The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation

Authors

  • Donald M. Gray,

    Corresponding author
    1. The Program in Molecular and Cell Biology, Mail Stop FO 31, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688
    • The Program in Molecular and Cell Biology, Mail Stop FO 31, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688
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  • Kenneth H. Johnson,

    1. The Program in Molecular and Cell Biology, Mail Stop FO 31, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688
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  • Marilyn R. Vaughan,

    1. The Program in Molecular and Cell Biology, Mail Stop FO 31, The University of Texas at Dallas, Box 830688, Richardson, Texas 75083-0688
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  • Patricia A. Morris,

    1. The Biology Department, Brookhaven National Laboratory, Upton, New York 11973
    Current affiliation:
    1. Vista Chemical Co., Box 500, Ponca City, OK 74602
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  • John C. Sutherland,

    1. The Biology Department, Brookhaven National Laboratory, Upton, New York 11973
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  • Robert L. Ratliff

    1. The Genetics Group, Life Sciences Division, Mail Stop 886, Los Alamos National Laboratory, Box 1663, Los Alamos, New Mexico 87545
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Abstract

CD spectra were obtained for eight synthetic double-stranded DNA polymers down to at least 175 nm in the vacuum uv. Three sets of sequence isomers were studied: (a) poly[d(A-C) · d(G-T)] and poly[d(A-G) · d(C-T)], (b) poly[d(A-C-C) · d(G-G-T)] and poly[d(A-C-G) · d(C-G-T)], and (c) poly[d(A) · d(T)], poly[d(A-T) · d(A-T)], poly[d(A-A-T) · d(A-T-T)], and poly[d(A-A-T-T) · d(A-A-T-T)]. There were significant differences in the CD spectra at short wavelengths among each set of sequence isomers. The (G · C)-containing sequences had the largest vacuum uv bands, which were positive and in the wavelength range of 180–191 nm. There were no large negative bands at longer wavelengths, consistent with the polymers all being in right-handed conformations. Among the set of sequences containing only A · T base pairs, poly[d(A) · d(T)] had the largest vacuum uv CD band, which was at 190 nm. This CD band was not present in the spectra of the other (A · T)-rich polymers and was absent from two first-neighbor estimations of the poly[d(A) · d(T)] spectrum obtained from the other three sequences. We concluded that the sequence dependence of the vacuum uv spectra of the (A · T)-rich polymers was due in part of the fact that poly[d(A) · d(T)] exists in a noncanonical B conformation.

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