Aggregated DNA in ethanol solution

Abstract

A recently developed mecbanocbemical method has provided a new, efficient tool for studies on the thermal stability and structure of aggregated DNA in ethanol-water solutions. At low ethanol concentrations DNA is fully soluble and is in the B form. However, with increasing ethanol concentration the melting temperature of DNA, T,,,, decreases. At a critical ethanol concentration, dependent on the nature and concentration of the counterion, aggregation of the DNA molecules sets in. This is reflected in a marked increase in T,,, indicating that the aggregated DNA molecules are thermally more stable than the dissolved ones. However, they are still in the B form. In general, T,,, of aggregated DNA also decreases with further increasing ethanol concentration and is dependent on the nature of the counterion, but T,,, is not affected by the concentration of the counterion (excess salt) in the ethanol-water solution. When the ethanol concentration reaches the range of 7040% (v/v), the B-to-A conformational transition occurs in the case of Na-, K-and CsDNA. Above this transition point the A form is more stable than the B form due to the reduced water activity and to increased interhelical interactions. At very high ethanol concentrations, above 85% and dependent on the nature of the counterion, a drastic change in the thermal behaviour is observed. Apparently such a strong interhelical interaction is induced in the aggregated DNA that the DNA is stabilized and cannot adopt a random coil state even at very high temperatures. This stability of DNA in the P form is fully reversed if the ethanol concentration is lowered and the activity of water, thereby, is restored.

On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension

“…Subsequently, some evidence existed to assume the presence of double-stranded P-DNA, but only under very particular conditions in dry DNA (29) or ethanol solutions (30) (see also ref. 31).…”

Fast Molecular Beacon Hybridization in Organic Solvents with Improved Target Specificity

“…52 As a result, we chose to perform most studies using 56% ethanol to achieve both high reaction rates as well as specificity.…”

“…Some solvents such as those tested alcohols are known to precipitate DNA and cause DNA aggregation at high solvent concentrations. 21,52 For most tested solvents at 75%, for example, very little fluorescence change was observed in the presence of the target DNA (Figure 4), possibly due to after DNA aggregation/precipitation, the diffusion and binding become more difficult. For most tested solvents under relatively dilute conditions (e.g.…”

“…For most tested solvents under relatively dilute conditions (e.g. less than 50-60% ethanol), 52 DNA is not known to aggregate and therefore, the observed kinetics change should be independent of such processes. Based on the Tm and kinetic data, the effect of organic solvents on the hybridization rate appears to stem from the decrease of activation energy for the hybridization and de-hybridization (or melting) reaction to a similar extent, such that the rate is enhanced without significantly shift the reaction equilibrium.…”

A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions

“…Variations in ionic strength and identity, sequence, water activity, and ligand/protein binding all can modulate DNA structure. ¶ An example is the B-DNA to A-DNA transition observed in 76%, 80%, or 84% ethanol (vol/vol) solutions of DNA fibers in the presence of Na ϩ , K ϩ , or Cs ϩ , respectively (9). In contrast, the more strongly hydrated counterions (Li ϩ and Mg 2ϩ ) inhibit the transition to A-DNA; instead, B-DNA to C-DNA (7) or B-DNA to P-DNA (8) transitions are observed.…”