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@article{493122,
author = {Štefl, Richard and Wu, Haihong and Ravindranathan, Sapna and Sklenář, Vladimír and Feigon, Juli},
article_number = {5},
keywords = {helical bending; NMR; structure; residual dipolar couplings},
language = {eng},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the U.S.A.},
title = {DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum},
volume = {101},
year = {2004}
}
TY - JOUR
ID - 493122
AU - Štefl, Richard - Wu, Haihong - Ravindranathan, Sapna - Sklenář, Vladimír - Feigon, Juli
PY - 2004
TI - DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum
JF - Proceedings of the National Academy of Sciences of the U.S.A.
VL - 101
IS - 5
SP - 1171-1176
EP - 1171-1176
SN - 00278424
KW - helical bending
KW - NMR
KW - structure
KW - residual dipolar couplings
N2 - 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.
ER -
ŠTEFL, Richard, Haihong WU, Sapna RAVINDRANATHAN, Vladimír SKLENÁŘ a Juli FEIGON. DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum. \textit{Proceedings of the National Academy of Sciences of the U.S.A.}. 2004, roč.~101, č.~5, s.~1171-1176. ISSN~0027-8424.
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