Victor A. Bloomfield

Sedimentation Coefficients of Linear and Cyclic Wormlike Coils with Excluded‐Volume Effects

The sedimentation coefficient for the Kratky—Porod wormlike coil is calculated with the effects of excluded volume taken into account. The statistical length of native DNA is found to be 900 A. The hydrodynamic diameter of the Watson—Crick helix is 26–27 A. Sedimentation coefficients are calculated to decrease by about 13% on going from a cyclic native DNA to a linear molecule of the same molecular weight.

Intrinsic Viscosity of Wormlike Chains with Excluded‐Volume Effects

The intrinsic viscosity [η] as a function of molecular weight M has been calculated for the Kratky‐Porod wormlike chain, taking into account excluded‐volume effects. The Peterlin theory of intrinsic viscosity was used for the calculation. The result for high molecular weights can be written [η] + bη′ ( 1 + β′M − (1 + e) / 2)M2e = KηM(1 + 3e) / 2, where e is an excluded‐volume parameter. The Kuhn statistical segment length for native double‐standard NaDNA in 0.195M [Na+] is found to be 542 A, in fair agreement with, but somewhat lower than, the values found by other techniques. The hydrodynamic diameter of the double helix is evaluated as 79–82 A, which is substantially higher than the value found from sedimentation coefficient measurements, and which appears physically unreasonable. Comparison with other theories of the intrinsic viscosity of wormlike coils, neglecting excluded‐volume effects, is made. The value of the Mandelkern‐Flory‐Scheraga parameter β has been calculated as 2.87 × 106, higher by abou...

The configuration of polysomes in solution

Abstract Sedimentation coefficients of polysomes containing from 1 to 12 ribosomes have been calculated and compared with experimental data obtained by other workers. Helical polysome models, in which the helix pitch is the same as the center-to-center nearest neighbor ribosome distance, give configurations which are too compact. Random coil polysome models, generated by complete enumeration or by Monte Carlo computer techniques on tetrahedral and five-choice cubic lattices and in free space, taking excluded volume effects into accounts, give configurations which are too extended. Satisfactory agreement with experiment may be obtained by increasing the helix pitch or by invoking small attractive interactions, of magnitude a few tenths of a kcal/mole, between ribosomes in random configurations. Although neither possibility can be definitely excluded, it is argued that the configuration of polysomes in solution is largely random. The effect of messenger RNA “tails” on the sedimentation of small polysomes is also discussed.

Light Scattering and Hydrodynamic Properties of Polymer Chains with Excluded Volume Effects

This paper considers the implications of the Domb–Gillis–Wilmers distribution function PN(R) = CNRδexp−(R / σ)δ for end‐to‐end distances R in polymer chains of N segments with excluded volume effects. CN is a normalizing constant; e is related to the standard deviation of R; and, according to Fisher, δ = 2 / (1 − e), where e is defined by 〈R2〉 = b2N1+e for polymers with step length b. We have calculated the angular dependence of light scattering, the translational frictional coefficient and intrinsic viscosity, and the dimensional statistics of cyclic chains. Comparison has been made with a previously used distribution function which took excluded volume effects into account in a less well‐founded way. The present distribution function gives properties which differ measurably from those obtained with the previous one, reflecting the greater average expansion of the chain implied by the distribution proposed by Domb et al.

Binding of proflavine and ethidium bromide to two forms of T2 bacteriophage with different sedimentation coefficients

Abstract Equilibrium and kinetic studies of binding of proflavine and ethidium bromide to T2 phage indicate that (1) most of the intraphage DNA is accessible to proflavine; (2) the bulkier ethidium cation binds to a limited amount of DNA within the phage head; (3) intraphage DNA and free DNA in solutions of high ionic strength have similar equilibrium constants for binding to proflavine and ethidium; (4) on a time scale of minutes to hours, there is little difference in the permeabilities of the fast sedimenting (1000 S) and slow sedimenting (700S) forms of T2 phage as measured by proflavine binding.

Estimation of High‐Polymer Excluded Volume from Numerical Studies on Short Chains

The mean‐square length 〈R2〉 of a polymer molecule composed of n segments is assumed to behave asymptotically as 〈Rn2〉 ∼ An1+e for large n, where A is a constant and e takes into account the excluded‐volume effect. This paper compares calculations of 〈Rn2〉 for the model of a polymethylene chain without excluded volume studied by Flory and Jerigan with the model of a polymer as a self‐avoiding walk on a crystal lattice which has been studied by the method of exact enumeration developed by Domb. For the first model e = 0, whereas for the second, which includes the excluded‐volume effect, e = 15. It is shown using the extrapolation technique of Neville tables that the exact‐enumeration method correctly predicts e = 0 for the Flory–Jernigan model. However, the rate of convergence is very much slower than comparable calculations using the fcc lattice and taking account of excluded volume.

Hydrodynamic study of short range interactions in single-stranded polynucleotides

Abstract Equations are presented for the analysis of sedimentation-molecular weight and viscosity-molecular weight data on flexible polymers, which enable determination of the effective monomer length b in nonideal solvents. The treatment is applied to published data on single-stranded polynucleotides. b decreases from 14.4 ± 0.8 A in 0.013 M Na+ to 12.9 ± 0.8 A in 0.2 M Na+, but appears to remain constant at higher ionic strengths. These results are consistent with the damping out of repulsive Coulombic interactions between the phosphates, and may also reflect an increase in the amount of single-stranded helix, with increasing salt.