Deoxyribonucleate Binding and Transformation in Rhizobium japonicum

Rhizobium japonicum, capable of binding high-molecular-weight donor (32)P-labeled deoxyribonucleic acid (DNA) during late log phase in a competence medium, was transformed for streptomycin resistance with a frequency of transformation ranging between 0.02 and 0.08%. Eight to 10% of the homologous native (32)P-labeled input DNA was bound irreversibly in a temperature-dependent manner. Homologous denatured (32)P-labeled DNA was incapable of binding to the recipient under similar conditions. CsCl density gradient banding of the donor and recipient DNA indicated homology. The low frequency of transformation could be due to one or more steps that occur between DNA uptake and integration.     

Restriction and modification in B. subtilis

Summary The effects of restriction in vivo by competent B. subtilis R cells and in vitro by purified endonuclease BsuR on transformation and transfection with native and denatured DNA were investigated.The results show that transformation by either native, or denatured DNA is not affected by restriction, whereas transfection both with native and denatured SPP1 DNA is severely restricted.In contrast to the results obtained in vivo, the biological activity of native and denatured transforming DNA is destroyed by BsuR in vitro, as is the transfecting activity of native and denatured SPP1 DNA. The sensitivity of denatured DNA, either with mixtures of the complementary strands or with separated single strands¹ alone, is significantly lower than that of native DNA.The results are discussed in the context of possible mechanisms underlying the different responses of transforming and transfecting DNA to in vivo restriction by B. subtilis R cells.Abbreviations EGTA ethyleneglycolbis-(aminoethylether)tetraacetic acid - m⁺ modified - m^- non-modified - moi multiplicity of infection - r⁺ m⁺ restricting and modifying - r^- m^- mon-restricting and non-modifying - SSC 0.15M NaCl+0.015 M trisodium citrate - SDS sodium dodecyl sulphate     

Photodynamic Action on Native and Denatured Transforming Deoxyribonucleic Acid from Haemophilus influenzae

The photodynamic inactivation of native or denatured transforming deoxyribonucleic acid (DNA) from Haemophilus influenzae is described. The inactivation at the same pH was higher for denatured than native DNA. At acidic pH, the inactivation both for native and denatured DNA was faster than at alkaline pH. The guanine content of photoinactivated native DNA at neutral pH was less than untreated DNA. The inactivation of biological activity was more extensive than the alteration of guanine. The absorption spectrum of photoinactivated native or denatured DNA was only slightly different than the control DNA at the different experimental conditions.     

Transforming activity of phage T4r+ DNA, treated with ultraviolet light, nitrous acid, hydroxylamine and visible light in the presence of methylene blue]

The efficiency of phages T4rIIB-638v+ and T4rIIB-638v- transformation by native and denatured DNA treated with UV, nitrous acid, hydroxylamine and visible light in the presence of methylene blue is studied. A greater transformation efficiency of UV-irradiated T4r+ phage native and denatured DNA was observed in the v+ recipient as compared with v- recipients. Denatured donor DNA treated with nitrous acid has higher transformation activity in spheroplasts infected with T4v+ phage than in those infected with T4v- phage. Native donor DNA, treated with methylene blue and visible light-irradiated, developed a decrease of the transformation activity in T4v- phage-infected spheroplasts as compared with T4v+ phage-infected spheroplasts. Hydroxylamine treatment of native and denatured donor DNA did not reveal any differences in the transforming activity for v+ and v- recipients. Denatured donor DNA was more resistant to the effect of hydroxylamine than native DNA.     

Polycyclic aromatic hydrocarbons physically intercalate into duplex regions of denatured DNA

We have investigated the physical binding of pyrene and benzo[a]pyrene derivatives to denatured DNA. These compounds exhibit a red shift in their absorbance spectra of 9 nm when bound to denatured calf thymus DNA, compared to a shift of 10 nm when binding occurs to native DNA. Fluorescence from the hydrocarbons is severely quenched when bound to both native and denatured DNA. Increasing sodium ion concentration decreases binding of neutral polycyclic aromatic hydrocarbons to native DNA and increases binding to denatured DNA. The direct relationship between binding to denatured DNA and salt concentration appears to be a general property of neutral polycyclic aromatic hydrocarbons. Absorption measurements at 260 nm were used to determine the duplex content of denatured DNA. When calculated on the basis of duplex binding sites, equilibrium constants for binding of 7,8,9,10-tetrahydroxy-7,8,9,10-tetrahydro-benzo[a]pyrene to denatured DNA are an order of magnitude larger than for binding to native DNA. The effect of salt on the binding constant was used to calculate the sodium ion release per bound ligand, which was 0.36 for both native and denatured DNA. Increasing salt concentration increases the duplex content of denatured DNA, and it appears that physical binding of polycyclic aromatic hydrocarbons consists of intercalation into these sites.     

