Hydrodynamic determination of polynucleotide chain discontinuities. Improved molecular weight correlations for denatured DNA

Monte Carlo simulation of DNA electrophoresis

This paper describes an attempt to study the electrophoresis mobility of a DNA molecule in a gel by means of a Monte Carlo simulation. We find that the electrophoresis mobility mu can be well described by the empirical equation mu v kappa 1/N + kappa 2E2 with N being the number of monomers of the model chain and E being the applied field. For small E the data can merge into the linear response result mu = kappa 1/N. The paper also discusses necessary extensions of the present approach.

Polydispersity and chain break effects on DNA intramolecular renaturation

The influences of sample polydispersity and of internal chain breaks are introduced in the formal description of intramolecular renaturation phenomenology, enhancing the usefulness of the involved methodology. In our method, renaturation is induced not by cooling but by increasing the sodium concentration. The single-stranded size distributions for the two types of samples employed (haplotomic and diplotomically degraded) are discussed. In the case of haplotomic cleavage, the variable is the strand size in the 'segment' between consecutive nicks in either of the native DNA strands. Our equations have been obtained by considering that the arrangement of DNA sequences may be approximately taken as random. These equations provide a good description of experimental data and a reasonable value (about 1000 base-pairs) for the size of the thermalite sequence, but show low sensitivity to departures from the random arrangement of sequences.

Local perturbation of the double helical DNA structure near single breaks

The influences of DNA composition and solvent modification on the stability of the native DNA structure near a single break have been studied. The value of the magnification parameter h of the double helix breakdown probability in a haplotomic degradation process is used as an index of the perturbation range. Methodological and technical details are discussed and comments are made on previously reported data on the h value. From this study it may be concluded that the width of the perturbation zone next to a nick is influenced by solvent-induced changes in the general stability of the native DNA molecule, and by compositional-dependent local interactions. Our results point to entropic effects as the more important contributions to stability perturbation near a discontinuity in the native DNA molecule.

Reversibility of partial denaturation of DNA

The hypochromicity recovery of a partially denatured DNA sample when salt concentration is suddenly increased at an intermediate stage of the transition, is studied. The results of CsC1 gradient analysis, polyethylenglycol/dextran partition analysis, and the behaviour in a new thermal transition, support the view that the process is an intramolecular double chain renaturation as that induced by cooling. The degree of denaturation irreversibility is dependent on the size of DNA segments between two nicks and on the helicity value at which salt concentration-jump is performed.