A three-component theory of sedimentation equilibrium in a density gradient

In the original analysis (1) of the behavior of macromolecules and viruses in a density gradient at equilibrium in the ultracentrifuge, only two incompressible components were considered to be present. These were the polymer and the solvent which forms the density gradient. The pressure-dependent terms and the cross terms in the chemical potential which describe the chemical reactions between the polymer and the solute were neglected. It has been pointed out from theoretical considerations (2-4) that these terms are important. In experimental studies of the buoyant behavior of bovine mercaptalbumin in aqueous cesium chloride,(5) it was observed that both solvation and pressure effects are large

Microsomal nucleoprotein particles from pea seedlings

Ultracentrifugal analysis of an extract of pea epicotyls, previously freed of debris and larger particles by centrifugation at 40,000 g for 10 minutes, has revealed the presence of a major component which possesses a sedimentation coefficient of 74 S. This component constitutes about 25 per cent of the TCA-precipitable material in the clarified epicotyl extract and is estimated to make up 1 to 2 per cent of the dry weight of the original tissue. In size, chemical composition, and morphology, the 74 S component resembles the nucleoproteins of the microsomes from animal tissues. The 74 S component of pea epicotyl extracts has been purified by repeated cycles of differential centrifugation to yield a preparation which is 80 per cent homogeneous in the analytical ultracentrifuge. It has been found to contain 30 to 37 per cent RNA as judged by a variety of analytical techniques. Approximately 55 per cent of the weight of the material is protein and a further 4.5 per cent phospholipide. Electron micrographs of air-dried specimens of the purified preparation show the 74 S constituent to be flattened spheres with an average height of 180 A and an average diameter of approximately 280 A. The molecular weight of the 74 S particles is computed from sedimentation, viscosity, and partial specific volume data to be 4.5 million ± 10 per cent in agreement with the value estimated from electron micrographs. The 74 S or microsomal component of pea epicotyls is rapidly aggregated in the presence of low concentrations of Mg ions or by somewhat higher concentrations of Ca or K salts. ATP on the contrary causes resolution of electrolyte-induced microsomal aggregates with simultaneous degradation of the particles to an ultracentrifugally inhomogeneous mixture of lower molecular weight materials

Mitochondrial DNA replication in sea urchin oocytes

Mitochondrial DNA (mtDNA) replicative intermediates from Strongylocentrotus purpuratus oocytes were isolated by ethidium bromide-CsCl density gradient centrifugation and examined by electron microscopy after formamide spreading. In some experiments, the mtDNA was radioactively labeled by exposing isolated oocytes to [3H]thymidine. Oocyte mtDNA replication appears to follow the displacement loop model outlined in mouse L cells. There are differences in detail. The frequency of D-loop DNA is much lower in oocytes, suggesting that the relative holding time at the D-loop stage is shorter. Duplex synthesis on the displaced strand occurs early and with multiple initiations. The frequency of totally duplex replicative forms, or Cairns' forms, is the highest reported for mtDNA. The differences may be related to the fact that oocyte mtDNA replication occurs in the absence of cell division and need not be coordinated with a cell cycle. Molecules with expanded D loops banded in the intermediate region between the lower and upper bands in an ethidium bromide-CsCl gradient, supporting the notion that displacement replication proceeds on a closed circular template which is subject to nicking-closing cycles. In mature sea urchin eggs, replicative forms are absent and virtually all the mtDNA is stored as clean circular duplexes. Some novel structural variants of superhelical circular DNA (molecules with denaturation loops and double branch-migrated replicative forms) are reported

Physical and Topological Properties of Circular DNA

Several types of circular DNA molecules are now known. These are classified as single-stranded rings, covalently closed duplex rings, and weakly bonded duplex rings containing an interruption in one or both strands. Single rings are exemplified by the viral DNA from φX174 bacteriophage. Duplex rings appear to exist in a twisted configuration in neutral salt solutions at room temperature. Examples of such molecules are the DNA's from the papova group of tumor viruses and certain intracellular forms of φX and λ-DNA. These DNA's have several common properties which derive from the topological requirement that the winding number in such molecules is invariant. They sediment abnormally rapidly in alkaline (denaturing) solvents because of the topological barrier to unwinding. For the same basic reason these DNA's are thermodynamically more stable than the strand separable DNA's in thermal and alkaline melting experiments. The introduction of one single strand scission has a profound effect on the properties of closed circular duplex DNA's. In neutral solutions a scission appears to generate a swivel in the complementary strand at a site in the helix opposite to the scission. The twists are then released and a slower sedimenting, weakly closed circular duplex is formed. Such circular duplexes exhibit normal melting behavior, and in alkali dissociate to form circular and linear single strands which sediment at different velocities. Weakly closed circular duplexes containing an interruption in each strand are formed by intramolecular cyclization of viral λ-DNA. A third kind of weakly closed circular duplex is formed by reannealing single strands derived from circularly permuted T2 DNA. These reconstituted duplexes again contain an interruption in each strand though not necessarily regularly spaced with respect to each other

