The origin of the A to B transition in DNA fibers and films.

Abstract

AbstractWe 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.