Electron microscopy of size and shape of viral DNA in solutions of different ionic strengths

High Resolution Shadowing of DNA

High resolution shadowing by electron beam evaporation was used to visualize DNA molecules. Its applicability to the study of macromolecules at this resolution level was previously demonstrated on monomeric and dimeric tRNA particles.

To utilize the potential of the high resolution shadowing for DNA, a mounting procedure was employed which provided a smooth substrate to which the naked molecules could be bound. This consisted of a two step process, modified from Kleinschmidt Lang, and Harford and Beer. When a 50μl droplet of cytochrome c (20 μg/ml in 0.2M Na acetate at pH 5) was allowed to stand on teflon for 20 minutes, a monolayer of protein formed on its surface. The film was picked up onto carbon coated grids, washed in ethanol and air dried. As test specimen, we used DNA from SV4O. The protein coated grids were floated for 30 minutes on buffer droplets containing 0.1-0.5 μg DNA/ml 10-3SSC and the molecules were bound to the protein monolayers by diffusion. Grids were then washed successively in 50% and absolute ethanol and air dried.

Effect of sodium and acetate ions on 8-hydroxyguanine formation in irradiated aqueous solutions of DNA and 2'-deoxyguanosine 5'-monophosphate

PURPOSE

The aim of this work was to study the combined effect of sodium and acetate ions on the radiation yield of 8-hydroxyguanine (8-OHG), one of the major DNA base lesions induced by free radicals.

MATERIALS AND METHODS

Aqueous solutions of DNA and 2'-deoxyguanosine 5'-monophosphate (dGMP) with various concentrations of sodium acetate and sodium perchlorate were γ-irradiated, enzymatically digested and analyzed by high-performance liquid chromatography (HPLC) methods.

RESULTS

It was found that both salts decrease the 8-OHG radiation yield in the concentration range studied for both DNA and dGMP, except in the case of dGMP wherein an increase in yield occurs in the concentration range from 0.1-1 mM. The dependence of the 8-hydroxy-2'-deoxyguanosine radiation yield on the concentration of both sodium acetate and sodium perchlorate have different shapes and have steeper slopes for the DNA compared with the dGMP solutions.

CONCLUSIONS

The observed decrease in the radiation yield of 8-OHG with increasing concentrations of sodium acetate is consistent with the hypothesis that sodium acetate produces two concentration-dependent effects in the DNA solutions: (1) A conformational change in the DNA caused by Na(+) counterions; and (2) free radical reactions related to the radiolysis of acetate ion.

[Ru(TAP)3]2+-Photosensitized DNA Cleavage Studied by Atomic Force Microscopy and Gel Electrophoresis: A Comparative Study

Topological modifications of plasmid DNA adsorbed on a variety of surfaces were investigated by using atomic force microscopy (AFM). On mica modified with 3-aminopropyltriethoxysilane (APS) or poly-L-lysine, the interaction between the plasmid DNA and the surface "freezes" the plasmid DNA conformation deposited from solution, and the AFM images resemble the projection of the three-dimensional conformation of the plasmid DNA in solution. Modified mica with low concentrations of Mg(2+) leads to a decrease in the interaction strength between plasmid DNA and the substrate, and the AFM images reflect the relaxed or equilibrium conformation of the adsorbed plasmid DNA. Under these optimized deposition conditions, topological modifications of plasmid DNA were produced under irradiation in the presence of [Ru(TAP)(3)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene), which is a non-intercalating complex, and were followed as a function of illumination time. The observed structural changes correlate well with the conversion of the supercoiled covalently closed circular form (ccc form) into the open circular form (oc form), induced by a single-strand photocleavage. The AFM results obtained after fine-tuning of the plasmid DNA-substrate interaction compare well with those observed from gel electrophoresis, indicating that under the appropriate deposition conditions, AFM is a reliable technique to investigate irradiation-induced topological changes in plasmid DNA.