The determination of the nature of the interaction of neutral Mn2+-dependent DNAse with DNA by immunoelectron microscopy

The interaction of neutral DNAase with native and denatured DNA was shown by immunoelectron microscopy method with the help of colloidal gold. The neutral DNAase of the rat liver nuclear chromatin is absorbed both to denatured DNA, in which the denatured regions are arranged at 5'-3' ends, and to DNA in which these regions are distributed along the whole molecule.     

Temperature dependence of the photosynthetic activities in the thylakoid membranes from the blue-green alga Anacystis nidulans.

The effects of temperature and ethidium bromide on the banding of heat-denatured DNA was studied during equilibrium centrifugation in density gradients of NaI. Centrifugation at 10 degrees C prevents the partial renaturation of Escherichia coli DNA and Clostridium perfringens DNA that occurs at 20 degrees C. A centrifugation temperature of --5 degrees C is required to prevent renaturation of T7 phage DNA. Ethidium bromide decreases renaturation of Escherichia coli DNA during centrifugation at 20 degrees C and causes a small shift in the buoyant density of both denatured and native DNA. Equilibrium centrifugation at lower temperatures prevents DNA renaturation and permits increased utilization of the large buoyant density difference between native and heat-denatured DNA in gradients of NaI.     

Multiple phases of competence occur during the Helicobacter pylori growth cycle

The gastric pathogen Helicobacter pylori undergoes genetic exchange at unusually high frequencies, primarily through natural transformation. Despite progress toward understanding the molecular mechanism of natural transformation in H. pylori, little is known about how competence is regulated or its relationship to DNA release. By measuring transformation incrementally throughout the growth curve, we show that H. pylori exhibits a novel pattern of competence with distinct peaks of transformation during both logarithmic and stationary growth phases. Furthermore, different H. pylori strains vary in the presence and timing of their competence peaks. We also examined the process of DNA release in relation to competence. Although extensive DNA release does not occur until late stationary phase, sufficient genomic DNA was present during the logarithmic phase to yield measurable transformants. These results demonstrate that the state of competence in H. pylori occurs in an unprecedented pattern during the growth curve with no clear relationship to DNA release.     

Bindings of RNAse to denatured and native deoxyribonucleic acids

The binding of pancreatic ribonuclease-A by denatured DNA, native DNA, poly-dA, and poly-dT, has been studied by a gel filtration method. With denatured DNA at pH 7.5, ionic strength 0.053M, there is one binding site per 12 nucleotides and the equilibrium binding constant per site is 9.7 × 10⁴ l./mole. The binding constant increases by a factor of 8 as the pH is decreased from 8 to 7. The strength of the binding of denatured DNA increases with decreasing ionic strength. At pH 7.5, native DNA binds about ? as strongly as does denatured DNA. The binding affinity increases in the order poly-dA, denatured DNA, and poly-dT. These results support the view that the binding of denatured DNA involves both electrostatic interactions between the negatively charged polynucleotide and the positively charged protein, and an interaction of the protein with a pyrimidine residue of the denatured DNA, and thus that the binding is basically similar to that between RNAse and its substrate RNA.     

Polarographic reducibility of denatured DNA

The de polarographic behavior of native and denatured DNA at pH 7.0 was studied. Whereas native DNA was polarographically inactive under the given conditions, denatured DNA yielded a reduction polarographic step at the potential of about ?1.4 V. Native DNA produced a single desorption wave on ac polarograms, while denatured DNA yielded, in addition to this wave, another more negative wave approximately corresponding, as to its potential, to the dc polarographic step of denatured DNA. The behavior of apurinic acid was similar to that of denatured DNA. The course of DNA denaturation at elevated temperature was studied by means of the two above techniques and changes at temperatures below the melting temperature observed. This finding is in agreement with earlier results obtained by oscillopolarographic and the pulse-polarographic method.     

