings suggest that phi 29 DNA replication occurs by a mechanism of strand displacement and that replication starts non-simultaneously from either DNA end, as in the case of adenovirus.

The organization of the ribosomal RNA genes of Chironomus tentans and some closely related species

Southern gel analysis of total DNA from Chironomus tentans showed that the rRNA genes (rDNA) are homogeneous in structure. After cloning in Escherichia coli plasmid pBR313, the rDNA organisation was further studied by restriction fragment analysis and R-loop mapping. No heterogeneity could be detected by heteroduplex analysis of six different cloned rRNA cistrons. R-loop sizes of 1.69 and 3.63 kilobases (kb) were measured for the 18S and 28S rRNA coding sequences. The two spacers are 0.75 and 1.77 kb long. Southern gel analysis showed also a homogeneous rDNA structure for a Canadian population of C. tentans and C. pallidivittatus. The same technique indicated, however, that the rDNA of two other closely related species of C. thummi and C. melanotus is heterogeneous in structure. A possible correlation between this heterogeneity and the presence of heterochromatin in these species is discussed.

Electron microscopic analysis of in vitro transcriptional complexes: mapping of promoters of the coliphage T5 genome

Transcriptional complexes formed in vitro with coliphage T5 DNA as template were analyzed by electron microscopy and the number and location of starting sites utilized by E. coli RNA polymerase were determined. Of the 40 promoters characterized in this way, 6 map in the two terminal "pre-early" regions, 29 in the "early" and 5 in the "late" region. The direction of transcription within the different regions determined in this study agrees with earlier findings derived from RNA synthesized in vivo.