AFM studies of DNA structures on mica in the presence of alkaline earth metal ions

As counterions of DNA on mica, Mg(2+), Ca(2+), Sr(2+) and Ba(2+) were used for clarifying whether DNA molecules equilibrate or are trapped on mica surface. End to end distance and contour lengths were determined from statistical analysis of AFM data. It was revealed that DNA molecules can equilibrate on mica when Mg(2+), Ca(2+) and Sr(2+) are counterions. When Ba(2+) is present, significantly crossovered DNA molecules indicate that it is most difficult for DNA to equilibrate on mica and the trapping degree is different under different preparation conditions. In the presence of ethanol, using AFM we have also observed the dependence of B-A conformational transition on counterion identities. The four alkaline earth metal ions cause the B-A transition in different degrees, in which Sr(2+) induces the greatest structural transition.

Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis

This paper reports a study of the deposition process of DNA molecules onto a mica surface for imaging under the scanning force microscope (SFM). Kinetic experiments indicate that the transport of DNA molecules from the solution drop onto the surface is governed solely by diffusion, and that the molecules are irreversibly adsorbed onto the substrate. A statistical polymer chain analysis has been applied to DNA molecules to determine the deposition conditions that lead to equilibrium and those that result in trapped configurations. Using the appropriate conditions, DNA molecules deposited onto freshly cleaved mica, are able to equilibrate on the surface as in an ideal two-dimensional solution. A persistence length of 53 nm was determined from those molecules. DNA fragments that were labeled on both ends with a horseradish peroxidase streptavidin fusion protein were still able to equilibrate on the surface, despite the additional protein-surface interaction. In contrast, DNA molecules deposited onto glow-discharged mica or H+-exchanged mica do not equilibrate on the surface. These molecules adopt conformations similar to those expected for a simple projection onto the surface plane, suggesting a process of kinetic trapping. These results validate recent SFM application to quantitatively analyze the conformation of complex macromolecular assemblies deposited on mica. Under equilibration conditions, the present study indicates that the SFM can be used to determine the persistence length of DNA molecules to a high degree of precision.

Analysis of the structure of dimeric DNA catenanes by electron microscopy

We analyzed the structure of open-circular and supercoiled dimeric DNA catenanes generated by site-specific recombination in vitro. Electron microscopy of open-circular catenanes shows that the number of duplex crossings in a plane is a linear function of the number of catenane interlinks (Ca/2), and that the length of the catenane axis is constant, independent of Ca. These relationships are similar to those observed with supercoiled DNA. Statistical analyses reveal, however, that the conformations of the individual rings of the catenanes are similar to those of unlinked circles. The distribution of distances between randomly chosen points on separate rings depends strongly on Ca and is consistent with a sharp decrease in the center-of-mass separation between rings with increasing Ca. Singly linked supercoiled catenanes are seen by microscopy to be linked predominantly through terminal loops in the respective superhelices. The observations suggest that chain entropy is a major factor determining the conformation of DNA catenanes.

The reliability of wormlike polysaccharide chain dimensions estimated from electron micrographs

Electron micrographs of alginate, xylinan, xanthan, and scleroglucan were prepared by vacuum-drying aqueous glycerol-containing solutions, and then heavy-metal, low-angle rotary replicated. Quantitative methods for excluding streamlining effects and deformation artifacts were developed and applied to the digitized polymer contours prior to analysis of stiffness. The apparent macromolecular dimensionalities were not obtainable on the basis of the change in the scaling coefficient alpha relating the rms end-to-end distance and the contour length, mean value of r2(1/2) approximately L alpha, for chains subject to the excluded volume effect in two and three dimensions. Using a two-dimensional model, the persistence length of these molecules was estimated to be (9 +/- 1) nm (alginate), (25 +/- 4) nm (xylinan), (30 +/- 4) nm (single-stranded xanthan), (68 +/- 7) nm (double-stranded xanthan), and (80 +/- 10) nm (scleroglucan). Monte Carlo calculations for wormlike chains close to an interacting surface or confined to the region between two surfaces showed that (1) strongly adsorbed molecules are essentially two-dimensional and (2) molecules restricted to the space between two surfaces separated by a distance less than 20% of the persistence length are two-dimensional in their directional correlation. The somewhat low estimates of the persistence lengths obtained from the electron micrographs compared with those reported from solution measurements can be accounted for by the adoption of a strictly two-dimensional model in the analysis, whereas the absorbed polymers are most likely intermediate between the two-and three-dimensional cases. The model calculations and the analysis of the electron micrographs suggest that stiffness parameters are obtainable from the electron micrographs when the proper theoretical description are used in the analysis.

