Compensating bends in a 16‐base‐pair DNA oligomer containing a T₃A₃ segment: A NMR study of global DNA curvature

Abstract

In-phase ligated DNA containing T(n)A(n) segments fail to exhibit the retarded polyacrylamide gel electrophoresis (PAGE) migration observed for in-phase ligated A(n)T(n) segments, a behavior thought to be correlated with macroscopic DNA curvature. The lack of macroscopic curvature in ligated T(n)A(n) segments is thought to be due to cancellation of bending in regions flanking the TpA steps. To address this issue, solution-state NMR, including residual dipolar coupling (RDC) restraints, was used to determine a high-resolution structure of [d(CGAGGTTTAAACCTCG)2], a DNA oligomer containing a T3A3 tract. The overall magnitude and direction of bending, including the regions flanking the central TpA step, was measured using a radius of curvature, Rc, analysis. The Rc for the overall molecule indicated a small magnitude of global bending (Rc = 138 +/- 23 nm) towards the major groove, whereas the Rc for the two halves (72 +/- 33 nm and 69 +/- 14 nm) indicated greater localized bending into the minor groove. The direction of bending in the regions flanking the TpA step is in partial opposition (109 degrees), contributing to cancellation of bending. The cancellation of bending did not correlate with a pattern of roll values at the TpA step, or at the 5' and 3' junctions, of the T3A3 segment, suggesting a simple junction/roll model is insufficient to predict cancellation of DNA bending in all T(n)A(n) junction sequence contexts. Importantly, Rc analysis of structures refined without RDC restraints lacked the precision and accuracy needed to reliably measure bending.

Dimerization and DNA recognition rules of mithramycin and its analogues

“… a The crystal structures were previously published as follows: 1CGC [44], 187D [45], 3ANA [46], 1VT9 [47], 1SS7 [48], 141D [49], 1D23 [50], 1BD1 [42], 28DN [51], 1D78 [51], 1SGS [52], 1D82 [53], and 1D93 [54]. …”

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“…Assessing the global bending magnitude in DNAprotein complexes is of particular interest, but classical NMR methods are inefficient in capturing DNA bending. However, the use of RDCs proved their ability to give a reliable view of bending in intrinsically curved DNA [46] or changes in DNA bending induced by protein binding.…”

“…Several dipolar couplings can be extracted on the protein backbone bonds, such as We have seen the importance of introducing RDCs in DNA structure determination to remedy the limited number of classical NOE restraints and to increase the accuracy of global DNA structures. The utility of employing RDCs was also established in the accurate determination of subtle structural features such as the DNA helix curvature, as in oligonucleotides containing AnTn segments [46]. Over the last decade, several pulse programmes have been developed for the measurement of residual dipolar couplings on DNA molecules [47][48][49].…”

Software Package aSHAPE as a Tool to Study the Spatial Conformation of the Bacterial Genome Sites

“…Это значит, что трехмерная структура свободной промоторной ДНК может иметь особую пространственную конфигурацию. О способности типичных для промоторов коротких фрагментов нуклеотидной последовательности формировать стабильные изгибы свидетельствуют данные, полученные методами рентгеноструктурного анализа [12] и ядерного магнитного резонанса (ЯМР) [13]. Однако такого типа анализ пока невозможен для полноразмерных промоторов.…”