Solution structure of unusual DNA sequences by high resolution NMR spectroscopy

Unusual DNA sequences are known to adopt interesting three-dimensional structures which might have important biological roles. For my thesis, I have tried to study the influence of various degrees of perturbations of DNA backbone, sequences, pH etc. on DNA structure by a quantitative NMR procedure including an NOE constrained simulated annealing procedure wherever necessary to ensure an exhaustive search of the conformational space. My studies on d(CG)r(CG)d(CG) and d(CG)r(C)d(TAGCG) show that, with a single RNA insertion into an octamer DNA, its overall conformation remains as the canonical B-DNA, except that the sugar pucker of rC3 residue is C3$\sp\prime$-endo (pseudorotation angle P = 3.6$\sp\circ$). But the hybrid hexamer is neither a pure B-DNA nor a pure A-DNA. Instead, we propose a model in which the DNA parts adopt B-, whereas the RNA part adopts A conformation, with the overall conformation closer to A-DNA. My results on d(TC)$\rm\sb n$ show that, there are three major pH-dependent conformational species: two antiparallel-stranded (APS) duplexes at pH 7 and pH 3, and a different structure near pH 5. Structural refinement of the duplexes at pH = 7.5 and pH = 2.9 using 2D-NOE data suggests that the C:T or C$\sp+$:T base pairs (with or without a bridging water) are continuously stacked. Structural refinement of d(CAATGG) and its related sequences based on the human centromere repeat by an NOE-constrained simulated annealing procedure reveals that the duplex form incorporates dynamic type-I G-A base pairs. From my studies on d(CCAGGCCTGG) and d(CCAGGC (araC) TGG), I find that there are no significant differences between the two structures that can be localized to the arabinosyl cytosine residue or its neighbours but the arabinosyl moeity may be causing local rigidity that propagates beyond the modified residue. My studies on four DNA tetra-thymine loop hairpins show that, though the loop region is well structured, it shows some degree of flexibility with an equilibrium between a conformation which has all loop residues stacked on each other and a conformation in which the second loop residue drops into the minor groove with some intermediates between the two extreme conformations also possible.U of I OnlyETDs are only available to UIUC Users without author permissio