DNA replication in Physarum polycephalum: characterization of replication products made in isolated nuclei

Nuclei isolated from synchronous S-phase plasmodia of the myxomycete $\text{Physarum polycephalum}$ were competent in production of low molecular weight DNA replication intermediates. Furthermore, these nuclei showed some competence in joining these fragments into DNA of intermediate molecular weight. The DNA molecules made $\text{in vitro}$ could be correlated with products made $\text{in vivo}$.     

The template specificities of DNA polymerase in cell free lysates of Xenopus laevis eggs, larvae and immature ovaries

DNA polymerase activities in cell-free lysates of unfertilized eggs, larvae and immature ovaries of $\text{Xenopus}\text{laevis}$ were compared to purified $\text{E.}\text{coli}$ DNA polymerase I using several natural and synthetic templates. The templates were tested as the native and denatured forms of normal and DNase I treated molecules. Although the $\text{Xenopus}$ polymerases tended to prefer DNase I treated Xenopus DNA over the other templates tested, so did the $\text{E.}\text{coli}$ polymerase I. In general, the template preferences of the polymerases studied depended in complex ways on both the form and the species of origin of the template.     

Thermal analysis of bacteriophage T4.

The process of bacteriophage T4 morphogenesis was studied using a heat leakage scanning calorimeter. Thermograms of defective mutant 49 (am NG727) in permissive and non-permissive cells of $\text{Escherichia coli}$ showed a difference in thermal properties between packaged and non-packaged DNA molecules. $\text{In vivo}$, non-packaged DNA carried out their thermal transition at 85°C, the same temperature as that of T4 DNA melting measured in the standard saline citrate buffer, while the packaged DNA gave a sharper peak at 87°C due to some interaction with the head shell structure. Empty head shells showed a sharp heat absorption peak at 89°C both $\text{in vivo}$ and $\text{in vitro}$, indicating the high degree of cooperativity in their conformational changes.     

Detection of sequence heterology by use of the N. Crassa nucleases

We have used the single-strand specific nucleases of $\text{Neurospora crassa}$ to detect sequence divergencies between two similar DNA molecules: restriction endonuc lease $\text{Eco}$RI produced linears from Simian Virus 40 and a variant of human origin, DAR. Enzyme treatment of the heteroduplex DNA resulted in specific cleavage into two fragments of one-third and two-thirds genome length. These two viral DNAs therefore have at least one region of heterology located about 0.35 map units from the $\text{Eco}$RI site. Due to the known specificities of the $\text{N.crassa}$ nucleases, this technique is applicable to detect mutations in RNA or DNA genomes.     

Detection and resolution of closely related satellite DNA sequences by molecular cloning.

Highly repeated satellite DNAs often consist of mixtures of DNAs with closely related repeating sequences. By cloning individual molecules we have resolved the 1.705 g/cm³ satellite DNA of Drosophila melanogaster into two distinct components: poly$\text{d}\text{A-A-G-A-G}\text{T-T-C-T-C}$ and poly$\text{d}\text{A-A-G-A-G-A-G}\text{T-T-C-T-C-T-C}$. The presence of two distinct sequences within this physically homogeneous satellite DNA had not previously been detected by standard physical, chemical, or sequencing techniques. Both cloning and direct sequence analysis suggest that the five-base-pair and seven-base-pair repeating units reside on separate molecules and are not interspersed with each other.     

Topography of nucleic acid helices in solutions. 28. Evidence for a dynamic structure of DNA in solution

Proton magnetic resonance (pmr), ultraviolet absorption, induced circular dichroism (CD), and viscometric evidence is presented which show that reporter molecules $\text{1}$ and $\text{2}$ bind to DNA via an intercalation process. Preliminary kinetic studies show that the DNA·$\text{1}$ complex forms rapidly (i.e., <1 msec), whereas the DNA·$\text{2}$ complex forms at a considerably slower rate ($\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{> 100 msec}$). The kinetic results, and the steric requirements for intercalation of $\text{2}$ can be explained on the basis of a dynamic structure of DNA.     

Molecular characterization of a stable Flac plasmid

F$\text{lac}$S is a thermostable extrachromosomal element isolated in $\text{Salmonella typhimurium}$ which is altered in its replication as compared to its precursor F_ts114$\text{lac}$. Sedimentation of both these plasmids in alkaline sucrose gradients has indicated a difference in their sizes. Contour length measurements of open circular plasmid DNA molecules photographed in the electron microscope have revealed the estimated molecular weight of F_ts114$\text{lac}$ to be 81 × 10⁶ daltons while that of F$\text{lac}$S is 109 × 10⁶ daltons. F$\text{lac}$S may carry a segment of $\text{S. typhimurium}$ chromosomal or cryptic plasmid DNA.     

