Buffered λ-DNA solutions at high shear rates

Abstract

We study buffered aqueous solutions of deoxyribonucleic acid isolated from bacteriophage lambda (λ-DNA) at shear rates up to 105 s−1. The shear rates are accessed with a narrow-gap rheometer at gap widths down to 20 μm. At lower shear rates, our data merge with the literature values. At high shear rates, the viscosity levels off into an infinite-shear viscosity plateau. Hence, the viscosity functions of buffered aqueous DNA solutions are now available for the entire shear-rate range from the first Newtonian plateau to that of infinite-shear viscosity. The latter hardly differs from the solvent viscosity. For the normal-stress differences, we observe a power-law dependence on the shear rate close to previous findings up to shear rates of about 104 s−1. Beyond this shear-rate range, we observe a stepwise change with the shear rate. By means of agarose gel electrophoresis, we confirm that the λ-DNA is not fragmented during our rheometric study at high shear rates. Yet, at the highest shear rates studied, shear-induced changes in the DNA to structures not being able to travel through the gel appear.

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

“…37,38 Only shear stresses are not effective for DNA fragmentation; Dakhil et al did a well-controlled shear experiment in which the highest shear rates were in the range of ∼10 5 s −1 (shear stresses about 100 Pa) without obvious DNA shearing. 54 Achieving uniform and random DNA fragmentation requires instantaneous release of huge mechanical energy. DNA fragmentation for NGS basically relies on ultrasonic treatment, which leads to DNA fragmentation through cavitation generated by the ultrasound.…”

Bubble-enhanced ultrasonic microfluidic chip for rapid DNA fragmentation

“…In well-controlled shear experiments by Dakhil et al the highest shear rates were in the range of ∼10 5 s −1 corresponding to shear stresses of about 100 Pa without any apparent DNA fragmentation. 53 Most hydrodynamic DNA shearing devices for fragmentation applications used elongation flows governed by tensile stress.…”

Narrow-Gap Rheometry: A Novel Method for Measuring Cell Mechanics

“…This is far below the reported effective zero-gap error of commercial rheometers of 25 µm to 70 µm [86], which, apart from being due to disk roughness and residual disk inclination, can be caused by squeeze flow during zeroing the rheometer [85]. The enhanced precision allows the extending of the measurement window to much higher shear rates [87,88] as well as studying the adhesion [89] and load limits [90] of cells in low viscous environments. With their device, Dakhil et al reached the linear viscoelastic range at small deformations, where the stress amplitude is proportional to the deformation amplitude [20,91].…”