Length, mass, and denaturation of double-stranded RNA molecules compared with DNA

The contour lengths of linear, double-stranded (ds) RNAs from mycovirus PcV and Pseudomonas bacteriophage phi 6 have been measured with samples prepared for the electron microscope from 0.05 to 0.5 M NH4Cl solutions. A linear dependence of contour length on the logarithm of ionic strength was found and compared with that of dsDNA (pBR322, linearized and open-circular forms). Conditions for molecular weight determinations of any natural dsRNA by electron microscopy have been established, and the method has been calibrated with phi 6 dsRNA of known nucleotide sequence. The results imply that dsRNA in 0.20 M NH4Cl solution has a rise per basepair of 0.271 nm, which is shorter than that in the A-conformation (4%) and in the A'-conformation (10%). The thermal behavior of dsRNA in terms of melting temperature and exhibition of fine structure of melting curves was found to be generally similar to that of dsDNA, as expected from the literature. Folding of dsRNA in ethanolic solution was similar to that of dsDNA. However, in contrast to dsDNA, coiled coils could not be induced by ethanol, which is consistent with dsRNA being stiffer than dsDNA. Concerning dsDNA, the results show that a contraction in rise per basepair by 0.1 nm is coupled with an increase in the winding angle between basepairs by 0.47 degrees, as qualitatively predicted by polyelectrolyte theory.

The structure of replicating bacteriophage T1 DNA: comparison between wild type and DNA-arrest mutant infections

Analysis of the structure of replicating phage T1 DNA has identified three major forms of T1+ intracellular DNA; (i) concatemeric molecules with single-stranded interruptions, (ii) monomer-length DNA with single-strand interruptions, and (iii) monomer-length molecules with completely intact single strands. The interruptions in concatemeric DNA are spaced at intervals, with a mean distance equivalent to one monomer length but with a broad distribution and many are in the form of gaps. Type (iii) molecules are probably derived from mature progeny phage particles disrupted during cell lysis. Under nonpermissive conditions, cells infected with amber mutants in T1 genes 3.5 and 4 show the premature arrest of phage DNA synthesis, failure to make concatemeric DNA, and reduced genetic recombination. Intracellular DNA from gene 3.5- and gene 4- infections consist of a uniform population of molecules approximately 10-12% shorter than mature monomers. They are stable throughout infection, contain single-stranded interruptions but not gaps, and are missing terminal sequences. These results are interpreted in terms of concatemer formation by end-to-end recombination between newly synthesised molecules whose terminal sequences are degraded in recombination-defective infections.

A physical map of the permuted genome of bacteriophage T1

A restriction map has been constructed for the DNA of coliphage T1 which locates the cleavage sites of the restriction endonucleases, BglI (6 cuts), BglII (16 cuts), EcoRI (2 cuts), HindIII (2 cuts) and PstI (2 cuts). Digestions with BglI and BglII reveal fragments which are present in sub-molar quantities. Two methods, one using the selective removal of molecular ends with exonuclease III and the other involving the comparison of digestion patterns of concatemeric and virion DNA, have shown that the submolar fragments are at or close to the ends of the molecules. Digestions with BglI show that one terminal fragment has a very precise molecular weight whereas all the others are of heterogenous molecular weight. These results are consistent with the model for DNA packaging in which maturation is initiated at a precise site on a concatemeric precursor and proceeds by the encapsidation of up to four successive 'headfuls' of 1.065 genome equivalents (MacHattie and Gill 1977).

