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D C Rau

Publications and source records attributed to D C Rau.

54 records · Page 3Linked to original sources
PubMed1984

Higher order structure in a short repeat length chromatin.

Polynucleosomes from calf brain cortical neurone nuclei have an average repeat length of less than 168 base pairs. The ability of this material to adopt higher order structure has been assessed by various physical techniques. Although containing on average less DNA per nucleosome than is required to form a chromatosome, this short repeat length chromatin folded in an H1 dependent manner to a structure with properties similar to those observed for longer repeat length chromatins such as that of chicken erythrocyte (McGhee, J.D., D.C. Rau, E. Charney, and G. Felsenfeld, 1980, Cell, 22:87-96). These observations are discussed in the context of H1 location in the higher order chromatin fiber.

Animals↗
PubMed1984

Water near intracellular surfaces.

In this paper we make the following points: Water is perturbed within several angstroms of the surfaces of soluble molecules. Removal of this water can require significant amounts of work, seen as an exponentially varying "hydration force" with respect to molecular separation. The favorable and specific attractions that occur in molecular assembly or in ligand binding imply that the specific association between the molecular surfaces is stronger than the association of those surfaces with water. The specificity of biochemical association is not simply a matter of protein-protein interaction but also of competing protein-water interactions. Small structural changes in molecular surfaces can evoke large changes in the contact energy of hydrated surfaces; surface hydration and the energetics of water displacement are a likely mechanism for the contact specificity of intracellular associations integrating the cell matrix.

Body Fluids↗
PubMed1983

Histone hyperacetylation has little effect on the higher order folding of chromatin.

HeLa cells were grown in the presence of 10 mM sodium butyrate and soluble chromatin containing hyperacetylated histones was prepared by mild micrococcal nuclease digestion and sucrose gradient fractionation. Sedimentation and electric dichroism were used to study the cation-induced folding of this acetylated chromatin from the 10 nm filament to the 30 nm solenoid conformation. Although under some conditions acetylated chromatin appears slightly less condensed than control chromatin, the major conclusion is that hyperacetylation of histones does not in itself prevent the formation of the higher order chromatin solenoid.

Centrifugation, Density Gradient↗
PubMed1983

Higher order structure of chromatin: orientation of nucleosomes within the 30 nm chromatin solenoid is independent of species and spacer length.

We have used electric dichroism to study the arrangement of nucleosomes in 30 nm chromatin solenoidal fibers prepared from a variety of sources (CHO cells, HeLa cells, rat liver, chicken erythrocytes, and sea urchin sperm) in which the nucleosome spacer length varies from approximately 10 to approximately 80 bp. Field-free relaxation times are consistent only with structures containing 6 +/- 1 nucleosomes for every 11 nm of solenoidal length. With very few assumptions about the arrangement of the spacer DNA, our dichroism data are consistent with the same orientation of the chromatosomes for every chromatin sample examined. This orientation, which maintains the faces of the radially arranged chromatosomes inclined at an angle between 20 degrees-33 degrees to the solenoid axis, thus appears to be a general structural feature of the higher order chromatin fiber.

Animals↗
PubMed1983

Electric dichroism of DNA. Influence of the ionic environment on the electric polarizability.

In order to test the diffuse ion atmosphere polarization model recently developed by us, the effects of ionic strength, titrating with Mg2+ and Co(NH3)3+6, and coion charge on the electric polarizability of short fragments of DNA are investigated. The results are consistent with the predictions of the theory and show that the diffuse ion atmosphere polarization contributes significantly to the overall orientation of DNA. At low ionic strengths, we attempt to separate the total dipole moment into two components: one that agrees well with the Debye-Hückel ion atmosphere calculations, while the other, presumably due to condensed counterion polarization, appears to be substantially independent of the ionic strength. At higher salt concentrations, however, a simple separation into dipole components is not possible, perhaps due to a significant coupling of ion flows between the diffuse atmosphere and the condensed counterion layer.

Animals↗
PubMed1983

Chromatin structure of the chicken adult beta-globin gene: is gene activity associated with local or long-range perturbations in chromatin structure?

