Studies on Agrobacterium tumefaciens. IV. Nonreplication of the bacterial DNA in mung beam (Phaseolus aureus).

DNA·DNA filter hybridization and DNA solution enrichment reassociation experiments showed that no $\text{Agrobacterium tumefaciens}$ DNA was replicated in mung bean seedlings under the conditions specified in published reports for the uptake, integration, and replication of bacterial DNA in higher plants. Residual presumptive DNA hybrids that formed in a few instances were characterized by thermal chromatography on hydroxylapatite. The Tm and melting profiles of these hybrids from DNA-treated plants were the same as those from untreated control plants. The sensitivities of these procedures were sufficient to detect $\text{A. tumefaciens}$ DNA in the order of 0.005% to 0.01% of the plant genome. These results do not concur with previous reports that large pieces of DNA (at least 30%) of the plant genome of bacterial-DNA-treated-plants is made up of bacterial donor DNA.     

Sequences of the 1.672 g/cm3 satellite DNA of Drosophila melanogaster.

The 1.672 g/cm³ satellite DNA of Drosophila melanogaster was purified by successive equilibrium centrifugations in a CsCl gradient, an actinomycin $\text{D}\text{CsCl}$ gradient, and a netropsin sulfate/CsCl gradient. The resulting DNA was homogeneous by the physical criteria of thermal denaturation, renaturation kinetics and equilibrium banding in each of the gradients listed above. In addition, the complementary strands could be separated in an alkaline CsCl gradient. Despite this rigorous purification procedure, nucleotide sequence analysis indicates the presence of two different DNA species in this satellite, poly $\text{A-A-T-A-T}\text{T-T-A-T-A}$ and poly$\text{A-A-T-A-T-A-T}\text{T-T-A-T-A-T-A}$. Further physical, chemical and template properties of the isolated complementary strands demonstrate that these two repeating sequences are not interspersed with each other. This result has biological significance since sequences of this particular satellite are known to be located primarily on two different chromosomes, Y and 2. These results further suggest that the sequence heterogeneity observed in satellite DNA of higher eukaryotes may result from mixtures of very closely related but molecularly homogeneous repeated sequences each restricted to a particular chromosome or chromosomal region.     

Differential effect of neomycin on DNA dependent -DNA and RNA synthesis in vitro

Neomycin inhibits $\text{in vitro}$ DNA dependent DNA and RNA synthesis catalyzed by DNA polymerase I and RNA polymerase from $\text{E. coli}$. The effect of the antibiotic is more pronounced towards DNA synthesis. The inhibition of DNA synthesis is competitive with template DNA, does not reverse with excess deoxynucleoside triphosphate, Mg²⁺ or enzyme $\text{E. coli}$ DNA polymerase I. Neomycin does not reduce the number of potential 3′ -OH end or primer. It seems to shorten the size of the newly formed polynucleotide.     

Effects of depurination on the fidelity of DNA synthesis.

