Calculations of the Mueller scattering matrix for a DNA plectonemic helix
- Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States) Graduate Group in Biophysics, University of California, Berkeley, California 94720 (United States)
- Department of Physics, Tennessee State University, Nashville, Tennessee 37209-1561 (United States)
- Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)
The polarization state of a beam of light is fully described by the four elements of the Stokes vector. How the Stokes vector is transformed upon scattering is described by the sixteen element Mueller scattering matrix. Polarized light scattering provides a useful tool to study macromolecular structure. In particular, measurements of Mueller matrix elements have been used to study chromosome structure; changes in these measured quantities can be used to monitor structure as a function of cell cycle. Such measurements done on helical structures can be compared to theoretical computations to determine the geometrical parameters describing the helix. The matrix elements that are most sensitive to the chiral parameters of the helix are largest when the wavelength of light is of the order of the pitch of the helix. Therefore, polarized light scattering measurements made on DNA plectonemic helices would provide the most information in the far ultraviolet (UV) and x-ray region. The Mueller matrix elements are calculated using the coupled dipole approximation in the orientation average at wavelengths in the visible, ultraviolet, and x-ray regions. Each base-pair of the idealized plectonemic helix is represented by a single dipole. A complex polarizability tensor is assigned to each dipole. Calculations are sensitive to the writhe and polarizability of the DNA molecule.
- DOE Contract Number:
- AC03-76SF00098
- OSTI ID:
- 7016872
- Journal Information:
- Journal of Chemical Physics; (United States), Vol. 101:5; ISSN 0021-9606
- Country of Publication:
- United States
- Language:
- English
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