Structural Study Of DNA Sequences Related To The Nucleosome Preferential Positioning

Nowadays, nucleosome positioning is being studied intensively due to the critical role in the regulation and transcription by modulating the accessibility of specific targeted sites for proteins in eukaryotic cell. As demonstrated by recent studies that positioning in vivo could be modulated by various factors, among which the role of DNA sequence is repeatedly underlined due to the form of preferred or excluding sequences.In an attempt to identify the structural and dynamic properties of sequences exhibiting strong ability to precisely position the nucleosome, we carried out a series of structural studies on free DNA oligomers corresponding to the core of this sequence. The synthetic601sequence was selected as a proper candidate for the experiment and the oligomers cover39bp of the5’half of the sequence. The utilization of NMR technology allows the observation of the oligomer properties in solution. However, it’s difficult to assign phosphorus resonances signals to long DNA oligonucleotides, which could be realized to divide the sequence of interested part into four equivalents (12bp).Analysis of a large set of NMR data on the four oligomers (72P (phosphorus chemical shift) and249sequential inter-proton distances) indicate the strong coupling between nanoseconde timescale motions of phosphate group and those involving sugar and bases. In the four dodecamers, the nanosecond timescale dynamics is dominated by the dinucleotide sequence, modulated at the tetranucleotide level. Importantly, the experimental data collected here validate our previously published NMR-based TRX scale that quantifies the nanosecond timescale intrinsic malleability of the ten complementary dinucleotides in B-DNA. The TRX annotation of the whole601sequence shows a10base-pair periodic alternation of stiff and flexible regions that can be exactly superimposed to the sinusoidal variations of minor groove width observed on the crystallographic structures of nucleosome. The TTAAA element was the subject of particular attention in this work. It is suspected to be crucial in the nucleosome formation context, exhibiting remarkable features, such as the constitution of a succession of BI-profiles (high-shifted P and short internucleotide distances) associated to a narrow minor groove. Furthermore, the results related to the residual dipolar couplings (RDC), which reflect the deflection angle between carbon-proton vectors and the long axis of DNA have shown that the differences between the residual dipolar couplings of two successive residues,△(RDC), are also correlated with P. This result definitively confirms that the structure and the dynamic of phosphate group, bases and sugars in B-DNA are highly coupled.In addition, our results start to decipher the indirect readout process underlying the nucleosome formation. Further, they establish that the TRX scale is a powerful, predictive tool for better understanding DNA-protein interactions, based on flexibility criteria. It represents a new step towards a simplified determination of properties of DNA by NMR.