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Notes: Abstract Measurements of viscoelastic retardation times of detergent-Pronase lysates of Drosophila cells demonstrated the presence of large numbers of DNA molecules of a size commensurate with that of the chromosomes. The values estimated from the retardation times for the molecular weights of the largest molecules ranged from about 20×109 to 80×109 daltons depending on the species of Drosophila. The molecular weights of the DNA molecules were independent of the metaphase shapes (i.e., metacentric or submetacentric), but were proportional to the DNA contents of the chromosomes in the case of translocations or deletions. It was concluded, therefore, that the DNA molecules must run the length of the chromosome and cannot be discontinuous at the centromere. When compared with the values of the DNA contents of Drosophila chromosomes determined by other methods, the results were consistent with the model of one, or possibly two, DNA molecules per chromosome; the simplest conclusion, that there is only one DNA molecule per chromosome (for simple chromosomes), rests on a long extrapolation of an empirical relation between retardation time and molecular weight, but is also favored by indirect evidence. Further possibilities which could not be excluded were that the large DNA molecules contained Pronase-resistant, non-DNA links, or that a fraction of smaller DNA molecules might also have been present in the chromosomes. Chromosome-sized DNA molecules were obtained almost quantitatively from unsynchronized cultured cells, suggesting that the size of the chromosomal DNA is conserved throughout much of the cell cycle. The molecules were stable for periods of up to several days at 50° C in solutions containing detergent, Pronase, and EDTA.

Notes: A simple model is introduced to investigate the stability of a sedimenting entanglement. The sedimenting entanglement is represented by a sedimenting sieve. Solvent can pass through it, but single-chain molecules that flow into it become entangled and their flow decreases or, if permanent entanglements form, ceases entirely. With this model we are able to find the conditions under which the mass of a sedimenting entanglement remains constant, grows or decays to a stable value, grows beyond limit, or decays to the mass of a single chain. The theory is applied to the sedimentation of small concentrations of large chain molecules in solutions of small chain molecules in solutions of small chain molecules for the case in which the entanglements are long-lived. Equations are derived which, (1) give the stable entanglement mass as a function of rotor speed and concentration and, (2) for a given concentration predict the rotor speed at which the entanglement mass grows without limit. Numerical results for small concentrations of T2 DNA sedimenting in solutions of T7 DNA are presented.

Notes: Zones of T2 DNA were sedimented through uniform solutions of T7 DNA to determine if the smaller DNA molecules would become entangled in the larger. No entanglement could be demonstrated even at high DNA concentrations. It is suggested that molecular entanglement is not responsible for the sudden loss of DNA from solution which occurs in high centrifugal fields. This communication also includes observations on the effects of rotor speed on the sedimentation behavior of DNA in high centrifugal fields, distortion of zone shape at high concentrations, and hydrodynamic interactions between DNA and MS2 bacteriophage particles.

Notes: The kinetics of the helix-coil transition have been investigated for T2 and T7 phage DNA in a formamide-water-salt mixed solvent using a slow temperature perturbation technique (applicable to kinetic processes with rate constants ≤ 3 min-1). In this solvent degradation of the DNA is effectively suppressed. Complex kinetic curves are observed by absorbance and viscosity measurements for the response to denaturing perturbations in the transition region. Analysis of the decay curves indicates that the denaturation reaction in this time range can be treated as a first-order reaction with a variable first-order rate parameter, k, the derivative of the logarithm of the absorbance or viscosity change with respect to time. In the approach to denaturation equilibrium in the transition region, the rate parameter is determined only by the instantaneous extent of denaturation of the molecules. Near equilibrium, the rate parameter assumes a constant value characteristic of the equilibrium state. In this region, where the denaturation reaction proceeds as a simple first-order process, both the decay of absorbance (reflected local conformational change) and the decay of solution viscosity (reflecting macromolecular conformational change) are characterized by the same constant value of k. In 83% formamide, 0.3M Na+, the rate parameter k for T2 DNA decreases from an extrapolated value of 2.0 min-1 at 0% denaturation to 0.11 min-1 at 90% denaturation. Rate parameters determined for T7 DNA at the same counterion concentration and fraction of denaturation are approximately five times as large as those cited for T2 DNA, indicating an inverse proportionality of rate constant to molecular length. On the other hand, simple first-order kinetic responses with constant k are obtained for renaturing perturbations within the transition, indicating that the mechanism of rewinding differs, in most cases, from that of unwinding. Only in the limit of very small perturbations about a given equilibrium position are the rate constants k obtained from denaturing and renaturing perturbations equal. For perturbations of finite size, it appears possible that an intramolecular initiation or nucleation event may precede rewinding and limit the rate of this reaction. The rate parameters again are approximately inversely proportional to molecular weight. The one exception to the first-power dependence on molecular weight appears when temperature jumps are made upward into the post-transition region. Here the molecular-weight dependence is second power, but complications arising from the different strand-separation properties of T2 and T7 DNA's make interpretation difficult. The previously used model of friction-limited unwinding appears to fit all the observations except for the molecular-weight dependence.

Notes: Sedimentation, diffusion, and hydrodynamic interaction are included in a simplified model for the behavior of a solution macromolecules in a centrifugal field. The model is simulated by a program on a digital computer. As the diffusion coefficient is allowed to decrease, the simulation shows that the molecules tend to cluster in high centrifugal fields. The clusters move through the solution in the direction of sedimentation in a wave-like fashion, acquiring new molecules at the front and shedding old ones to the rear. It is suggested that this tendency to cluster could account for the loss of DNA and other very large molecules from solution which is observed to occur at high centrifugal fields.