Elongation flow studies of DNA as a function of temperature

Abstract

ABSTRACT:The response of T4-phage DNA molecules to an elongational flow field was monitored by flow-induced birefringence as a function of temperature. The flow-induced birefringence observed in this study was localized in the pure elongational flow area with a critical strain rate, indicating that the birefringence was attributed to a coilstretch transition of DNA molecules. The slight decrease in the birefringence intensity with increases in temperature to 40°C was explained by a thermal-activation process. At temperatures above 50°C, flow-induced birefringence decreased remarkably, and no birefringence was observed at temperatures above 60°C. After the flow experiments, ambient temperature was reduced back to room temperature, and flow experiments at room temperature were performed again. Flow-induced birefringence was recovered almost completely in samples for which the first flow measurements were made at temperatures below 53°C. Irreversible changes were observed for samples for which the first flow experiments were performed at temperatures above 55°C. The temperature dependence of UV-absorption spectra revealed that the double-strand DNA helix began to partially untwine at a temperature over 50°C, and duplexes became almost completely untwined at a temperature over 55°C. A comparison of electrophoresis patterns for untwined molecules showed that flow-induced scission of DNA molecules occurred in a sample solution in flow experiments performed at 65°C, while no molecular weight reduction was observed in the sample solution at 55°C. In this article, this difference between the untwined DNA molecules is discussed on the basis of the thermally activated bond scission (TABS) model.

λ-DNA Induced Turbulent Drag Reduction and Its Characteristics

“…This could also explain why there was no further development of the degradation process in this condition. As far as concerned on this half-cut phenomenon, Sasaki et al 41 explained it within a theoretical framework known as the thermally activated barrier to scission (TABS) model. 42 According to the this model, molecular degradation in an elongational flow field proceeds in two-stage processes: molecular stretching and fracture.…”

Turbulent Drag Reduction and Degradation of DNA

“…These experiments found that polymers can be stretched by weak flows [5] and broken by strong extensional flows [6]. Since there are strong correlations [7] between dragreduction efficiency and extensional viscosity in polymer solutions, a study of MMD will provide a good opportunity not only in the understanding of the basic DR mechanism but also in the turbulent structures at such a small scale in the presence of polymers.…”

DNA Dynamics under Turbulent Flow

“…[22] Based on the higher molecular weight of CT-DNA and the analysis of l-DNA under turbulent flow condition, [7] it can be assumed that major mechanical degradations of the CT-DNA intensively occurred right after the injection of CT-DNA into turbulent flow just in a few second. As far as this half-cut phenomenon is concerned, Sasaki et al [23] explained that molecular degradation in an elongational flow field proceeds as a two-stage process; molecular stretching and fracture. In this process, scission of the extended conformation always occurs near the midpoint, where the stress in the molecule reaches a maximum value.…”

“…In this process, scission of the extended conformation always occurs near the midpoint, where the stress in the molecule reaches a maximum value. [24] Regarding the critical condition of molecular degradation, they [23] also explained that the critical strain rate ( _ " f ) for fracture is related to the contour length (L) and molecular weight (M w ) of a polymer chain in an inverse square mode as:…”