A THREE-COMPONENT THEORY OF SEDIMENTATION EQUILIBRIUM IN A DENSITY GRADIENT

States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM

Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.

Double-walled carbon nanotube processing

Single-walled carbon nanotubes (SWCNTs) have been the focus of intense research, and the body of literature continues to grow exponentially, despite more than two decades having passed since the first reports. As well as extensive studies of the fundamental properties, this has seen SWCNTs used in a plethora of applications as far ranging as microelectronics, energy storage, solar cells, and sensors, to cancer treatment, drug delivery, and neuronal interfaces. On the other hand, the properties and applications of double-walled carbon nanotubes (DWCNTs) have remained relatively under-explored. This is despite DWCNTs not only sharing many of the same unique characteristics of their single-walled counterparts, but also possessing an additional suite of potentially advantageous properties arising due to the presence of the second wall and the often complex inter-wall interactions that arise. For example, it is envisaged that the outer wall can be selectively functionalized whilst still leaving the inner wall in its pristine state and available for signal transduction. A similar situation arises in DWCNT field effect transistors (FETs), where the outer wall can provide a convenient degree of chemical shielding of the inner wall from the external environment, allowing the excellent transconductance properties of the pristine nanotubes to be more fully exploited. Additionally, DWCNTs should also offer unique opportunities to further the fundamental understanding of the inter-wall interactions within and between carbon nanotubes. However, the realization of these goals has so far been limited by the same challenge experienced by the SWCNT field until recent years, namely, the inherent heterogeneity of raw, as-produced DWCNT material. As such, there is now an emerging field of research regarding DWCNT processing that focuses on the preparation of material of defined length, diameter and electronic type, and which is rapidly building upon the experience gained by the broader SWCNT community. This review describes the background of the field, summarizing some relevant theory and the available synthesis and purification routes; then provides a thorough synopsis of the current state-of-the-art in DWCNT sorting methodologies, outlines contemporary challenges in the field, and discusses the outlook for various potential applications of the resulting material.

Hydrodynamic characterization of surfactant encapsulated carbon nanotubes using an analytical ultracentrifuge

The hydrodynamic properties of surfactant encapsulated single-walled carbon nanotubes (SWNTs) have been characterized by optically measuring their spatial and temporal redistribution in situ in an analytical ultracentrifuge. The measured redistribution profiles are fit to the Lamm equation, thus determining the sedimentation, diffusion, and hydrodynamic frictional coefficients of the surfactant encapsulated SWNTs. For sodium cholate encapsulated SWNTs, we demonstrate that the technique of analytical ultracentrifugation can be utilized to determine the linear packing density of surfactant molecules along the length of the SWNTs, 3.6 +/- 0.8 nm(-1), and the anhydrous molar volume of the surfactant molecules on the SWNT surfaces, 270 +/- 20 cm(3) mol(-1). Additionally, analytical ultracentrifugation is used to measure and compare the sedimentation rates of bundled and isolated carbon nanotubes. This study should serve as a guide for designing centrifuge-based processing procedures for preparing samples of SWNTs for a wide variety of applications and studies. Additionally, the results obtained here should aid in understanding the hydrodynamic properties of SWNTs and the interactions between SWNTs and surfactants in aqueous solution.

Adair was right in his time

The subunit molar mass of hemoglobin was established in the 19th century by chemical analysis, the tetramer structure by osmotic pressure determination in 1924 and by the newly developed analytical ultracentrifuge in 1926, which became a powerful tool for biological macromolecule molar mass determinations. The Svedberg equation was derived by eliminating the translational friction coefficient relating to sedimentation and diffusion in the ultracentrifuge in a strictly solute/solvent vanishing concentration two-component system analysis. A differential equation describing the radial equilibrium concentration distribution in the ultracentrifuge was also derived, both yielding the buoyant molar mass (1-nu2rho)M2 term. Many years later it was realized that solutions of biological macromolecules are multicomponent systems and the two-component analysis leads to minor or major erroneous results. Thermodynamic derivation of an equation for multicomponent systems redefines the buoyant molar mass terms by (deltarho/deltac2)muM2, leading to correct molar mass (g/mol) values following determination of the density increment at constant chemical potentials of diffusible solutes, and powerfully connects the analytical sedimentation equation to the osmotic pressure concentration derivative and, in a broad complementary sense, to light, X-ray and neutron scattering experiments. Macromolecular interactions can be studied with high precision and solute-solvent interactions yield powerful information relating to "thermodynamic" hydration, closely related to hydration derived from X-ray diffraction, as well as solute-cosolute interactions. A series of examples is given to demonstrate the correctness and usefulness of the thermodynamic multicomponent system approach. It is a strange fact that in current analytical ultracentrifugation analysis the elegant and powerful multicomponent solution technology is almost totally disregarded and the classical limited validity Svedberg approach is used uniquely.

