Biomedical subjects

J L Viovy

Publications and source records attributed to J L Viovy.

25 records · Page 2Linked to original sources

PubMed1994

[Sequencing of DNA by mechanical opening of the double helix: a theoretical evaluation].

We propose and evaluate a model experiment, in which the sequence of a DNA fragment is determined by mechanically opening the double helix in a controlled manner (e.g. pulling on the 3' end of one strand), and measuring the variation of the force exerted by the base pairs on a nanodynamometer (e.g. on a bead in an optical trap or a glass microneedle attached to the 5' end of the other strand). We show that the major limitation of the approach is the longitudinal elasticity of the already sequenced single strand sections, which soften the displacement-force function, and facilitate spontaneous thermal opening of the base pairs.

DNA↗

PubMed1993

Control of electrohydrodynamic distortion of sample streams in continuous flow electrophoresis using oscillating fields.

Continuous flow electrophoresis is a method to separate ions contained in a sample continuously injected into a laminar flow of electrolyte as a cylindrical stream. Usually, the sample is more conductive than the electrolyte, and the charges created at the sample-electrolyte interface lead to electrohydrodynamic distortions which reduce the separation power of this technique. We demonstrate theoretically that the rate of electrohydrodynamic distortion of a cylindrical sample stream can be reduced to zero, by superimposing to the AC field responsible for the separation of a DC field transverse to it and to the flow direction, with an appropriate frequency, and an effective strength equal to that of the DC field. Using a continuous flow electrophoresis chamber, in which such a field is produced using capacitive electrodes, the major predictions of the theory are confirmed. In particular, it is shown that a sample stream more conductive than the carrying electrolyte, which was seriously deformed in the absence of a transverse AC field, recovers its cylindrical shape in presence of the field. The implications of this discovery for the separating power of continuous-flow electrophoresis are discussed.

Buffers↗

PubMed1993

DNA electrophoresis in polymer solutions: Ogston sieving, reptation and constraint release.

The electrophoresis of long polyelectrolytes is considered theoretically, with special attention to duplex DNA. We first discuss quantitative approaches to determine unambiguously the entanglement properties of polymer solutions. Following an idea proposed by Grossman and Soane, we then assume that the "mesh" size of the solution plays the role of a dynamic "pore size" in order to apply theories for gel electrophoresis. In the framework of the Ogston model, we predict that duplex DNA up to 1 kb or more should be separable in dilute (i.e. nonentangled) solutions of high molecular weight polymers. In an entangled solution, and for DNA larger than the pore size, we use a recently developed fluctuation-reptation model to predict the range of sizes in which separation should be possible as a function of electric field E and pore size zeta b. For zeta b larger than the Kuhn length of DNA, we predict a separation up to a size N*scaling as E-1 zeta b-1. For zeta b smaller than the Kuhn length, two different regimes are expected. For small electric fields (typically of the order of 10 V/cm), N*should be proportional to E-1 zeta b-3/2, whereas for high electric fields such as encountered in capillary electrophoresis, we expect that N*is proportional to E-2/5 zeta b-12/5. These predictions are qualitatively different from earlier ones. Finally, we demonstrate that the finite lifetime of the "pores" in an entangled solution (as opposed to a gel) may lead to a new migration mechanism by constraint release, which is not size-dependent.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemical Phenomena↗

PubMed1989

Generalized tube model of biased reptation for gel electrophoresis of DNA.

A theoretical analysis of the reptational motion of DNA in a gel that includes the effects of molecular fluctuations has been used to explain the main features found in experiments involving periodic inversion of the electric field. The resonance-like decrease of the electrophoretic mobility as a function of pulse duration is related to transient "undershoots" in the orientation of the molecule, in agreement with recent experimental data. These features arise from a delicate interplay of internal and center of mass motion of the molecules under pulsed field conditions, and are important for the separation of DNA molecules in the size range 0.2 to 10 million base pairs.

Chemical Phenomena↗

PubMedDate not supplied

Reptation-breathing theory of pulsed electrophoresis: dynamic regimes, antiresonance and symmetry breakdown effects.

We apply the concepts of tube and reptation to the pulsed electrophoresis of DNA, considering both biased reptation and "breathing" modes (internal modes of the chain). Using suitable preaveraging approximations, analytical expressions are derived which relate displacement in crossed field electrophoresis to molecular weight, field strength, field period, pore size of the gel, and the angle between the field. These expressions provide scaling laws for the change of mobility when one (or more) of the parameters is varied as well as "universal" velocity versus molecular weight versus pulse time curves. These results are quantitatively compared with experiments. At some point which depends on field angle, field strength and chain length, however, we predict a failure of this model due to symmetry breakdown and loss of ergodicity. Qualitatively, this should lead to considerable band spreading and/or splitting of the highest DNA bands into two bands migrating sideways from the diagonal. The case of field inversion is also investigated. It is shown that only breathing modes can explain the strong differences in mobility experienced by chains of different length when opposite fields of equal amplitude are applied: the "trapping" of chains in conformations of low mobility is associated with an antiresonance-like coupling between the external field and the internal modes.

Chromosomes↗

PubMedDate not supplied

Irreversible trapping of DNA during crossed-field gel electrophoresis.

Using an original protocol with a rotating gel electrophoresis apparatus, it is shown that duplex DNA undergoing crossed-field electrophoresis in agarose gets trapped in the gel when the field is increased above a threshold value which decreases with the chain length and depends on the angle between the fields in a non-monotonous manner. This trapping is irreversible, i.e. once trapped at a high field strength, chains are unable to resume their motion when the field is returned to a lower value at which they moved prior to trapping. A model of trapping by "tight knots" is proposed. It predicts a trapping threshold proportional to the inverse square of the electric field, in qualitative agreement with the data. The implications of our results for the separation of large DNA molecules are discussed.

Chromosome Banding↗

PubMedDate not supplied

Gel electrophoresis of an end-labeled DNA. I. Dynamics and trapping in constant fields.

A theory for the gel electrophoresis of a flexible polyelectrolyte, bearing an uncharged bulky label or an uncharged section at one end, is presented. We first consider a gel that is fully permeable to the label: we calculate the degree of stretching of the polyelectrolyte and its mobility as a function of chain size, electric field and label friction. Various regimes are identified, and their "existence domains" are calculated. For increasing friction, we predict a transition from a mobility decreasing with chain size to a mobility increasing with chain size. Secondly, we consider the possibility that the label may get trapped at some locations of the gel, a situation relevant to a method of "trapping electrophoresis" recently proposed by Ulanovsky et al. for DNA sequencing. A molecular model for detrapping by thermally activated "backward reptation" is constructed and solved using the Kramers rate-equation theory. Different closed analytical expressions and approximate scaling laws corresponding to different regimes of stretching and field strengths are predicted. The most striking result is a mobility which exponentially decreases past a critical size Np*, which decreases with increasing field. In the regime relevant to the experiments by Ulanowsky et al., we predict Np* approximately E-2/3. The predictions are in good qualitative agreement with presently available experiments, but further experimental investigations are suggested.

Chemical Phenomena↗