The effect of depurination of polynucleotide templates on the fidelity of DNA synthesis in vitro has been determined. The fidelity of DNA synthesis with Escherichia coli DNA polymerase I, avian myeloblastosis virus DNA polymerase and human placenta DNA polymerase-β is decreased as a result of depurination of the poly[d(A-T)], poly[d(G-C)]and poly[d(A)]templates. The error rate with poly[d(A-T)]increased from $\text{1}\text{17,500}$ to $\text{1}\text{2100}$ using E. coli Pol I, and from $\text{1}\text{4100}$ to $\text{1}\text{1500}$ using the myeloblastosis virus DNA polymerase. Depurination of poly[d(A)]increased the error rate from $\text{1}\text{21,000}$ to $\text{1}\text{6500}$ using E. coli Pol I, and from $\text{1}\text{19,300}$ to $\text{1}\text{6100}$ using the DNA polymerase-β from human placenta. Depurination of poly[d(G-C)]resulted in an increase in the error rate with E. coli Pol I from $\text{1}\text{9200}$ to $\text{1}\text{2200}$, and with the virus DNA polymerase from $\text{1}\text{2400}$ to $\text{1}\text{1300}$. This misincorporation is shown to be directly proportional to the extent of depurination. Deletion experiments and alkaline sucrose gradient analyses suggest that the incorporation of complementary and non-complementary nucleotides is dependent on polymerization, and occurs in the same newly synthesized product. Kinetic studies and nearest-neighbor analyses indicate that the incorporation of non-complementary nucleotides occurs randomly as single-base substitutions. The nearest-neighbor studies also suggest that any of the four deoxynucleotides can be incorporated opposite apurinic sites. The number of each nucleotide incorporated relative to the number of apurinic sites was determined to be $\text{1}\text{490}$ for dGTP, $\text{1}\text{115}$ for dCTP, $\text{1}\text{2·5}$ for dATP and $\text{1}\text{1·7}$ for dTTP with both the poly[d(A-T)] and poly[d(A)] templates. The frequencies of misincorporation relative to the number of apurinic sites with the poly[d(G-C)]template were $\text{1}\text{230}$ for dATP, $\text{1}\text{120}$ for dTTP, $\text{1}\text{2·4}$ for dGTP and $\text{1}\text{1·8}$ for dCTP. Hydrolysis at the apurinic sites by alkali treatment reversed the effects of depurination on fidelity. The error rates with the depurinated templates were reduced to within 2% of those obtained prior to depurination, providing additional evidence that the misincorporation after depurination results from apurinic sites on the template. These results suggest a possible relationship between depurination of DNA and errors in DNA replication and/or repair.     

Cloning of the replication origin from Drosophila virilis mitochondrial DNA.

Mitochondrial DNA from $\text{Drosophila}$ contains high “A+T”-rich region. Its DNA replication starts in the “A+T”-rich region and proceeds unidirectionally around the molecule. In order to determine precise location of the DNA replication origin and elucidate unique feature of its nucleotide sequence, the “A+T”-rich region of mitochondrial DNA from $\text{Drosophila}\text{virilis}$ has been cloned in $\text{Escherichia}\text{coli}$. The chimeric plasmid DNA containing the “A+T”-rich region stimulates $\text{in}\text{vitro}$ DNA replication system from $\text{Drosophila}\text{virilis}$ mitochondria about ten fold higher than the parental plasmid DNA, as does native mitochondrial DNA.     

Specificity of DNA uptake in genetic transformation of gonococci

Genetic transformation of gonococci to streptomycin resistance was inhibited by homologous DNA or by DNA from related $\text{Neisseriae}$, but not by high concentrations of heterologous DNAs. Gonococci were capable of adsorbing large quantities (up to about 50 μg per 10⁸ cells) of both homologous and heterologous DNA, which could not be eluted by strong shearing forces. Treatment with externally added DNase removed virtually all the heterologous DNA while a small fraction of the homologous DNA, not influenced by the presence of excess heterologous DNA, remained cell-bound in a form resistant to nuclease treatment. Competing homologous DNA suppressed nuclease-resistant binding. These findings suggest that gonococci have two types of DNA binding components at their surface. Competence of gonococci for genetic transformation undergoes a rapid decay if the cells are incubated with homologous (but $\text{not}$ with heterologous) DNA.     

Preferential synthesis of yeast mitochondrial DNA in alpha factor-arrested cells

α factor is a diffusible substance produced by $\text{S. cerevisiae}$ cells of the $\text{α}$ mating type which inhibits cell division (1) and the initiation of nuclear DNA synthesis (2) in cells of the $\text{a}$ mating type. In this report, it is shown that mitochondrial DNA synthesis continues at a normal rate in $\text{a}$ cells for at least 6 hours in the presence of α factor, resulting in a 5-fold increase in the amount of mitochondrial DNA per cell. The continued synthesis of mitochondrial DNA in the absence of nuclear DNA synthesis allows specific labeling of yeast mitochondrial DNA.     

Effect of aphidicolin on viral and human DNA polymerases.

DNA polymerases induced by Herpes simplex and Vaccinia viruses are inhibited by aphidicolin and this inhibition is probably the basis of its antiviral activity $\text{in vivo}$. Its possible clinical use is however hampered by the concomitant effect on human replicative DNA polymerase α. The inhibition of human α-polymerase is reversible both $\text{in}$$\text{vitro}$ and $\text{in vivo}$ and the changes in the rate of incorporation of thymidine into DNA, following treatment with aphidicolin for a generation time, indicate the likely synchronization of the cells due to this agent. DNA polymerase β, which has recently been shown to carry out repair synthesis of damaged nuclear DNA, is not inhibited by aphidicolin either $\text{in vitro}$ on $\text{in vivo}$ suggesting that the drug could allow a rapid and simple evaluation of DNA repair synthesis due to DNA polymerase β.     