Evidence for an increase of DNA contour length at low ionic strength

The polyion chain expansion of DNA was studied by viscometry within the Na+ concentration range c5 = 0.002 M to 0.4 M. The DNA molecular weights M were between 0.5 x 10(6) and 13 x 10(6). The relative change of intrinsic viscosity [eta] is linearly correlated to c5(-1/2) with a slope that increases with increasing M. This behaviour reflects the predominance of helix stiffening in chain expansion. At c5(112) > 0.01(-1/2 M-1/2 (Debye-Hückel screening radius 1/chi > (1/chi)*=3nm) the relative change of [eta] rises with a steeper slope. This effect increases with decreasing M suggesting that helix lengthening contributes to the chain expansion. Our model enables us to interpret other ionic-strength dependent effects known from literature. The start of the significant duplex elongation at (1/chi)* can be correlated to the polyion-charge arrangement. In accordance with our interpretation (1/chi)* is found to be greater for DNA-intercalator complexes.

Electron microscopy of DNA: determination of absolute molecular weights and linear density

The molecular lengths of several phage DNA's and one plasmid DNA have been measured and the molecular linear density of double stranded DNA under standard conditions has been determined. This determination was possible since the absolute molecular weight for phi X 174 DNA has become known from sequence work. RF DNA of phi X 174 phage consists of 5375 +/- 20 basepairs equivalent to a molecular weight of (3.558 +/- 0.013) x 10(6) dalton and since the length of this DNA has been determined to be 1.71 +/- 0.02 micrometer the molecular linear density of double stranded DNA prepared for electron microscopy under the conditions described is (2.08 +/- 0.03) x 10(6) dalton micrometer-1. These data have been used to determine the molecular weights of several phage DNA's and of the plasmid DNA PML 21. The latter DNA exhibits a remarkable heterogeneity with respect to its size.

Mapping and length measurements of restriction enzyme fragments by electron microscopy

1. We have mapped by electron microscopy the DNA-fragments formed by the action of the restriction endonuclease from Arthrobacter luteus of phi X 174 replicative form DNA. These fragments were separated by polyacrylamide gel electrophoresis and hybridized to phiX 174 single stranded DNA. The partial duplex molecules were inspected in the electron microscope. In this way the relative order of eleven fragments ranging in size from approximately 100 to 1000 nucleotide pairs has been established and compared with that deduced from reciprocal digestion studies. 2. The measured lengths of the fragments agreed well with the lengths found by gel electrophoresis. 3. The purity of the isolated fragments was checked. Most of the contaminating fragments derive from nearest neighbours in the preparative polyacrylamide gels.

The structure of kinetoplast DNA. 1. The mini-circles of Crithidia lucilae are heterogeneous in base sequence

We have analysed limit digests of mini-circles from kinetoplast DNA of Crithidia luciliae by gel electrophoresis. Endonucleases HapII and AluI cut the circles into at least 37 and 21 fragments, respectively, and leave no circles intact. In both cases the added molecular weights of the fragments, estimated from mobility in gels, exceeds 18 X 10(6), i.e. more than 12 times the molecular weight of the mini-circle DNA. Endonucleases HindII + III, EcoRI and HpaI cut only part of the circles. These results show that the mini-circles are heterogeneous in base sequence. Different sequence classes are present in different amounts. DNA-DNA renaturation analysis of mini-circle DNA yields a complexity of about 3 X 10(6), i.e. twice the molecular weight on one mini-circle. The delta tm of native and renatured duplexes is about 1 degree C, showing that the sequence heterogeneity is a micro-heterogeneity. Electron microscopy, gel electrophoresis and sedimentation analysis show that the circles that are not cut by endonucleases HindII + III remain catenated in very large associations. These associations lack the 'rosette' structures and the long edge loops characteristic of intact kinetoplast DNA. This suggests that the mini-circle classes cut by endonucleases HindII + III are present throughout the network and that the maxi-circle component of the network (see accompanying paper) is not essential to hold the network together. Prolonged electrophoresis on 1.5% or 2% agarose gels resolves the open mini-circles into three and linearized mini-circles into four bands, present in different amounts. We conclude that the mini-circles are also heterogeneous in size, the difference in size between the two extreme size classes being 4% of the contour length. Digestion with endonuclease HapII shows that at least three out of these four bands differ in sequence. Possible mechanisms that could account for the micro-heterogeneity in sequence of mini-circles are discussed.

