DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum

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FONTE

National Academy of Sciences

RESUMO

DNA A-tracts have been defined as four or more consecutive A·T base pairs without a TpA step. When inserted in phase with the DNA helical repeat, bending is manifested macroscopically as anomalous migration on polyacrylamide gels, first observed >20 years ago. An unsolved conundrum is why DNA containing in-phase A-tract repeats of A4T4 are bent, whereas T4A4 is straight. We have determined the solution structures of the DNA duplexes formed by d(GCAAAATTTTGC) [A4T4] and d(CGTTTTAAAACG) [T4A4] with \documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \pagestyle{empty} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{NH}}_{4}^{+}\end{equation*}\end{document} counterions by using NMR spectroscopy, including refinement with residual dipolar couplings. Analysis of the structures shows that the ApT step has a large negative roll, resulting in a local bend toward the minor groove, whereas the TpA step has a positive roll and locally bends toward the major groove. For A4T4, this bend is nearly in phase with bends at the two A-tract junctions, resulting in an overall bend toward the minor groove of the A-tract, whereas for T4A4, the bends oppose each other, resulting in a relatively straight helix. NMR-based structural modeling of d(CAAAATTTTG)15 and d(GTTTTAAAAC)15 reveals that the former forms a left-handed superhelix with a diameter of ≈110 Å and pitch of 80 Å, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 Å and diameter of ≈50 Å. Results of gel electrophoretic mobility studies are consistent with the higher-order structure of the DNA and furthermore depend on the nature of the monovalent cation present in the running buffer.

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