Repetitive blocks of guanine- and cytosine-rich sequences, such as those occurring in centromeric and telomeric DNA regions and promoter regions of protein coding genes, have ability to form G- and C-quadruplex structures, respectively. These non-B DNA structures are involved in more than 40 pathological human conditions including cancer. From a biophysical point of view, a common property to both G- and C-rich sequences is their inherent sensitivity to non-specific, physical-chemical environmental factors promoting their conformational polymorphism. Notable sensitivity of these DNA motifs towards the environmental factors implies that conventional XRD and/or NMR techniques, which served thus far as a primary source of structural information on these DNA, have to be used with caution when addressing the question which is the physiologically relevant structure of these DNA molecules.
Both XRD and NMR examine the structural properties of the isolated DNA. Whereas environmental conditions in XRD studies are constrained to conditions that support monocrystal growth, the choice of NMR conditions is limited by the fact that not all factors that can modulate folding topologies of these DNA structures in vivo are known a priori. Experimental observations that the structures of these non-B DNA motifs depend on environmental factors have strongly suggested that quantitative characterization of their physiologically relevant structures needs to be performed as close to native conditions as possible, preferably in vivo. To address physiological relevancy of the environmentally observed conformational polymorphism of the non-B-DNA DNA sequences observed in vitro, I propose to characterize structures formed by DNA sequences corresponding to centromeric, telomeric, and proto-oncogene promoter DNA regions under native conditions in vivo using state-of-the art technique of in-cell NMR spectroscopy and in-cell single pair FRET.

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