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Notes: We have measured the refractive indices of highly crystalline Li- and Na-DNA wet-spun films as a function of their water content using an immersion technique. We calculated the molecular polarizabilities of a DNA base pair using the Lorentz-Lorenz relation for anisotropic materials, the measured water contents, and densities corrected for void formation. For Li-DNA, the polarizabilities are independent of the relative humidity, whereas for Na-DNA, there are large changes at the A-B transition and also at low humidities. The average polarizability of A-Na-DNA is in agreement with that calculated from refractive index increments and also as calculated by a simple addition of bond polarizabilities, whereas the values for Li- and B-Na-DNA are about 30% larger than the calculated values. We propose that these anomalous values are due to nonlinear polarizabilities of the phosphate group.

Notes: We have used Brillouin spectroscopy to study the velocities and attenuation of acoustic phonons in wet-spun films of Na-DNA and Li-DNA as a function of the degree of hydration at room temperature. Our data for the longitudinal acoustic (LA) phonon velocity vs water content display several interesting features and reveal effects that we can model at the atomic level as interhelical bond softening and relaxation of the hydration shell. The model for interhelical softening makes use of other physical parameters of these films, which we have determined by gravimetric, x-ray, and optical microscopy studies. We extract intrinsic elastic constants for hydrated Na-DNA molecules of c11 ≃ 8.0 × 1010 dynes/cm2 and c33 ≃ 5.7 × 1010 dynes/cm2, which corresponds to a Young's modulus, E ≃ 1.1 × 1010 dynes/cm2 (with Poisson's ratio, σ = 0.44). The negative velocity anisotropy of the LA phonons indicates that neighboring DNA molecules are held together by strong interhelical bonds in the solid state. The LA phonon attenuation data can be understood by the relaxational model in which the acoustic phonon is coupled to a relaxation mode of the water molecules. Na-DNA undergoes the A to B phase transition at a relative humidity (rh) of 92% while Li-DNA (which remains in the B form in this range) decrystallizes at an rh of 84%. We find that our Brillouin results for Na- and Li-DNA are remarkably similar, indicating that the A to B phase transition does not play an important role in determining the acoustic properties of these two types of DNA.

Notes: We have studied the hydration of Na-DNA and Li-DNA fibers and films, measuring water contents, x-ray fiber diffraction patterns, low-frequency Raman spectra (below 100 cm-1), high-frequency Raman spectra (600-1000 cm-1), and swelling, as a function of relative humidity. Most samples gain weight equilibrium (though not conformational equilibrium) in one day. The volume occupied by a base pair as the DNA is hydrated (obtained from the x-ray and swelling data) shows anomalies for the case of Na-DNA in the region where the A-form occurs. Our Raman and x-ray data reproduce the well-known features of the established conformational transitions, but we find evidence in the Raman spectra and optical properties of a transition to what may be a disordered B-like conformation in Na-DNA below 40% relative humidity. We have studied the effects of crystallinity on the A to B transition. We find that the transition to the B-form is impeded in highly crystalline samples. In most samples, the transition occurs in three days (after putting the sample at 92% relative humidity) but in highly crystalline samples, the transition may take months. By comparing the high-frequency Raman spectra of highly ordered and disordered films, we show that the extent of crystallinity controls the amount of A-DNA formed when ethanol is used to dehydrate the films. We show that rapid dehydration (by laser heating) does not result in a B to A transition. A fiber that gives A-type x-ray reflections probably contains B-like material in noncrystalline regions. The low-frequency Raman spectrum is dominated by a band at about 25 cm-1 in both Na- and Li-DNA. Another band is seen near 35 cm-1 in Na-DNA at humidities where the sample is in the A-form. In contrast to earlier reports, we find that the Raman intensity does not depend on fiber orientation relative to the scattering vector. The “35-cm-1” band is largely depolarized (i.e. vertical polarization incident and horizontal polarization scattered, VH, or vice versa, HV) while the “25-cm-1” band appears in both VV, VH and HV polarizations. These bands are all weaker in HH polarization. The “25-cm-1” band may be due to a shearing motion of the phosphates and their associated counterions, while the “35-cm-1” band may be characteristic of A-DNA crystallites. We consider mass-loading, relaxational coupling to the hydration shell, and softening of interatomic potentials as possible explanations of the observed softening of the low-frequency Raman bands on hydration. Relaxation data suggest that the added water binds tightly (on these time scales) and a mass-loading model accounts for the observed softening rather well.We conclude that the A to B transition is not driven by softening of the “25-cm-1” band. Rather, it is most probably a consequence of crystal-packing forces, with the more regular A-form favored in crystals when these forces are strong.