DNA Thermal Stability Depends on Solvent Viscosity

Abstract

Capillary electrophoresis has been used to measure the thermal stability of small DNA hairpins in solutions containing 0.3 M cation, comparing the results observed in Na+ and NH4 + with those observed in solutions containing various tetraalkylammonium ions. The midpoint melting temperatures of the hairpins decreased nonlinearly with cation radius but linearly with solvent viscosity, suggesting that the reversible melting transition involves DNA migration through the solvent to find stable base-pairing partners. The normalized melting temperatures increased linearly with the inverse viscosity of the solvent and agreed with values calculated from literature data for another small DNA hairpin, a small RNA duplex, and sonicated calf thymus DNA in tetraalkylammonium ion solutions. The normalized melting temperatures calculated from literature data for poly­(A)·poly­(U) and two proteins, ribonuclease and lysozyme, in tetraalkylammonium ion solutions also increased linearly with inverse solvent viscosity. By contrast, the normalized melting temperatures calculated from literature data for DNA in solutions containing ethylene glycol or glycerol to modify the viscosity increased linearly with the logarithm of inverse solvent viscosity, not the first power of inverse solvent viscosity.

Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects

“…In addition to what is generally referred to as molecular crowding effects, correlations to water activity were concluded along the lines of earlier work by Spink and Chaires (52). However, the picture is complex as water activity is affected via several parallel mechanisms such as electrostatic, solvent viscosity, and dehydration effects—in combination with the excluded volume and osmotic effects (53, 54). In our case dehydration is judged less important since dioxane, diglyme, and PEG give very similar effects despite their widely different hydration properties.…”

Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

“…We have used CE to measure the thermal stability of DNA hairpins in solutions containing various monovalent cations [43,98,99]. CE is a relatively straightforward method of analyzing the helix/coil transition because the free-solution mobility depends primarily on the ratio between the effective charge and the frictional coefficient.…”

“…CE is a relatively straightforward method of analyzing the helix/coil transition because the free-solution mobility depends primarily on the ratio between the effective charge and the frictional coefficient. When a hairpin (or duplex) is denatured, the conformation becomes less compact, increasing the frictional coefficient while the effective charge remains approximately constant [33,43,98,99]. Hence, the mobility of a duplex or hairpin will decrease upon denaturation until becoming equal to that of a random coil containing the same number of nucleotides.…”

Electrophoretic Mobility of DNA in Solutions of High Ionic Strength

“…We have been using free-solution capillary electrophoresis (CE) to evaluate the properties of small ssDNA and dsDNA in solutions containing various monovalent cations. Our previous studies have addressed the dependence of the electrophoretic mobility of DNA on molecular weight (22)(23)(24), ionic strength (25,26), curvature (27)(28)(29)(30), charge density (23,(30)(31)(32), and solution viscosity (33). Here, we have used CE to determine the dependence of the electrophoretic mobility of ssDNA and dsDNA on ionic strength in solutions containing high concentrations of Na þ ions.…”