Graduate Thesis Or Dissertation
 

Studies on the hydrophobic effect and its contribution to the stability, crystallization, and helix packing of Z-DNA

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  • The studies presented here use the B- to Z-DNA transition and Z-DNA crystallization as model systems to determine the contribution of solvent interactions to macromolecular structures. The substituent groups of naturally occurring and modified nucleotide bases affect the hydration and thus the stability of right-handed B-DNA and left-handed Z-DNA. The free energy for alternating pyrimidine-purine sequences in the B- and Z-conformations are quantitated as solvent free energies (SFE) from their solvent-accessible surfaces. The effect of methylation of the C5 carbon of pyrimidine bases on the stability of Z-DNA was analyzed in comparisons of d(TA) versus d(UA) dinucleotides. In the minor groove, the N2 amino group of purine bases was examined by comparing the stability of d(CG) versus d(CI), and d(TA) versus d(TA') dinucleotides as Z-DNA. These comparisons correctly accounted for the observed effects of the major and minor groove substituent groups on the relative stability of Z-DNA. These predictions were confirmed by comparing the amount of salt required to crystallize various hexanucleotides as Z-DNA. The relative contribution of solvent and steric interactions in DNA assembly were studied crystallographically using an asymmetric hexanucleotide which assumes two discrete and discernible orientations in the crystal lattice. How this sequence orients in the lattice is a direct measure of the DNA-DNA interactions at the surface of the crystal. These interaction free energies were directly correlated with differences in solvation for 5 sequences where there was effectively no differences in steric interactions for the two orientations. In the singular case where a large steric clash was expected, the orientation was in fact determined by this interaction. The comparisons indicate that both solvent and van der Waals interactions are significant in DNA assembly with van der Waa ls interactions dominating in situations with large steric interactions. The analyses of the B- to Z-DNA transition and Z-DNA crystallization based on SFEs support the significance of solvent interactions in determining the structure and assembly of macromolecules.
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