Bibliothek

Notizen: The quantum theory of light absorption by a pair of neighboring absorbers is developed in the point dipole approximation for the circumstance where excited states decay only by radiative damping. Comparison with classical local field theories, in which the monomers are represented by constant, frequency-dependent complex polarizabilities, shows that these local field theories are valid for non-harmonic absorbers only in the weak interaction limit, and only when there exist no states with both monomers simultaneously excited (e.g. one excited vibrationally, the other electronically) that are nearly degenerate with the single excitation states and also connected to them by appreciable transition moments. Failure of the local field theories is, thus, shown to be a consequence of the non-harmonic nature of real absorbers.Using a general relation between the level-shift function and complex polarizability, a recipe is formulated for calculating the complex polarizability and spectrum of a dimer.

Notizen: A function analogue of the formal operator theory of Goldberger and Watson for the decay of prepared states is developed with a modification that permits treatment of degenerate, interacting intermediate states. The theory is applied to the problem of absorption of radiation by an absorber in a very intense monochromatic beam. In particular, a simple two-level absorber in a resonant monochromatic beam of sufficient intensity to induce transitions from the ground state at a rate exceeding the spontaneous emission rate from the excited state, but still lying well below the optical frequency characterizing the transition, is investigated with the conclusion that the absorption cross-section falls off with the one-half power of the incident intensity. Conditions for the possible experimental verification of this result are presented.

Notizen: The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.

Notizen: The pertinent correlation function for nmr dipolar relaxation of 31P by its neighboring protons in DNA is derived for a comparatively realistic model of the internal Brownian motions. These motions include the collective torsional deformation modes of the elastic filament, uncoupled local overdamped reorienting motions of the P-H vectors in harmonic potential wells within the nucleotide unit, and the compartively slow end-over-end rotations of the local helix axis. These latter slow axial tumbling motions essentially completely determine T2 but have virtually no effect on T1 or the nuclear Overhauser effect (NOE), which are governed almost exclusively by rapid torsional deformations and local reorientations on the nanosecond time scale. The essential behavior of the relevant correlation function for the collective torsional motions has recently been determined experimentally in this laboratory using the decay of fluorescence polarization anisotropy of bound ethidium dye [J. C. Thomas et al. (1980) Biophys. Chem. 12, 177-180]. By using that result to carry out nmr relaxation calculations for various amplitudes and time constants of the uncoupled local motions and comparing them with the experimental data, it can be demonstrated that (within this model of purely dipolar relaxation), only rather small rms amplitudes of local reorientations (〈7°) occur and that their relaxation times are near 1 ns. Contrary to previous conclusions in the literature, the collective torsional deformation modes actually make the dominant contribution to T1 and NOE. At t = 1 ns the total rms azimuthal displacement of the P-H vector in this model is 19.5°, which results from a superposition of torsional deformations with rms displacement 18.2° and uncoupled local motions with rms displacement 7°. The contribution of pure chemical shift anisotropy (CSA) to the 1/T1 relaxation rate is calculated for the first time for the case when torsional deformation modes predominate, and it is predicted to be 46% of the corresponding dipolar relaxation rate or 31% of the total relaxation rate. Unusual magnetic field strength dependence of the pure CSA and dipolar contributions is predicted to arise as a consequence of the collective torsional deformation modes. This seriously weakens empirical arguments in favor of a small (〈10%) CSA contribution. In any case, a detailed interpretation of T1 and NOE incorporating both dipolar and CSA relaxation must await the evaluation of the CSA:dipolar interference term, or crossterm, contribution to the relaxation rate. The contribution of pure CSA to 1/T2 relaxation is likewise calculated for the case when local reorienting motions are negligible; it is found to be ≲16% of the corresponding dipolar relaxation rate for the comparatively short (300-600-base-pair) DNA fragments of interest. For high-molecular-weight DNAs we predict that the slow Rouse-Zimm coil-deformation modes will dominate 1/T2 relaxation and the linewidth. Dynamic light-scattering and other evidence is presented that the remarkable loss of nmr signal from DNA on addition of ethidium bromide, as reported by Hogan and Jardetzky, is actually a consequence of phase separation in such concentrated solutions. A pronounced decrease in T2, due to greatly hindered axial tumbling in the more concentrated phase, is advanced as a plausible line-broadening explanation for the apparent loss of nmr signal from DNA in that phase.

