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

Abstract

SynopsisWe 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-I), high-frequency Raman spectra (soO-lOOO cm-'), 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-' in both Na-and Li-DNA. Another band is seen near 35 cm-l 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-crn-'" band is largely depolarized (i.e. vertical polarization incident and horizontal polarization scattered, VH, or vice versa, HV) while the "25-cm-'" band appears in both W, VH and HV polarizations. These bands are all weaker in HH polarization. The "25-cm-'" band may be due to a shearing motion of the phosphates and their associated counterions, while the "35-cm-" 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-'" 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. INTRODUCTIONThe earliest fiber diffraction studies established that DNA can take up secondary structures that differ dramatically. Sodium-salted fibers give ...

The Influence of Packing on Free Radical Yields in Solid-State DNA: Film Compared to Lyophilized Frozen Solution

“…DNA conformation is known to vary with changes in DNA hydration (27)(28)(29). Vacuum-dried DNA [~2.5 waters per nucleotide (8,9)] is denatured; slightly wetter DNA (~3 < Γ < ~10) is in a B-like conformation; more fully hydrated DNA (~10 < Γ < ~25) tends to be in the A conformation; at greater hydrations, DNA is in the B conformation.…”

Ionic mobility in DNA films studied by dielectric spectroscopy

“…The larger value of the activation energy and the lower carrier mobility in the Na-DNA film, in which the molecules are in the A-form, is consistent with what is known about the structures of DNA fibers. The fibers of the B-form, which are more hydrated, leave more room for the motion of the counter-ions, whereas the fibers of the A-form have a higher crystalline content in which the molecules are closely packed [17]. The average volume per base pair is approximately two times larger in Li-DNA at 92% RH than in Na-DNA at 56% RH and therefore it is not surprising to find a significantly higher barrier for ionic motion in the Na-DNA film, and a lower charge carrier mobility.…”

“…In the presence of Li + ions DNA remains in the B-form in a wider watercontent [17]. This is why we use Li-DNA to study DNA in its B-form and Na-DNA to investigate the A-form.…”

Terahertz optical measurements of correlated motions with possible allosteric function

“…Similar results have been found for a variety of proteins, thus suggesting the possibility that specific vibrations can be identified using optical spectroscopy. A number of proteins have been measured spectroscopically with Raman and traditional Fourier transform infrared (FTIR) transmission techniques (Lindsay et al 1988;Lisy et al 1997;Powell et al 1987Powell et al , 1991. While extensive Raman spectroscopy studies have been performed, there is some disagreement among various research groups on band identification, possibly due to the application of complex Lorentzian line-fitting procedures for extracting weak contributions to the main elastic scattering peak (Lisy et al 1997;Weidlich et al 1990).…”