Partial specific volume and preferential hydration of low density lipoprotein subfractions

We have determined the partial specific volume (v-) for five low density lipoprotein (LDL) subfractions (n = 5-7) and evaluated preferential hydration (n = 2) for LDL subfraction 3 in normolipoproteinemic subjects in order to characterize these highly atherogenic components of the human plasma lipoprotein spectra. Values for v- at 1 g were determined by sixth place density measurements of the solvent and lipoprotein solutions and carbon, hydrogen and nitrogen (CHN) absolute mass of the lipoprotein concentrations. Mean values for v- were 0.9757 +/- 0.0019, 0.9701 +/- 0.0007, 0.9674 +/- 0.0016, 0.9616 +/- 0.0016 and 0.9550 +/- 0.0025 ml/g for subfractions 1, 2, 3, 4 and 5, respectively. However, molecular densities (sigma) obtained from rho (rho) = 1/v- for respective LDL subfractions were 1.0249, 1.0308, 1.0337, 1.0399 and 1.0471 g/ml, respectively. The preferential hydration of lipoprotein subfraction 3 (n = 2) in NaCl/H2O solutions was 2.9-4.8 wt percent, whereas values were much lower (0.3-0.6 wt percent) in NaCl/NaBr/H2O solvent system. Unhydrated densities for LDL subfraction 3 (n = 2) at 1 g (sixth-place density meter) were 1.0287 and 1.0269 g/ml, whereas at 200,000 X g (used in D2O flotation eta F degrees vs rho determinations) both values were 1.0308 g/ml, indicating that these similar LDL fractions have 23 and 53% higher compressibility than the solvent at 200,000 X g force. It was observed that the linearity of eta F degrees vs rho may not be valid for solvents NaCl/NaBr/H2O of density as high as 1.4744 g/ml. Thus, flotation velocity data using extreme salt concentrations (1.4744 g/ml and higher) may be viewed with caution.

The early melting of closed duplex DNA: analysis by banding in buoyant neutral rubidium trichloroacetate

Aqueous RbTCA permits the buoyant banding of both native and denatured DNA at room temperature and neutral pH. A unique property of this solvent is the bouyant resolution of closed circular, underwound DNA (I) from the corresponding nicked (II) species. Conditions are reported here in which PM-2 DNA I is physically resolved from native PM-2 DNA II, the buoyant separation being 1.27 mq/ml in 3.3 M RbTCA at 25 degrees C. The separation between nicked and closed DNAs increases with temperature up to 35.5 degrees C, at which PM-2 DNA II cooperatively melts and subsequently pellets. The isothermal buoyant density of a cloed DNA increases linearly as the linking number (Lk) of the closed DNA decreases. The early melting of closed DNA may be monitored with high precision by buoyant banding in RbTCA, it being possible to detect the disruption of as few as 40 base pairs in PM-2 DNA (10,000 base pairs). The constraint that the linking number be conserved in closed DNA requires that a change in duplex winding be accompanied by a compensating change in supercoiling. We estimate the linking number deficiency of PM-2 DNA I to be 0.094 turns per decibase pair. This result permits the estimation of the EtdBr unwinding angle, phi, by comparison with alternative determinations of the linking number deficiency which depend upom the value of phi. The result obtained here is that phi = 27.7 degrees +/- 0.5 degrees and is approximately independent of temperature over the range 15 degrees-35 degrees.

