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The DNA Phosphate orientation. Infrared data and energetically favorable structures
Author(s) -
Pohle Walter,
Zhurkin Victor B.,
Fritzsche Hartmut
Publication year - 1984
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360231131
Subject(s) - chemistry , crystallography , infrared , phosphate , linear dichroism , twist , nucleic acid , orientation (vector space) , infrared spectroscopy , dna , tilt (camera) , fiber diffraction , dichroism , diffraction , circular dichroism , optics , x ray crystallography , geometry , physics , organic chemistry , biochemistry , mathematics
The conformation of nucleic acids can be probed reliably by the geometrical arrangement of the PO 2 ‐ groups in the backbone. The phosphate arrangement is described by two angles, θ OO and θ OPO, which can be determined by several methods. In the present paper, the two angles obtained for the A, B, and C forms of DNA, experimentally by ir linear dichroism (LD) of oriented films as well as theoretically from energy‐minimized structures. The methodology of the phosphate angle determination from the ir dichroism spectra is presented in detail, elucidating the potentialities and limitations of this method. Advantageously, tilt and twist angles of the DNA bases, found by theoretical calculations, were used in the ir data processing. The phosphate angles were compared with the corresponding x‐ray and nmr results from the literature. Regarding the rather high flexibility of the double helix, as well as the sequence‐dependent variation of the conformational angles, a fairly good agreement between our results and the majority of all discussed data can be established. Thus ir LD provides reliable data on the orientation of phosphate groups in DNA. Reasons for discrepancies with some literature data from x‐ray fiber‐diffraction analysis, published several years ago, will be discussed.