We review our physical studies on the higher-order structure of bulk chromatin. Using the method of electric dichroism, we determine the arrangement of DNA in the 30-nm solenoid or thick chromatin fiber. With few assumptions, our results lead to a detailed model, in which the chromatosomes are arranged radially but tilted approximately 25 degrees from the solenoid axis. We then attempt to determine if the chromatin of the adult beta-globin gene in embryonic chicken red cells normally exists in a solenoidal configuration. We conclude that it does and that the stability of this globin gene-containing solenoid is similar to that of bulk DNA. Furthermore, the solenoid stability is not measurably perturbed by the binding of the nonhistone chromosomal proteins HMG 14 and 17. We describe the nature of a hypersensitive site close to the 5' end of the adult beta-globin gene. Approximately 200 bp of DNA appear accessible to nuclease digestion and moreover a substantial portion of this region can be excised as naked DNA. Overall there is strong evidence that gene activity is associated with local perturbations in chromatin structure but much weaker evidence that gene activity is associated with a perturbation in chromatin higher-order structure.

Animals↗
PubMed1982

Length changes in solution accompanying the B-Z transition of poly (dG-m5dC) induced by Co(NH3)63+.

Transient electric dichroism measurements have been used to observe the rotational relaxation times of 145 base pair fragments of poly (dGm5dC) and random sequence DNA to solution. From these the lengths of the fragments are calculated and the interbase pair separation or rise per base pair (RPB) calculated. The observations show that even in low salt, the addition of very low concentrations of trivalent Co(NH3)63+ results in a transition of the dGm5dC polymer from B-form to Z-form with a change in the RPB from 3.4 +/- .06A to 3.7 +/- .06A, the latter form defined by the criterion of an inverted circular dichroism spectra similar to that observed at high salt in the absence of Co(NH3)63+. The 145 base pair DNA and poly (dGm5dC) are found to be essentially fully extended rods in low salt (0.2 - 2 mM Na+) solutions.

Base Composition↗
PubMed1982

The high mobility group proteins HMG 14 and 17, do not prevent the formation of chromatin higher order structure.

The high mobility group proteins, HMG 14 and 17, have been associated with the chromatin of active genes (refs 1-8), although how they function is not known. We use sedimentation and electric dichroism to investigate the effect of HMG 14 and 17 on the condensation of chicken erythrocyte chromatin into higher order structure. We find no evidence that excess HMG 14 and 17 induce an extended configuration, either in bulk chromatin or in the chromatin of the chicken beta-globulin gene.

Animals↗
PubMed1982

Participation of core histone "tails" in the stabilization of the chromatin solenoid.

We show here that the solenoid is maintained by the combination of linker histones and the nonglobular, highly basic "tails" of the core histones, which play only a minor part in the formation of the nucleosome core (Whitlock and Simpson, 1977. J. Biol. Chem. 252:6,516--6,520; Lilley and Tatchell, 1977. Nucleic Acids Res. 4:2,039--2,055; and Whitlock and Stein, 1978. J. Biol. Chem. 253:3,857--3,861). Polynucleosomes that contain core histones devoid of tails remain substantially unfolded under conditions otherwise favorable for the formation of solenoids. The tails can be replaced by extraneous basic polypeptides and in the presence of the linker histones the solenoid structure is then spontaneously recovered, as judged by a wide variety of structural criteria. The inference is that the core histone tail segments function by providing electrostatic shielding of the DNA charge and at the same time bridging adjacent nucleosomes in the solenoid. Our results carry the further implication that posttranscriptional modifications, such as acetylation of epsilon-amino groups, that reduce the positive charge of the core histone tails will tend to destabilize the higher-order structure and could thus render the DNA with which they are associated more readily available for transcription.

Centrifugation, Density Gradient↗
PubMed1981

Polarization of the ion atmosphere of a charged cylinder.

The dipole moment is calculated for an electric-field-induced polarization of a Debye-Hückel ion atmosphere surrounding a charged rod. If L is the length of a thin rod. Q is its linear charge density, Z is charge of the salt ion in solution, and k is the Debye-Hückel shielding parameter, then for KL less, similar 10, the calculated polarizability is proportional to Z(2)Q(2)L(1.8)/K(1.2). Comparison with experimental data for DNA shows that the ion atmosphere dipole is of the correct magnitude and is consistent with observed variations with Z, Q, L and k.