Rearrangement of mitochondrial DNA molecules during the differentiation of mitochondria in yeast. I.-Electron microscopic studies of size and shape

Size and shape of purified mitochondrial DNA was analyzed by electron microscopy as a function of mitochondrial differentiation. The mitochondrial DNA was extracted at fourth growth stages corresponding to different steps of mitochondria repression and depression. It was heterogeneous both in form and length. The size of linear molecules ranged from 1 mu to 25 mu but most of the molecules could be assigned into four Gaussian subpopulations with mean lengths of 2.2 mu to 4.0 mu, 6.0 mu and 10.0 mu. The circular molecules were all open and sized varied from 0.5 mu to 10 mu. Their length repartition was congruent with a logarithmic Gaussian distribution. The relative proportion of the different classes of molecules changed according to the stage of the growth cycle: during the repression most of the mitochondrial DNA molecules were short: the population of 2.2 mu was predominant. The longest linear molecules were observed during derepression where the populations of 4.0 mu and 10.0 mu were only found as well as the highest proportion of circular molecules. At the stationary phase the mitochondrial DNA became short again and the circles disappeared completely. The mitochondrial DNA extracted from a cytoplasmic "petite" was composed of linear and circular molecules. The linear molecules ranged from 0.1 mu to 32 mu and most of them could be assigned to two subpopulations of 1.3 mu and 4.2 mu. The circular molecules which accounted for 11 percent had contour lengths of 0.7 mu and 1.5 mu. The physiological meaning of the change in the relative proportion of different classes of mitochondrial DNA is discussed.

Fragmentation of purified mammalian DNA molecules by ultrasound below human therapeutic doses

Because of the increasing medical use of ultrasound, especially in obstetrical diagnosis, it has become important to check its genetic harmlessness. Purified calf thymus DNA in solution was exposed to both therapeutic and obstetrical diagnostic doses of ultrasound. Intensities lower than those used in therapy have a drastic effect on purified DNA in solution, although intensities used in obstetrical diagnosis caused no visible effect.

Round of replication mutant of a drug resistance factor

A derivative of the R factor NR1 (called R12) has been isolated which undergoes an increased number of rounds of replication each division cycle in Proteus mirabilis, Escherichia coli, and Salmonella typhimurium. The alteration resulting in the increased number of copies (round of replication mutation) is associated with the transfer factor component of the R factor. R12 has the same drug resistance pattern as NR1, is the same size as shown by sedimentation in a sucrose gradient and electron microscopy (63 x 10(6) daltons), and has the same partial denaturation map. The level of the R factor gene product chloramphenicol acetyltransferase has been examined in P. mirabilis and was found to be consistent with gene dosage effects. The plasmid to chromosomal deoxyribonucleic acid ratio of NR1 increases several fold after entry into stationary phase, whereas this ratio for R12 remains approximately constant. Individual copies of R12 are selected at random for replication from a multicopy plasmid pool. A smaller percentage of R12 copies replicate during amino acid starvation than has previously been found for NR1 in similar experiments.

Studies of nondefective adenovirus 2-simian virus 40 hybrid viruses. VI. Characterization of the DNA from five nondefective hybrid viruses

Certain biophysical characteristics of the DNA from each of the five nondefective adenovirus 2 (Ad2)-simian virus 40 (SV40) hybrid viruses (Ad2(+)ND(1), Ad2(+)ND(2), Ad2(+)ND(3), Ad2(+)ND(4), Ad2(+)ND(5)) have been determined. The guanine plus cytosine content varied from 55 to 57% and was not significantly different from that of nonhybrid Ad2 (56%), and the hybrid DNA molecules had mean molecular lengths which were similar to that of the standard, Ad2. The Ad2 and SV40 components of each hybrid were linked by alkali-resistant, presumably covalent bonds. The percentage of SV40 DNA in each hybrid virus was determined by hybridization with SV40 complementary RNA in a calibrated system. The results indicate that each hybrid virus DNA contains a different percentage of SV40 nucleotide sequences. The estimated size of the SV40 DNA component varies from 48,000 daltons for Ad2(+)ND(3) to 840,000 daltons for Ad2(+)ND(4), the latter being equivalent to between one-fourth and one-third of the SV40 genome.