| The NMR solution structure of self-complementary deoxyribonucleic acid (DNA) molecules, namely; d(CGGATCCG)2, d(CAGATCTG)2, d(CCXX'GG)2 and d(CTXX'AG) 2 (where X = A, G, C, or T and X' is complementary base-pair of X), have been determined in order to investigate the building block of DNA duplex; tetramer block unit, using NMR interproton distances, endocyclic sugar torsion angles, backbone torsion angles and hydrogen bond constraints (Chapter 2). The A-T base-pair steps of the G-A-T-C tetramer are compared (RMSD= 0.38A) among the sequences d(CGGATCCG)2, d(CAGATCTG)2 and d(CGATCG)2. Further, the solution structural features of eight hexamers, i.e. d(CCXX'GG)2 and d(CTXX'AG)2, at 10°C are described in Chapter 4. An improved structure function, SigmaLS(backbone), composed of the sum of the contributions from the twist (O), the roll (rho), the base-pair slide (Deltadelta), the propeller twist (o), and the sugar-phosphate backbone (Deltabeta, Deltaepsilon and Deltazeta), is defined to described the geometry of base-pair step by considering a tetramer unit (Chapter 5). It follows to demonstrate a correlation between DeltaG 10°C and SigmaLS(backbone) of self-complementary tetramers, namely; X-A-T-X', X-G-C-X', X-C-G-X ' and X-T-A-X', demonstrates the conformation of a DNA duplex is a consequence of relief of steric clashes. The degree of conformational changes is sequence-specific and is cooperation between different types of helical motions. From the DeltaG10°C - Sigma LS(backbone) correlation, the hydrogen bond energy (0.8 kcal mol -1) is approximated. It experimentally demonstrates that the contribution of stacking and hydrogen bond energies corresponding to the base-pair step. The degree of conformational changes of base-pair steps, T-A (97°/kcal mol-1) > A-T (53°/kcal mol-1) > G-C (18°/kcal mol-1), is reported.;The SigmaLS(backbone) allows an understanding of the DNA duplex local structural variation in a tetramer motif. The behavior of sugar-phosphate backbone of a tetramer has also been discussed. The SigmaLS(backbone) may form a basis for the development of a model for the prediction of sequence-specific local structure of deoxyribonucleic acid molecule. |