Lysogenic conversion for multiple characters in a strain of Staphylococcus aureus

Lysogenization of nonlysogenic strains of Staphylococcus aureus was performed with two different bacteriophages, LS1 and LS2, that were unable to plaque on any of the strains of S. aureus tested. Infection of recipient strains was achieved when protoplasts were inoculated with LS1 or LS2 or when bacterial cultures were simultaneously inoculated with a virulent phage together with LS1 or LS2. Lysogenization was demonstrated by changes in phenotypic characters of the host strain and by liberation of bacteriophages from the modified strains as shown by electron microscopic examination. The lysogenic strains differed from the host strains by the following characters: they were coagulase, deoxyribonuclease, and lipase negative; they were untypable by the basic set of phages; they did not ferment mannitol under anaerobic conditions; and they produced only l-(+)-lactic acid by glucose fermentation. Their cell walls contained less glycine and concomitantly more serine than those of the host strains. Furthermore, they were devoid of protein A. Conversely, some antigenic factors as well as the presence of ribitol in the cell wall teichoic acid, indicated a parental relationship between the host strains and the derived lysogenic ones. Phages LS1 and LS2 could be excluded from the lysogenic strains by invading phages, and the revertant nonlysogenic strains recovered all of the characteristics of the initial host strains. It was thus concluded that the phenomenon described was due to lysogenic conversion. The origin of phages LS1 and LS2 is discussed.

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.

Macromolecular distribution near the limits of density-gradient columns. Some applications to the separation and fractionation of glycoproteins

1. Expressions are derived for the distribution at density-gradient equilibrium of macromolecules whose densities are (a) close to the values characterizing the solution limits or (b) outside the span of the gradient. 2. Density-distribution predicted by the expressions agree with those obtained by rigorous methods. 3. The distribution equations are applied to hypothetical mixtures of proteins and glycoproteins in commonly used density-gradient media to simulate separation and fractionation conditions. 4. It is shown that CsBr, although less efficient than CsCl for fractionation, is nevertheless adequate for most purposes; in analytical experiments it may often have advantages over CsCl. Limitations on the use of LiBr are explored. 5. An expression is derived which allows the variance of the partial specific volume of the macromolecular component to be determined from the variance of the buoyant density. It is shown that the relative resolving powers of different salts is expressed by their values of the quantity (formula: see text). 6. The equations are applied to a well-characterized glycoprotein preparation at equilibrium in CsCl and in Cs2SO4:it is shown that the much wider distribution in CsCl than in Cs2SO4 is explicable in terms of the variance in buoyant density and the solvation properties of the salts. 7. Limitations of the expressions arise when dispersity in density is represented by a low apparent molecular weight; realistic simulations can then only be obtained when the component is fully banded.

Purification and quantitative changes of mitochondrial DNA in etiolated cucumber seedlings

The mtDNA (mitochondrial DNA) extracted from etiolated seedlings of Cucumis sativus L. has been purified by a three-step procedure: RNase and pronase treatment, bio-gel filtration, analytical CsCl gradient centrifugation. This procedure appeared rapid, suitable for small quantities of DNA and gave highly reproducible results. It was used to follow the quantitative variation of the mtDNA in hypocotyls and cotyledons of dark-grown cucumber seedlings.The major feature occurring during the etiolation process appeared to be an important accumulation of the mtDNA in hypocotyls between 3 and 5 days of culture. The amount of the mtDNA per hypocotyl increased 5 times, the hypocotyl length and the total DNA increased 6 and 12 times respectively, between these two stages. It was demonstrated that at least during the first week of culture in the dark, endogeneous hormone-induced elongation in the cucumber hypocotyl (a non-dividing tissue) was associated to an important accumulation of mtDNA.

Composition and size of Shope fibroma virus deoxyribonucleic acid

Deoxyribonucleic acid (DNA) extracted from purified virions of Shope fibroma virus (SFV) (by using DNA from Microccocus lysodeikticus as marker) had a buoyant density of 1.6996 +/- 0.0003 g/ml), hence a guanine plus cytosine (G + C) content of 40.4 +/- 0.3%, which is close to the G + C content of the DNA of susceptible rabbit cells (40.9 +/- 0.4%) and different from that of vaccinia virus DNA (35.5 +/- 0.4%). For the determination of the molecular weight of DNA, SFV and vaccinia purified virions, treated with Pronase and detergent, were cosedimented in sucrose density gradients. Results showed that SFV-DNA has a molecular weight of about 153 x 10(6) daltons. By electron microscopy, only one molecule corresponding to this value was observed (its length was 80.3 mum). The others had a median size of 49.8 mum +/- 0.9.