Cytoplasmic DNA in the unfertilized sea urchin egg: Physical properties of circular mitochondrial DNA and the occurrence of catenated forms

The mitochondrial DNA in the unfertilized egg of the sea urchin Lytechinus pictus is present in an amount approximately seven times that of the haploid nuclear DNA.(1) The mitochondrial DNA has a higher buoyant density than the nuclear DNA and consists of circular duplex molecules of a uniform size of about 5µ. The circular DNA has been recovered(1) in both the intact (closed) and nicked (open) states characteristic of the circular duplex viral DNA's(2) and the mitochondrial DNA's from birds and mammals.(3, 4

The Buoyant Behavior of Viral and Bacterial DNA in Alkaline CsCl

In equilibrium density gradient centrifugation, the banding polymer species is electrically neutral. The banding species for a negative polyelectrolyte with a polyanion P_(n)^(-z)n (where n is the degree of polymerization, and z the titration charge per monomer unit) in a CsCl salt gradient is CS_(zn)P_n. If the ion P_(n)^(-z)n is itself a weak acid, it may be titrated to the state P_(n)^(-(Zn+y)) by CsOH; the banding species is then Cs_(zn+y)P_n. Because of the large mass and high effective "density" of a Cs^+ ion, it is to be expected that the buoyant density in a CsCl gradient of a polymer acid will be increased by such a partial alkaline titration with CsOH. This expectation has been confirmed for polyglutamic acid (where z = 0 at low pH). The guanine and thymine monomer units of DNA are weak acids. The present communication is concerned with the increase in buoyant density of DNA in alkaline CsCl solutions. It is well known that the guanine and thymine protons are more readily titrated in denatured DNA than in native DNA. We find that the buoyant density of denatured DNA and of single strand ϕX-174 DNA gradually increases as the pH of the solution is increased beyond pH 9.8. The density of native DNA is not affected until a critical pH > 11 is reached, where the DNA abruptly denatures and increases in density. Similar increases in buoyant density have been observed independently by Baldwin and Shooter in their studies of 5BU[overbar]-substituted DNA's in alkaline solutions

THE ISOLATION OF MYXOMYOSIN, AN ATP-SENSITIVE PROTEIN FROM THE PLASMODIUM OF A MYXOMYCETE

1. A procedure has been developed for the preparation of an active concentrate from the myxomycete, Physarum polycephalum. This concentrate responds with a lowered viscosity to the addition of small amounts of ATP. The preparation recovers in viscosity, and the process may be repeated. 2. In the most active concentrates, 75 per cent of the non-dialyzable material moves as a single boundary both in the descending limb in electrophoresis and in the ultracentrifuge. It contains about 10 per cent ribonucleic acid, which is at least in part reversibly bound to the protein. 3. The active material has been designated myxomyosin because of its origin and its similarity to actomyosin in ATP response

OBSERVATIONS ON AN ATP-SENSITIVE PROTEIN SYSTEM FROM THE PLASMODIA OF A MYXOMYCETE

1. Extracts of the plasmodia of the myxomycete, Physarum polycephalum, exhibit reversible decreases in viscosity in response to the addition of ATP under appropriate conditions. The protoplasm material prepared by extraction with KCl solution can apparently exist in either a high or a low viscosity state. As prepared, it is in the low viscosity condition. Rapid and extensive increases in viscosity of the extract are brought about by addition of AMP, inorganic phosphate, or, under certain conditions, of ATP. Only after the high viscosity state has been attained does addition of appropriate quantities of ATP cause a reversible decrease in viscosity. 2. The active principle of crude plasmodial extracts may be concentrated by fractional precipitation with ammonium sulfate and is found in the fraction precipitated between 30 and 40 per cent saturation. This material possesses a higher viscosity than does the original crude extract and is apparently in the high viscosity state since the addition of ATP causes an immediate reversible decrease in viscosity. 3. The ATP-sensitive fraction of myxomycete plasmodia possesses a viscosity which is dependent upon its previous thermal treatment. Extracts incubated at 0° for a period of a few hours increase greatly in viscosity when they are returned to 24.5°. This increased viscosity is structural in nature, is destroyed by mechanical agitation of the solution, and may be reversibly destroyed by addition of ATP. 4. It is suggested that the ATP-responsive protein of myxomycete plasmodia may be related to sol-gel transformations which have been observed in intact plasmodia and may participate in the protoplasmic streaming of the intact organism. This suggestion is based upon the following facts: (a) the protoplasmic streaming of myxomycete plasmodia is increased by microinjection of ATP; (b) the gel portion of the cytoplasm at the site of the microinjection of ATP is extensively converted to the sol state. The changes in structure of the intact cytoplasm are thus similar in nature to the changes exhibited in response to ATP by the purified ATP-sensitive protein. 5. The ATP-sensitive protein of myxomycete plasmodia appears to undergo reversible aggregation to form a high viscosity state. The function of ATP is to break down the aggregates thus formed. Since a specific ATPase activity is associated with the purified material, added ATP is gradually destroyed and recovery of viscosity attends the spontaneous reconstitution of aggregates