Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers

Nearly 40 years ago, Franklin and Gosling (1953a, b) observed that the diffraction pattern of DNA fibres was sensitive to the relative humidity of the sample. Two forms of DNA were identified, one preferred at lower humidity designated ‘A’, and the other preferred at high humidity, designated ‘B’. Examples of the A- and B-forms of DNA have now been studied extensively, first by fibre diffraction (Arnott et al., 1976) and later by single-crystal X-ray crystallography (Dickerson, 1991). Both are righthanded forms of a DNA double helix, with the B-form corresponding closely to the double helix proposed by Watson and Crick (1953). Another form of DNA was discovered more recently, the left-handed or Z-form (Wang et al., 1979). The A-, B- and Z-forms of DNA, shown in Figure 6.1, now establish the main basis for classification of DNA structures into families (Saenger, 1983). However, crystallographic variations have led to a number of subcategories (Fuller and Mahendrasingam, 1987), and, within each family, the DNA is expected to manifest a certain dynamical range of motions as well as exhibiting sequence-dependent fine structure (Dickerson, 1988; Kennard, 1984; Kennard and Hunter, 1989; Shakked and Rabinovich, 1986) and axis bending (Sundaralingam and Sekharudu, 1988).