Density invariance of cultured Chinese hamster cells with stage of the mitotic cycle

Isopycnic banding of Chinese hamster line CHO cells in Ficoll gradients shows that a population in balanced, exponential growth is very homogeneous with respect to density, the coefficient of variation of the density distribution spectrum being less than 5% of the mean reduced density (i.e. density minus one). Similar measurements on synchronized cultures indicate that reduced density varies by less than 2% around the life cycle. The mean density of CHO cells in F-10 growth medium is calculated to be 1.051 after correction for osmotic effects of the Ficoll gradient.

The use of equilibrium-density-gradient methods for the preparation and characterization of blood-group-specific glycoproteins

1. The method of sedimentation equilibrium in a gradient of caesium chloride has been applied to the preparation of blood-group-specific glycoproteins from human ovarian-cyst fluids: it is shown that virtually complete separation from contaminating protein is easily accomplished in a single step. 2. The glycoproteins isolated in this way have been characterized by analytical density-gradient experiments in both caesium chloride and caesium sulphate and values of the buoyant density, selective solvation and apparent molecular weight have been obtained. 3. In some cases, materials prepared from the same cysts by solvent extraction methods have also been characterized in these terms. 4. The selective solvation values are about 0.1 and 0.5g of water/g of glycoprotein in caesium chloride and caesium sulphate respectively. 5. The apparent molecular-weight values are much lower than the weight-average molecular weights, and it is shown that the origin of the discrepancy is heterogeneity in density of the glycoproteins. 6. Some sources of error in the interpretation of density-gradient schlieren patterns are examined.

Comparison of two serologically distinct ribonucleic acid bacteriophages. II. Properties of the nucleic acids and coat proteins

Overby, L. R. (University of Illinois, Urbana), G. H. Barlow, R. H. Doi, Monique Jacob, and S. Spiegelman. Comparison of two serologically distinct ribonucleic acid bacteriophages. II. Properties of the nucleic acids and coat proteins. J. Bacteriol. 92:739-745. 1966.-The ribonucleic acid (RNA) molecules and coat proteins of two RNA coliphages, MS-2 and Qbeta, have been characterized. MS-2 RNA shows an S(20,w) of 25.8 and a molecular weight by light scattering of 10(6). The corresponding parameters for Qbeta-RNA were 28.9 and 0.9 x 10(6). A difference in base composition was reflected in the adenine-uracil ratio, which was 0.95 for MS-2 and 0.75 for Qbeta. The two RNA preparations are readily separated by chromatography on columns of methylated albumin. Both gave identical bouyant densities in cesium sulfate of 1.64 g/ml. The coat protein subunits were of similar molecular weights: 15,500 (Qbeta) and 14,000 (MS-2). They differed, however, in that the Qbeta-protein lacked tryptophan and histidine, whereas the MS-2 protein lacked only histidine.

Zone centrifugation in a cesium chloride density gradient caused by temperature change

In this communication is described a new technique for the determination of sedimentation coefficients of macromolecules banded in equilibrium density gradients. Initially, the macromolecules are banded in the analytical ultracentrifuge at a low temperature of about 5 degrees C. After equilibrium has been obtained, the temperature is increased to 25 degrees C. The equilibrium band will now sediment to a new equilibrium position in the ultracentrifuge cell: (a) By following the position of the migrating band as a function of time, sedimentation coefficients may be determined. (b) If several species having different sedimentation coefficients are present in the original band, then during the course of the migration the band may split into several new bands which eventually reunite at the final equilibrium position. (c) If different chemical species of macromolecules such as nucleic acids and carbohydrates are present, in general they will exhibit different temperature density relationships, and can move different distances and directions in response to temperature change.