Pyridoxal 5' phosphate: a selective inhibitor of oncornaviral DNA polymerases.

Pyridoxal 5′ phosphate at concentrations < 0.5 mM inhibits $\text{polymerization}$ of deoxynucleoside triphosphate catalysed by variety of DNA polymerases isolated from type C RNA tumor viruses, as well as $\text{E.}\text{coli}$, but $\text{does}\text{not}$ affect the polymerase associated RNase H activity. Both phosphate and aldehyde groups of pyridoxal phosphate are essential for the inhibition which appears to be mediated through the reversible Schiff base.     

Studies on invitro DNA synthesis: II. Isolation of a protein which stimulates deoxynucleotide incorporation catalyzed by DNA polymerases of E.coli

Purified RNA polymerase, DNA polymerase III and unwinding protein of $\text{Escherichia}\text{coli}$ catalyze limited rifampicin sensitive fd or ØX 174 DNA-dependent DNA synthesis. A protein has been partially purified from $\text{E.}\text{coli}$ which stimulates rifampicin sensitive dXMP incorporation in this system 20 to 30 fold. This protein also stimulates DNA synthesis catalyzed by DNA polymerases I and II; the stimulation occurs in reactions primed with natural and synthetic DNAs as well as RNA-DNA hybrids. The protein is not a product of the known dna genes. In contrast to the above system of purified enzymes, rifampicin sensitive dXMP incorporation in crude extracts of $\text{E.}\text{coli}$ is specifically dependent on fd but not ØX 174 DNA. An additional factor has been isolated from extracts of $\text{E.}\text{coli}$ which restores specificity to the purified rifampicin sensitive system by preventing ØX 174 DNA from serving as a template.     

Transformability of DNA polymerase-deficient mutants of Bacillus subtilis

The effect of a deficiency in DNA polymerase on recombination in $\text{Bacillus}$$\text{subtilis}$ has been studied. It is concluded that the major DNA polymerase of $\text{B.}$$\text{subtilis}$ is not required for recombination, and that the recombination deficiency of a previously described DNA polymerase-deficient mutant is actually due to a $\text{rec}$ mutation. Genetic crosses imply that this recombination deficiency is not $\text{recA}$ or $\text{recB}$.     

A spectrofluorimetric investigation of calf thymus DNA modified by BP diolepoxide and 1-pyrenyloxirane

7β,8α-Dihydroxy-9α,10α-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BP diolepoxide, $\text{1}$) and 1-pyrenyloxirane ($\text{2}$) bind chemically to calf thymus DNA. The fluorescence efficiency of pyrenyl groups in mutagen modified DNA varies appreciably with its conformation and decreases in the order: pyrenees, modified denatured DNA and modified native DNA. A particularly interesting observation is that the fluorescence efficiency of mutagen modified DNA intensifies substantially upon denaturation. Our results suggest that the pyrenyl groups in mutagen modified DNA are intercalated between the base pairs of DNA. Since both $\text{1}$ and $\text{2}$ are powerful frame-shifting mutagens for S. typhimurium TA-98, the intercalative covalent binding of these compounds to DNA may provide a molecular basis for their mutagenic activity.     

Characterization of the stimulatory effect of T4 gene 45 protein and the gene 4462 protein complex on DNA synthesis by T4 DNA polymerase

On a variety of single-stranded DNA templates, the overall rate of in vitro DNA synthesis catalyzed by the bacteriophage T4 DNA polymerase is increased about fourfold by addition of the T4 gene $\text{44}\text{62}$ and 45 proteins. Several different methods suggest that this stimulation reflects an increase in the average DNA polymerase “sticking distance”, or processivity, from 800 to about 3000 nucleotides per initiation event. Both the $\text{44}\text{62}$ protein complex and the 45 protein must be present to obtain this effect, and either ATP or dATP hydrolysis is required. Rapid-mixing experiments indicate that the polymerase stimulation is maximized within a few seconds after addition of these “polymerase accessory proteins.”     

