Mechanochemical study of conformational transitions and melting of Li‐, Na‐, K‐, and CsDNA fibers in ethanol–water solutions

Abstract

SYNOPSISHighly oriented fibers of Li-, Na-, K-, and CsDNA were prepared with a previously developed wet spinning method. The procedure gave a large number of equivalent fiber bundle samples (reference length, Lo, typically = 12-15 cm) for systematic measurements of the fiber length L in ethanol-water solutions, using a simple mechanochemical set up. The decrease in relative length L / Lo with increasing ethanol concentration at room temperature gave evidence for the B-A transition centered at 76% ( v / v ) ethanol for NaDNA fibers and at 80 and 84% ethanol for Kand CsDNA fibers. A smaller decrease in L / L o of LiDNA fibers was attributed to the B-C transition centered at 80% ethanol. In a second type of experiment with DNA fibers in ethanol-water solutions, the heat-induced helix-coil transition, or melting, revealed itself in a marked contraction of the DNA fibers. The melting temperature T,, decreased linearly with increasing ethanol concentration for fibers in the B-DNA ethanol concentration region. In the B-A transition region, Na-and KUNA fibers showed a local maximum in T,. On further increase of the ethanol concentration, the A-DNA region followed with an even steeper linear decrease in T,. The dependence on the identity of the counterion is discussed with reference to the model for groove binding of cations in B-DNA developed by Skuratovskii and co-workers and to the results from Raman studies of the interhelical bonds in A-DNA performed by Lindsay and co-workers. An attempt to apply the theory of Chogovadze and Frank-Kamenetskii on DNA melting in the B-A transition region to the curves failed. However, for Na-and KDNA the T , dependence in and around the A-B transition region could be expressed as a weighted mean value of T , of Aand B-DNA. On further increase of the ethanol concentration, above 84% ethanol for LiDNA and above about 90% ethanol for Na-, K-, and CsDNA, a drastic change occurred. T , increased and a few percentages higher ethanol concentrations were found to stabilize the DNA fibers so that they did not melt at all, not even at the upper temperature limit of the experiments ( -80°C). This is interpreted as being due to the strong aggregation induced by these high ethanol concentrations and to the formation of P-DNA. Many features of the results are compatible with the counterion-water affinity model. In another series of measurements, T,,, of DNA fibers in 75% ethanol was measured at various salt concentrations. No salt effect was observed (with the exception of LiDNA at low salt concentrations). This result is supported hy calculations within the Poisson-Roltzmann cylindrical cell model.

Aggregated DNA in ethanol solution

“…This is in agreement with other studies suggesting hat intermolecular bonds are important for the existence of the \ conformation [36]. Aggregated KDNA behaves similarly vhile aggregated CsDNA lacks the local maximum in r,,, [28]. The data are from ref.…”

“…However, the increase in the transition width at these ethanol concentrations (Fig. 2) is probably a kinetic effect [28]. At a certain ethanol concentration, DNA does not melt at all, not even when the ethanol solution has reached the boiling point (Fig.…”

“…Therefore, it seems that the thermal stability of DNA in ethanol varies inversely with the size of the solvated counterion which is just the opposite of the results obtained in solutions lacking ethanol. Furthermore, while the melting of dissolved DNA in water is strongly influenced by the salt concentration, no salt effect on T,,, is observed for aggregated DNA [28] (Table l), possibly with the exception of LiDNA at very low salt concentrations [28]. One explanation is that the salt dependence of the electrostatic contribution to the free energy difference between coil and helical conformation (s) is negligible in the highly packed fiber system.…”

“…In the case of MgDNA, such transitions were not observed. The B-to-A transition was centered at 76% ethanol in the case of NaDNA, at 80% for KDNA and at 84% for CsCl; and the B-to-C transition was centered at 80% ethanol for LiDNA [28]. The A form is believed to be more firmly stabilized by aggregation and interhelical bonds.…”

“…This method was early modified for the preparation of a long fiber bundle of oriented DNA molecules from which a large number of reproducible samples could be taken for mechanochemical study [26]. Recently, a simple set-up was suggested for mechanochemical studies of conformational and helix-to-coil transitions in such DNA fiber samples [27,28,29,30]. A DNA fiber was held straight by a small weight in a measuring cylinder containing ethanol-water solution.…”