Molecular weights and hydrodynamic properties for homogeneous native DNA, derived from diffusion, sedimentation, and viscosity measurements on polydisperse samples

Abstract

SynopsisThe diffusion, sedimentation, and viscosity behavior of native DNA has been studied as a function of molecular weight absolutely determined by diffusion and sedimentation measurements between 106 and 20 X lo6 Daltons. Only data for monodisperse subfractions of the polydisperse DNA samples investigated have been compared. They were derived by means of calculations based on individual sedimentation constant distribution and polymer parameters. The inconstancy of these parameters for the semirigid DNA molecules over the range of different subfractions of the polydisperse samples has been taken into account. A detailed description of the corresponding mathematical background as well as of the diffusion measurements has been given in the two preceding papers. For the homologous series of monodisperse native DNA molecules, three-parameter equations have been determined representing the so-[q], so-M, and [q]-M relations as well as the DO-@ and DO-M interdependence over the entire molecular weight range of interest. Furthermore a simple equation is given describing the molecular weight dependence of the Maridelkern-Flory-Scheraga parameter B in terms of so and [?I. The asymptotic value 8" has been determined, primarily by measurements a t finite molecular weights, to be 2.39 X 106, resulting in values near 2.50 X 106 a t M = 108 Daltons. The hydrodynamic properties of our two calf thymus DNA samples of highest molecular weight proved to be influenced by residual protein interactions resulting in a more compact conformation. Further data are given demonstrating the influence of the individual polydispersity of the investigated samples on diffusion constant and molecular weight averages.

Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes

“…2M NaCl, 20°C) from a nonlinear leastsquares analysis of the sedimentation data of Kovacic and van Holde (see above). Inclusion of the data of Reinert et al , 31 Prunell and Bernardi, 32 Record et al, 33 and Godfrey, 34 which together cover the size range 50-40 000 base pairs [ (3 x 10 4 }-(3 x 10 7 ) daltons ], in our analysis gave essentially identical results b = 13. 3 ± 0.…”

Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides

“…Viscosity measurements were performed as previously described (12,22,23). The intrinsic viscosity ffllwas approximated by lnlirele/c and used for the estimation of the DNA molecular weights (23)(24)(25). The interpretation of relative viscosity 2m66 Nucleic Acids Research changesAy = AfJ/ rC; in terms of changes of the persistence length and contour length was based on a first order approximation (12,23,34).…”

The intrinsic viscosity of linear DNA

“…In this figure, we included constants directly reported or calculated here from published works 38,39,41,45,49,52,53 as well as the ones from our own measurements. The constants from the linear fit of Eq.…”

“…Very early on, viscometric studies 38,39,49,69 of rather long DNA chains recorded that the linearity of log-log plots was broken around the value of M % (3 6 1) 3 10…”