A comparison of DNA content between two substrains of Escherichia coli B/r.

The average DNA content per cell was measured in steady-state cultures of two substrains of $\text{E. coli}\text{B}\text{r}$ growing at various rates at 37°C. The DNA content of substrain $\text{B}\text{r}$ F was consistently lower than that of substrain $\text{B}\text{r}$ A. It is suggested that the differences in DNA contents are consequences of strain-specific differences in the relationship between chromosome replication and the division cycle of $\text{E. coli.}$     

Replication of repeated DNA in human cells

The replication pattern of the repeated sequence families of human DNA has been studied by means of DNA reassociation curves. Early- and late-replicating DNA fractions were obtained from synchronized cultures of KB cells by labeling cells with bromodeoxyuridine (BUdR) early or late in the DNA synthesis period and isolating the BUdR-containing DNA by CsCl density-gradient centrifugation. Highly repeated and moderately repeated sequence classes labeled with ${}^{14}\text{C-deoxycytidine}$ either early or late in the DNA synthesis period were also prepared. The effect of the isolated early- or late-replicating BUdR-DNA on the rate of reassociation of the ${}^{14}\text{C-labeled}$ repeated sequences was then tested. Increasing concentrations of early- or late-replicating BUdR-DNA were added to a constant amount of either ${}^{14}\text{C-labeled}$ early- or late-replicating repeated sequences, and the fraction of label in double-stranded DNA was determined. Analysis of the DNA reassociation curves so obtained indicates that some repeated sequence families are replicated throughout the DNA synthesis period whereas others are replicated primarily in the second half. This is true for both the highly-repeated and moderately-repeated sequence classes.     

Effects of aphidicolin on retrovirus DNA synthesis in vivo

Renaturation of $\text{Aequorea}$ green-fluorescent protein (A-GFP) was achieved for the first time following denaturation in guanidine-HCl or acid. Denaturation was accompanied by the concerted loss of visible fluorescence, alteration of absorption characteristics, and large negative deflection of CD signal in the far UV. Dialysis of a guanidine-denatured sample at pH 8 resulted in 64% renaturation (return to native absorption) and neutralization of an acid-denatured sample restored 90% of the native absorption. Renatured GFP is highly fluorescent and indistinguishable from native GFP with respect to the shape of excitation and emission spectra. Both native and denatured proteins exhibit resistance to trypsin hydrolysis and have identically broad pH and heat stability profiles, all of which suggest full renaturation.     

Chloramphenicol damages bacterial DNA.

L(+)-$\text{threo}$-chloramphenicol induces reversion of His^?$\text{Salmonella typhimurium}$ strains TA100 and TA1535 in the conventional Ames' assay without microsomal activation. Any mutagenicity of D(?)-$\text{threo}$-chloramphenicol was masked by toxicity. Similarly, a sensitive fluctuation test showed mutagenesis with L(+)-$\text{threo}$-chloramphenicol at concentrations of 0.5 μM and above but the D(?) isomer proved to be toxic even at these low levels. The L(+) isomer caused single strand breaks in the DNA of $\text{Escherichia coli}\text{B}\text{r}$ and $\text{Salmonella typhimurium}$ strains TA1535, TA100 and TA1976. The D(?) isomer caused breaks in $\text{Escherichia coli}\text{B}\text{r}$ and $\text{Salmonella typhimurium}$ TA1976 although it was less effective and it did not produce DNA breaks in TA1535 or TA100.     

Synthesis and decay of lambda DNA replication proteins in minicells

The coliphage λ DNA replication proteins, the $\text{O}$- and $\text{P}$-gene products, have been identified by infection of nonpermissive $\text{Escherichia coli}$ minicells with the appropriate λ amber mutants as proteins of a molecular weight of about 34000 and 23000, respectively. Proteins of exactly the same size were found in minicells harbouring the plasmid $\text{λ}\text{dv}$. Both proteins seem to be synthesized at the same rate. In λ-infected minicells, as well as in $\text{lambda;}\text{dv}$-harbouring minicells the pulse-and-chase experiments have shown an exceptionally rapid decay of the O-protein.