Notizen: Internal Brownian motions of clean φ29 and λ-DNAs have been studied using photon-correlation techniques at both visible (λ0 = 632.8 nm) and uv (λ0 = 363.8 nm) wavelengths. The present dynamic light scattering data, which extend to K2 = 19 × 1010 cm-2, can in every case be satisfactorily simulated by a Rouse-Zimm model polymer with an appropriate choice of the three model parameters. The effects of pH, salt concentration, single-strand breaks, and molecular weight on those model parameters have also been investigated. Intact clean DNAs exhibit surprisingly little variation with pH from 7.85 to 10.25, with salt concentration from 0.01 NaCl to 5.4M NH4Cl, or with molecular weight or GC content. The single-strand breaks have no effect at pH 9.46, but produce dramatic changes in the model parameters at pH 10.0 and 10.25, indicating the introduction of titratable joints at those pHs. The failure of either single-strand breaks or a large change in GC content to alter the model parameters in the neutral pH range is a strong indication that local denaturation is not required for those flexions and torsions that dominate the relaxation of fluctuations in the scattered light. The Langevin relaxation time for the slowest internal mode of a particular Rouse-Zimm model derived from the dynamic light scattering data is compared with pertinent literature data extrapolated to the same molecular weight. The present algorithm for determining model parameters from the light-scattering Dapp vs K2 curve actually yields a Langevin time in fairly good agreement with the literature value. For unknown reasons the light-scattering D0 values generally exceed those obtained from the molecular weight and sedimentation coefficient by about 20%.

Notizen: Dynamic light-scattering techniques are employed to study the internal Brownian motions of a commercial calf thymus DNA, clean and contaminated φ29 DNAs, and a clean φ29 DNA with bound spermidine as a function of pH. The Rouse-Zimm model parameters of both calf thymus and contaminated φ29 DNAs differ substantially from those of clean φ29 DNA in the neutral-pH region. However, this difference is largely removed by adding 0.01M EDTA (which has no effect on clean φ29 DNA) to the calf thymus DNA sample. These findings imply the existence in that preparation of polycation contaminants, presumably basic proteins, that can substantially alter the local mechanical properties of the DNA near their binding sites. The internal motion parameters kBT/f and b of both calf thymus and contaminated φ29 DNAs are found to exhibit pronounced characteristic variations between pH 8.5 and 10.5, over which range there is essentially no detectable titration to a resolution of about 1% of the base pairs. These variations, which are not observed for clean φ29 DNA, are qualitatively similar to those previously reported for a φ29 DNA with 21 single-strand breaks per chain. This indicates the formation of titratable joints associated with bound polycation contaminants. These basic ligands presumably facilitate local denaturation by stabilizing the titration of one or more protons on base-ring nitrogens near their binding sites. Spermidine binding up to 85-87% of neutralization of the total DNA charge has only a relatively minor effect on the internal motion parameters at neutral pH in 0.01M NaCl. However on raising the pH to 10.2, the internal motion parameter kBT/f undergoes a marked decrease similar to that observed for both calf thymus and contaminated φ29 DNAs and also φ29 DNA with single-strand breaks. This indicates that spermidine, too, is capable of inducing titratable joints. Evidence is presented that the titratable joints associated with bound polycations on the calf thymus DNA may serve primarily as torsion joints, as was found previously for the titratable joints associated with single-strand breaks.

Notizen: The hexamer of phycocyanin from Phormidium luridum has been isolated and purified by ammonium sulfate fractionation and gel chromatography. The protein is characterized by the sedimentation constant S°20, w = 10.2S, the diffusion coefficient D20, w = 4.73 × 10-7 cm2/sec, and intrinsic viscosity [η] = 3.89 ml/g. The molecular weight of the aggregate is 209,000. The shape and dimensions of the hexamer are discussed in terms of a model consisting of subunits arranged with C6 symmetry. The monomers, assumed to be spherical, are found to have a radius of 22 Å, and the diameter across the hexamer is 132 Å. The latter figure agrees closely with dimensions observed in electron micrographs.