Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA

The stability of DNA duplex and tripler structures not only depends on mole cular forces such as base pairing or tripling or electrostatic interactions but also is sensitive to its aqueous environment. This gaper presents data on the melting of Escherichia coli and poly(dA).poly(dT) duplex DNA and on the poly(dT).poly(dA).poly(dT) tripler in a variety of media to assess the contributions from the osmotic status and salt content of the media. The e ffects of volume exclusion on the stability of the DNA structures are also studied. From thermal transition measurements in the presence of low-molecu lar weight osmotic stressors, the number of water molecules released upon m elting is found to be four waters per base pair for duplex melting and one water for the conversion of tripler to single-strand and duplex. The effect s of Na+ counterion binding are also determined in ethylene glycol solution s so that the variation of counterion binding with water activity is evalua ted. The data show that there is a modest decrease in the extent of counter ion binding for both duplex and tripler as water activity decreases. Finall y, using larger polyethylene glycol cosolutes, the effects on melting of vo lume exclusion by the solutes are assessed, and the results correlated with simple geometric models for the excluded volume. These results point out t hat DNA stability is sensitive to important conditions in the environment o f the duplex or tripler, and thus, conformation and reactivity can be influ enced by these solution conditions.