Deoxyribonucleases in phytohemagglutinin-stimulated lymphocytes

The in situ assay of deoxyribonucleases in DNA-containing polyacrylamide gels following their separation by microdisc electrophoresis was used to determine the deoxyribonuclease pattern of human lymphocytes during stimulation with phytohemagglutinin (PHA). Two additional neutral deoxyribonuclease activities are detectable in stimulated cells, one only active with denatured DNA, the other active with native and denatured DNA as substrate, showing a maximum activity after 36 h and increasing in waves respectively. A group of acid deoxyribonuclease activities also shows a maximum after 36 h of stimulation. A neutral deoxyribonuclease active only with native DNA is missing in stimulated lymphocytes. It is suggested that the acid deoxyribonuclease activities and the neutral deoxyribonuclease active only with denatured DNA are involved in DNA synthesis, whereas the involvement of the neutral deoxyribonuclease active with native and denatured DNA in processing of DNA excreted in stimulated lymphocytes is discussed.     

Low-angle light-scattering studies on alkali- and heat-denatured DNA

The molecular weight of native DNA is shown to decrease by at least a factor of two on denaturation by heat or alkali. This result is obtained only if low-angle (<30°) light-scattering measurements are used. High-angle measurements (>30°) do not reveal a decrease in molecular weight on denaturation due to the incorrect value for native DNA. The dn/dc value for both native and denatured DNA is 0.166 ml/g ± 0.003 ml/g. Methods are described for the clarification of native and denatured DNA solutions for light scattering by the use of membrane filters.     

DNA replication in Escherichia coli: physical and kinetic studies of the replication point

DNA replication in Escherichia coli was followed using analytical composite agarose-acrylamide gel electrophoresis of native and denatured DNA samples from cells that had been pulse-labeled in vivo. The results obtained with samples of native DNA, combined with the different sensitivities of the various electrophoretic fractions of native DNA to enzymatic attack, led us to conclude that a significant amount of single-strandedness exists in the region of the replication site. Data obtained from kinetic analyses of the labeling of both the high molecular weight DNA and the fragments formed on denaturation of native DNA samples were consistent with the Okazaki model (Okazaki et al., 1968a,b) of DNA replication. Furthermore, the data indicated that eight to ten precursor fragments are present per fork during bacterial growth at both 20 and 37 °C, under the conditions used in this study.     

Tracing the Evolution of Competence in Haemophilus influenzae

Natural competence is the genetically encoded ability of some bacteria to take up DNA from the environment. Although most of the incoming DNA is degraded, occasionally intact homologous fragments can recombine with the chromosome, displacing one resident strand. This potential to use DNA as a source of both nutrients and genetic novelty has important implications for the ecology and evolution of competent bacteria. However, it is not known how frequently competence changes during evolution, or whether non-competent strains can persist for long periods of time. We have previously studied competence in H. influenzae and found that both the amount of DNA taken up and the amount recombined varies extensively between different strains. In addition, several strains are unable to become competent, suggesting that competence has been lost at least once. To investigate how many times competence has increased or decreased during the divergence of these strains, we inferred the evolutionary relationships of strains using the largest datasets currently available. However, despite the use of three datasets and multiple inference methods, few nodes were resolved with high support, perhaps due to extensive mixing by recombination. Tracing the evolution of competence in those clades that were well supported identified changes in DNA uptake and/or transformation in most strains. The recency of these events suggests that competence has changed frequently during evolution but the poor support of basal relationships precludes the determination of whether non-competent strains can persist for long periods of time. In some strains, changes in transformation have occurred that cannot be due to changes in DNA uptake, suggesting that selection can act on transformation independent of DNA uptake.     

DNA Polymerase Activity Associated with the Membrane Fraction of E. coli

Spheroplasts were disrupted with 0.2% Brij 58 and the separation of intact cells, spheroplasts, disrupted spheroplasts, fragmented membrane, and supernatant was performed on a linear 40~55% sucrose gradient. About half an amount of nucleic acid components was distributed in disrupted spheroplast fractions, while only a small amount of protein components was found in these fractions.

DNA polymerase in the fragmented membrane fraction incorporated ³H-TTP more rapidly than that in the supernatant fraction for the first 5 to 6 min, and then the incorporation rate decreased, while DNA polymerase in the supernatant fraction incorporated ³H-TTP linearly up to 20 min when native DNA was used as a primer. The former required native DNA as a primer and showed little activity towards denatured DNA, while the latter incorporated ³H-TTP at a similar rate to both the primer DNA’s.

DNA polymerase of the fragmented membrane fraction synthesized various sizes of DNA from short to a size of primer when native DNA was used as a primer, while when denatured DNA was used, products were only short. DNA polymerase of the supernatant fraction synthesized various sizes of DNA when both native and denatured DNA’s were used as primers.     

