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Title: Linear dichroism of DNA: Characterization of the orientation distribution function caused by hydrodynamic shear

Linear dichroism provides information on the orientation of chromophores part of, or bound to, an orientable molecule such as DNA. For molecular alignment induced by hydrodynamic shear, the principal axes orthogonal to the direction of alignment are not equivalent. Thus, the magnitude of the flow-induced change in absorption for light polarized parallel to the direction of flow can be more than a factor of two greater than the corresponding change for light polarized perpendicular to both that direction and the shear axis. The ratio of the two flow-induced changes in absorption, the dichroic increment ratio, is characterized using the orthogonal orientation model, which assumes that each absorbing unit is aligned parallel to one of the principal axes of the apparatus. The absorption of the alienable molecules is characterized by components parallel and perpendicular to the orientable axis of the molecule. The dichroic increment ratio indicates that for the alignment of DNA in rectangular flow cells, average alignment is not uniaxial, but for higher shear, as produced in a Couette cell, it can be. The results from the simple model are identical to tensor models for typical experimental configuration. Approaches for measuring the dichroic increment ratio with modern dichrometers are furthermore » discussed.« less
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  1. Augusta Univ., Augusta, GA (United States). Dept. of Chemistry and Physics; Brookhaven National Lab. (BNL), Upton, NY (United States). Dept. of Biology; East Carolina Univ., Greenville, NC (United States). Dept. of Physics
Publication Date:
Grant/Contract Number:
SC0012704; SC001270; Sc001270
Publisher's Accepted Manuscript
Journal Name:
Analytical Biochemistry
Additional Journal Information:
Journal Volume: 523; Journal Issue: C; Journal ID: ISSN 0003-2697
Research Org:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Augusta Univ., Augusta, GA (United States)
Country of Publication:
United States
59 BASIC BIOLOGICAL SCIENCES; DNA ligands; Couette cell; polarized absorption; scalene ellipsoid; photoelastic modulator; equivalent orthogonal orientation; dichroic increment ratio
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1424978