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Proceedings Paper

Cartesian coordinates of DNA from Raman scattering and molecular modeling
Author(s): Warner L. Peticolas; Zhongy Dai; Manuel Dauchez; G. A. Thomas
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Paper Abstract

Although a great deal of work has been done lately on unusual conformations of DNA, it is not always clear how relevant these structures are to the conformations found in the genome of living organisms. It appears that it an unusual form of DNA, such as the Z form, exists in the genome, it must exist as short sections of a specific sequence such as an alternating CG Z form sequence in the midst of very long sections of B-form DNA. To examine this problem of DNA structure, we have determined the minimum length of a string of alternating CG base pairs that can go into the Z form in the middle of a long section of B-form. Rules have been developed for determining the sequence lengths required to generate Z form in the presence of B form. Although Raman spectroscopy has been very useful as a semiquantitative indication of the conformation of proteins and nucleic acids it has not been by itself capable of giving precise structural parameters such as torsional angles or Cartesian coordinates. Recently we have shown how it is possible by a combination of Raman spectroscopy, thermodynamic analysis, hydrogen-deuterium exchange and molecular modeling to generate Cartesian coordinates for oliognucleotides in solution or in the crystal. In this paper we review the principles that lead to the actual structure determination. The possible extension of these techniques to the determination of the Cartesian coordinates for bent DNA is also discussed.

Paper Details

Date Published: 17 June 1993
PDF: 10 pages
Proc. SPIE 1921, Laser Spectroscopy of Biomolecules, (17 June 1993); doi: 10.1117/12.146138
Show Author Affiliations
Warner L. Peticolas, Univ. of Oregon (United States)
Zhongy Dai, Univ. of Oregon (United States)
Manuel Dauchez, Univ. of Oregon (United States)
G. A. Thomas, Univ. of Oregon (United States)

Published in SPIE Proceedings Vol. 1921:
Laser Spectroscopy of Biomolecules
Jouko E. Korppi-Tommola, Editor(s)

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