Structure and properties of hemocyanins. XIV. Reassociation of Helix pomatia alpha-hemocyanin

Helix pomatia α-hemocyanin dissociates within minutes into $\text{1}\text{10}$-size and $\text{1}\text{20}$-size molecules, on increase of pH in the alkaline region.The rate and final state of reassociation of $\text{1}\text{10}$-size and $\text{1}\text{20}$-size molecules have been studied, by turbidity measurements and ultracentrifugation, on lowering of pH or on the addition of calcium ions.Reassociation of $\text{1}\text{10}\text{-size}$ molecules proceeds in two phases, with half-times in the order of minutes and one hour, respectively. The slow phase is linked to the disappearance of transitory intermediates, presumably dimers and tetramers of $\text{1}\text{10}$-size molecules.A hysteresis is observed in the final state of pH-dependent and Ca²⁺-dependent dissociation-reassociation.Reassociation of $\text{1}\text{20}$-size molecules depends on the initial (isomeric) state of these molecules. The F(fast sedimenting)-$\text{1}\text{20}$-size molecules reassociate almost completely to whole molecules, whereas the S(slow sedimenting)-form does not reassociate at all.     

A catenated DNA molecule as an intermediate in the replication of the resistance transfer factor R6K in Escherichia coli

Pulse-labeling of an $\text{Escherichia coli}$ strain harboring the resistance transfer factor R6K results in a transient increase in labeled catenated R6K DNA molecules. After a chase the level of labeled catenated DNA molecules is greatly reduced concomitant with a marked increase in labeling of the supercoiled DNA form of R6K. The data presented support a role for the catenated DNA molecule as an intermediate in the replication of the plasmid R6K.     

Action of the S1 endonuclease from Aspergillus oryzae on simian virus 40 supercoiled component I DNA

The digestion products of superhelical component I of SV40 DNA incubated with various concentrations of nuclease S₁ from $\text{Aspergillus Oryzae}$, an enzyme specific for single-stranded nucleic acid, were studied. The enzyme shows a preference for supercoiled DNA I as opposed to relaxed DNA II molecules, and converts SV40 DNA I into linear molecules. Conditions have been developed under which the majority of SV40 DNA I molecules is converted into form II DNA. By using high concentrations of enzyme, it was possible to introduce further breaks in the DNA molecule; by increasing ionic strengh or using SDS this activity was not eliminated.     

Structure and properties of hemocyanins. XII. Electron microscopy of dissociation products of Helix pomatia alpha-hemocyanin: quaternary structure

Electron microscopy of the dissociation products of α-hemocyanin of the snail Helix pomatia reveals two distinctly different conformations of $\text{1}\text{10}$-size molecules: a C(compact)-form at high ionic strength and pH near 8, and an L(loose)-form at low ionic strength and/or higher pH.The size and shape of the C-$\text{1}\text{10}$-size molecules indicate a dissociation of the $\text{1}\text{2}$-size molecules along the (10,9) helical grooves, which have been shown to be boundaries between the morphological units of the cylinder wall (Mellema &; Klug, 1972). The 5-fold collar is distributed evenly among the C-$\text{1}\text{10}$-size molecules.The C → L conformational change is characterized by a drastic loosening of the $\text{1}\text{10}$-size molecules to a flexible cluster of globules, with a concomitant decrease of sedimentation coefficient and increase of intrinsic viscosity and frictional ratio.The $\text{1}\text{20}$-size molecule appears as a flexible, linear chain of seven or eight globules with a diameter of 55 to 60 Å. These globules are inferred to be the minimal oxygen binding units with a molecular weight of about 50,000, linked together by short stretches of the polypeptide chain.Stable intermediate dissociation products, $\text{2}\text{10}$, $\text{3}\text{10}$ and $\text{4}\text{10}$-size molecules, were obtained by intramolecular crosslinking of $\text{1}\text{2}$-size molecules with dimethyl-suberimidate prior to dissociation.     

Structural investigations of mode of action of drugs. I. Molecular structure of mitomycin C.