Journal Article↗
PubMed1980

Orientation of the nucleosome within the higher order structure of chromatin.

We have used electric dichroism to investigate chromatin fragments isolated from chicken erythrocytes. Both within the extended "10 nm filament" present at low salt and the condensed "30 nm solenoid" induced by the addition of divalent cations, the data give a quantitative description of the DNA conformation in the higher order structure of chromatin. In the 10 nm filament both the spacer DNA and the flat faces of the core particle discs must be oriented within 20 degrees of the fiber axis. Within the Mg++-induced 30 nm solenoid the flat faces of the core particles must also be oriented close to parallel to the solenoid axis, the estimated angle depending upon the disposition of the spacer DNA. We suggest a model for the 30 nm solenoid.

Animals↗
PubMed1980

Polyelectrolyte effects in DNA condensation by polyamines.

The conditions required for the counterion induced collapse of T7 bacteriophage DNA are briefly reviewed. Using Manning's counterion condensation theory we calculate a striking unity among collapse conditions: collapse occurs when from 89% to 90% of the DNA phosphate charges are neutralized by condensed counterions. The forces involved in collapsed DNA are investigated with emphasis on electrostatic repulsion. It is concluded that polyelectrolyte repulsion is the dominant force opposing collapse. Comparison of the results or polyelectrolyte repulsion calculation made using numerical methods and the Poisson-Boltzmann equation, with values of the attractive energies due to London dispersion interactions, leads to the conclusion that dispersion forces are probably large enough to cause collapse when the repulsions have been reduced by the presence of multivalent counterions.

Calorimetry↗
PubMed1980

Comparison of polyelectrolyte theories of the binding of cations to DNA.

Predictions of the binding of counterions to DNA made using the counterion condensation theory developed by Manning are compared with those made using the Poisson-Boltzmann equation, solved numerically by the Runge-Kutta procedure. Ions are defined as territorially or atmospherically bound if they fall within a given distance, defined by counterion condensation theory, from the DNA surface. Two types of experimental situations are considered. The first is the delocalized binding of a single type of counterion to DNA. In this case the Poisson-Boltzmann treatment predicts somewhat lower extents of binding TO DNA, modeled as a 10-A radius cylinder, than does Manning theory. The two theories converge as the radius decreases. The second type of experiment is the competition of ions of different valence for binding to DNA. The theories are compared with literature values of binding constants of divalent ions in the presence of monovalent ions, and of spermidine 3+ in the presence of Na+ or Mg2+. Both predict with fair accuracy the salt dependence of the equilibrium constants.

Cations↗
PubMed1978

A unified theory of nucleation-rate-limited DNA renaturation kinetics.

DNA renaturations under nucleation-rate-limiting conditions on simple DNA such as bacterial and bacteriophage DNA show significant deviation from ideal second-order kinetics when followed by optical density measurements at 260 nm. Ideal second-order kinetics yield linear plots when the data is plotted in the standard reciprocal second-order (RSO) manner. The observed deviations from ideal second-order behavior take the form of steadily downward-curving RSO plots. In this paper, experiments are presented for E. coli and T2 DNA documenting this non-ideal behavior. Since experiments using T4, T5 and B, subtilis DNA yield identical non-ideal behavior, this behavior appears to be a property of DNA renaturation followed by optical density, not a peculiarity of a particular DNA. Identical non-ideal behavior is also seen in kinetics followed by S1 nuclease assay. A theory is developed to explain this deviation from ideal second-order kinetics. The theory also explains why kinetics followed by hydroxyapatite chromatography show nearly ideal second-order kinetics. In contrast to the approach taken by others in developing equations that describe S1 nuclease monitored reactions, our view is that nonideal second-order kinetics are fundamentally due to the reacton of free single strands to yield partially helical duplex species. Later reactions of these species tend to reduce the deviations from non-ideal second-order kinetics.

DNA↗