Probing Hydration of Monovalent Cations Condensed Around Polymeric Nucleic Acids

Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

“…These results, together with other studies in the literature (1)(2)(3)(4)(5)(6)(7)(8)(9), suggest that all, or nearly all, monovalent cations bind to randomsequence dsDNA in aqueous solutions. The apparent K D observed for the binding of Tris + to ds26 is somewhat smaller than observed for the binding of other cations, suggesting that Tris-DNA complexes are stabilized by the formation of hydrogen bonds with the DNA bases (45), as well as by electrostatic interactions with the phosphate residues.…”

Effect of cesium on the volume of the helix–coil transition of dA·dT polymers and their ligand complexes

“…Since the partial molar volume of Cs + is about 22.8 cm 3 mol − 1 larger than Na + [45], V DNA of the Cs + form is about 3.2± 2.5 cm 3 mol − 1 nt or 6.4 ± 5.0 cm 3 mol − 1 bp smaller than the Na + form. Similarly, the adiabatic compressibility of DNA-Cs is about 5.2 ± 4.0 × 10 − 3 cm 3 mol − 1 MPa − 1 more positive than DNA-Na [44] with the difference between Cs + and Na + being about 12.8± 0.7 × 10 − 3 cm 3 mol − 1 MPa − 1 [33,46]. Thus, the cesium form is about 7.6 ± 4.0 × 10 − 3 cm 3 mol − 1 nt MPa − 1 or 15.2 ± 8.0 × 10 − 3 cm 3 mol − 1 bp MPa − 1 less compressible than the sodium form.…”

“…We propose that this effect originates from the higher affinity of this cation for DNA and a stronger neutralizing effect on DNA phosphate, which causes dehydration of the phosphate, a change in conformation of the backbone, and compaction of DNA. We interpret the lack of an effect with poly(dA)·poly(dT) in terms of the fact that the first layer hydration water in the minor groove of poly(dA)·poly(dT) only has hydrogen bonds with the bases, while the hydrogen bonding with backbone sugars are also involved in case of poly in CsCl and NaCl, both at 50 mM, 25°C [44]. The partial molar volume of DNA-Cs (183.0 cm 3 mol − 1 ) is reported to be about 19.6 ± 2.5 cm 3 mol − 1 larger than DNA-Na (163.4 cm 3 mol − 1 ) [44].…”

“…We interpret the lack of an effect with poly(dA)·poly(dT) in terms of the fact that the first layer hydration water in the minor groove of poly(dA)·poly(dT) only has hydrogen bonds with the bases, while the hydrogen bonding with backbone sugars are also involved in case of poly in CsCl and NaCl, both at 50 mM, 25°C [44]. The partial molar volume of DNA-Cs (183.0 cm 3 mol − 1 ) is reported to be about 19.6 ± 2.5 cm 3 mol − 1 larger than DNA-Na (163.4 cm 3 mol − 1 ) [44]. Since the partial molar volume of Cs + is about 22.8 cm 3 mol − 1 larger than Na + [45], V DNA of the Cs + form is about 3.2± 2.5 cm 3 mol − 1 nt or 6.4 ± 5.0 cm 3 mol − 1 bp smaller than the Na + form.…”

“…This would also contribute to the volumetric differences observed between sodium and cesium forms. Tikhomirova and Chalikian [44] interpreted their data as arising from the partial dehydration …”