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Journal Article

Turbulence decay in stopped flow experiments by measurements of electric dichroism


Porschke,  D.
Research Group of Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Porschke, D. (2000). Turbulence decay in stopped flow experiments by measurements of electric dichroism. Journal of Physical Chemistry B, 104, 1115-1121.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0012-F928-4
Various macromolecules of widely different chemistry and structure show unusual rotational diffusion time constants in stopped flow experiments. These effects have been characterized by measurements of electric dichroism in a combined stopped-flow-electric-field-jump instrument. DNA restriction fragments in the range of chain lengths up to 179 base pairs do not show anything unusual yet: the dichroism decay times correspond to the standard values reflecting unperturbed rotational diffusion. For fragments with more than 200 base pairs, the dichroism measured directly after stop of the flow revealed decay time constants clearly smaller than the corresponding values found without flow. The reduction of the time constants for overall rotational diffusion is similar to 10% for a fragment with 256 bp and increases to similar to 70% for DNA with 800 bp. The decay time constants return to the usual values within a few ms after stop of flow. The limiting electric dichroism of the flow induced state is virtually identical with that of standard DNA and, thus, the local secondary structure remains in the B-form. However, the polarizability of the flow induced state is clearly reduced. These results seem to indicate a flexible state of DNA induced by shear stress, resulting from breaking of stacking interactions. The kinetics can be described by a model with parallel reactions leading to the native state with a time constant of similar to 1 ms. Effects observed for single stranded poly(A) are virtually identical to those of double stranded DNA for samples of corresponding hydrodynamic dimensions. The time constants for the transition to the standard state are again similar to 1 ms, although stacking reactions of poly(A) occur in the time range less than or equal to 1 mu s. Further experiments with other macromolecules or macromolecular aggregates indicate that acceleration of rotational motion is a general phenomenon under stopped flow conditions: for example bacteriorhodopsin membrane disks and colloidal suspensions of the fibrous claylike silicate attapulgite show very high accelerations of their rotational diffusion time constants after stopped flow by factors of about 3000. The return to the usual state both for bacteriorhodopsin and for attapulgite extends over a broad time range up to similar to 100 ms. Although it cannot be excluded that these effects are partly due to kinking of the structures, the similarity of the data for materials of very different structures indicates that the acceleration of rotational diffusion is mainly due to the existence of turbulence. The rotational motion of small molecules, such as 95 bp DNA, is much faster than rotational motion of corresponding volume elements of the solvent and, thus, these molecules do not indicate turbulence. The data demonstrate that turbulence decays over a broad time range: small vortices with high rates of rotational motion decay first, merge into larger ones with lower rotation rates, until finally the largest ones compatible with the dimension of the observation chamber are reflected only by particles with relatively large dimensions and slow rotational diffusion. These results demonstrate the mode of turbulence in stopped flow observation cells, the scaling of its decay, and the utility of electrooptical techniques for the characterization of turbulence.