Southern transfer of native DNA using nylon membranes

Transfer of native or denatured DNA from gels or filter manifolds was compared using nylon or nitrocellulose membranes. The results were comparable when denatured DNA was used, but only nylon membranes were able to retain native DNA. Although retention of the native DNA was less efficient the bound DNA could be rapidly denatured in situ, avoiding the need to soak gels in alkaline denaturation solution and neutralizing buffer.     

Duplication of single stranded DNA catalyzed by calf thymus DNA polymerase alpha.

Purified calf thymus DNA polymerase alpha is inactive with native DNA as template and shows little activity with denatured DNA. DNA synthesis with denatured DNA as template is greatly stimulated by the addition of a nuclease which initially copurifies with DNA polymerase but is separated from the polymerase on DEAE-cellulose chromatography. A limit digest of nuclease treated native DNA which is then denatured is replicated 80-95%; extensive replication is also obtained with native DNA partially degraded by pancreatic DNase and then denatured. The product of the reaction with calf thymus nuclease-treated DNA as template is double-stranded DNA with a hairpin (looped back) structure.     

The properties of native and denatured DNA in buoyant rubidium trichloroacetate at neutral pH

Aqueous RbTCA is generally suitable as a buoyant solvent for both native and denatured DNA at neutral pH and room temperature. Native PM-2 DNA II, for example, is buoyant at 3.29 M salt, 25 degrees C; whereas the denatured strands band together at 4.52 M. Two properties of the solvent make this system uniquely useful for separations based upon the extent of secondary structure. First, the melting transition temperature for chemically unaltered DNA is depressed to room temperature or below. Second, the buoyant density increase accompanying denaturation is extraordinarily large, 174 mg/ml for PM-2 DNA II. This value is three times that found in aqueous NaI and ten times that for CsCl. The properties of the RbTCA buoyant solvent presented here include the compositional and buoyant density gradients and the buoyant density dependence upon base composition. The DNA remains chemically unaltered after exposure to RbTCA as shown by the absence of strand scissions for closed circular DNA and by the unimpaired biological activity in transformation assays. Intact virion DNA may be isolated by direct banding of whole virions in RbTCA gradients without prior phenol extraction. Strongly complexed or covalently bound proteins may be detected by their association with the buoyant polymer in the denaturing density gradient.     

Volume changes accompanying the thermal denaturation of deoxyribonucleic acid. I. Denaturation at neutral pH

Dilatometric measurements were made to determine the change in apparent specific volume φ of DNA resulting from thermal denaturation in neutral solution, φ increased continuously with temperature in the range 10–85°C. No deviations from a monotonically rising curve were observed in the φ versus temperature profile in the region of the melting temperature. The results are interpreted in terms of a partial loss of the preferentially bound DNA hydration shell. The nature of the well known buoyant density difference between native and denatured DNA was investigated by evaluating the densities in a series of cesium salt gradients at constant temperature. Extrapolation of the results to zero water activity indicates that the partial specific volumes of anhydrous native and denatured DNA are equal. The density difference at nonzero water activities is attributed to decreased hydration in the denatured state. The absence of a related change in φ accompanying the denaturation in the dilatometric experiments suggests that the probable volume change associated with loss of bound water during denaturation is accompanied by other compensatory volume effects. The possible nature of these volume effects is discussed.     

Factors affecting transformation of Bacillus licheniformis

Thorne, Curtis B. (Fort Detrick, Frederick, Md.), and Harold B. Stull. Factors affecting transformation of Bacillus licheniformis. J. Bacteriol. 91:1012-1020. 1966.-Transformation systems involving two types of transformable mutants of Bacillus licheniformis 9945A were compared. Each system required its specific growth medium, but a single transformation medium could be used for both. Cells from a culture of optimal age were not competent, at least to any great extent, but they developed competence during incubation in a transformation medium. With each system, 3 to 5% of the recipient cells were transformed upon exposure to wild-type deoxyribonucleic acid (DNA) for 2 to 3 hr. When competent cells were exposed to DNA for 30 min, 1 to 2% of them were transformed. The data are interpreted to mean that cells were heterogeneous with respect to development of competence, and when properly grown cells were incubated in transformation medium some of them gained competence, whereas others lost it. If DNA was present during the entire period, the cells were transformed as they became competent and the transformants accumulated. However, during any short period of exposure to DNA, only those cells that were competent at the time were potential transformants. The high frequencies of transformation obtained in these studies made it feasible to prepare marked strains by transforming markers into recipient cells. These experiments demonstrated that the characteristics of the two transformation systems could not be attributed to specific nutritional markers. Presumably, each of the two series of highly transformable auxotrophic mutants also carried at least one other mutation that resulted in development of competence under the specific conditions.