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

Warning

This publication doesn't include Faculty of Arts. It includes Faculty of Science. Official publication website can be found on muni.cz.
Authors

ŠTEFL Richard WU Haihong RAVINDRANATHAN Sapna SKLENÁŘ Vladimír FEIGON Juli

Year of publication 2004
Type Article in Periodical
Magazine / Source Proceedings of the National Academy of Sciences of the U.S.A.
MU Faculty or unit

Faculty of Science

Citation
Field Biophysics
Keywords helical bending; NMR; structure; residual dipolar couplings
Description 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 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 A and pitch of 80 A, similar to DNA in the nucleosome, whereas the latter has a gentle writhe with a pitch of >250 A and diameter of 50 A. 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.
Related projects:

You are running an old browser version. We recommend updating your browser to its latest version.