The crystal and molecular structure of the antitumor antibiotic mitomycin C has been determined by X-ray diffraction. The space group is monoclinic P2₁ with cell dimensions $\text{a}\text{=77.988(3)}$, $\text{b}\text{=20.355(7)}$, $\text{c}\text{=9.679(3)}\text{A}\text{?}$, β=95.99°(1) and Z=4. The structure was solved by direct methods. There are two independent molecules per asymmetric unit. The structure was refined to an R value of 0.049 for 2151 observed reflections measured on diffractometer. The benzoquinone ring is slightly deviated from planarity. The N4 in the indole ring behaves like an amide nitrogen owing to its participation in the conjugated benzoquinoid system. The five membered ring through C1, C2, C3, N4 and C9a adopts an envelope conformation. The molecules are held together in crystal by the hydrogen bonds. All nitrogens except N4 are involved in the hydrogen bonding. Studies with models of drug and DNA indicate two different kinds of mechanism for crosslinking.     

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.     

Interfacial spin trapping in model membrane systems

The nature of mitochondrial DNA replication during the synchronous cell cycle in the yeast, $\text{Saccharomyces}\text{cerevisiae}$ has been investigated by examining the rate of labeled DNA precursor incorporation into specific segments of the mitochondrial genome at defined points during synchronous growth. The movement of label uptake from one area of the DNA to another at different times during the synchronous cell cycle indicates mitochondrial DNA replication to be a synchronous process during this time with most or all molecules at the same point in replication at any given time during the cell cycle.     

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 $\text{recB}$.     

Transfection of Vibrio cholerae by bacteriophage phi 149 DNA

DNA isolated from Choleraphage ø149 of Group IV was infectious when mixed with competent $\text{V.}\text{cholerae}$ cells. The cells were competent during mid-log phase of growth. The infectivity of phage DNA was destroyed by deoxyribonuclease but not by ribonuclease or pronase. About 5 min is required for the establishment of the DNase resistant state. The dose response curve for transfection suggested that 2 to 3 molecules of DNA are required to produce one infections center. An infectivity of 5 × 10⁴ infectious center per μg of DNA was obtained.     

Kinetics of hydrolysis to tetraols and binding of benzo(a)pyrene-7,8-dihydrodiol-9,10-oxide and its tetraol derivatives to DNA. Conformation of adducts

When the major reactive metabolite of benzo(a)pyrene, $\text{trans}$ -7,8-dihydroxy - $\text{anti}$-9,10-epoxy -7,8,9,10-tetrahydrobenzo(a)pyrene ($\text{anti}$-BPDE) is incubated with DNA in aqueous solution at 25°C, both covalent binding and hydrolysis of $\text{anti}$-BPDE to its tetraols occur. Using fluorescence and absorption spectroscopy it is shown that hydrolysis of $\text{anti}$-BPDE is markedly accelerated by DNA. In the presence of 5A₂₆₀ units of DNA per ml in cacodylate buffer solution, at an initial concentration of DNA phosphate/$\text{anti}$-BPDE ratio of 100, both the extent of covalent binding to DNA ( < 7% of the total $\text{anti}$-BPDE initially present) and hydrolysis of $\text{anti}$-BPDE reach their maximum levels within less than five minutes after mixing. Absorption and electric linear dichroism spectra indicate that the tetraols bind non-covalently to DNA by an intercalation mechanism, whereas the covalent product displays the characteristics of an externally bound complex.     

Cryptic plasmid in Bacillus pumilus ATCC 7065

Approximately 2% of the deoxyribonucleic acid (DNA) extracted from $\text{Bacillus pumilus}$ ATCC 7065 can be isolated as covalently closed, circular duplex molecules. The 7065 plasmid-like DNA appears homogeneous with respect to size and has a molecular weight of approximately 6 million daltons. A biological function for this circular DNA element has not been determined.     

The effect of 5-azacytidine on E. coli DNA methylase.

5-Azacytidine, when added to growing $\text{E.}$$\text{coli}$ K12, causes a decrease in DNA methylation assayed $\text{in}$$\text{vitro}$. This decrease is greater when $\text{E.}$$\text{coli}$ DNA is used as substrate than when calf thymus DNA is used. The decrease in activity is not due to the inhibition of protein synthesis caused by this drug, since neither chloramphenicol nor rifampin causes a decrease in enzyme activity. The effect is specific for the DNA(cytosine-5)methylase; the methylation of adenine is not affected. The concentration of drug that inhibits the DNA methylase by 50% is the same concentration that inhibits cell growth by 50%.