Differential effect of tetramethylammonium chloride and sodium chloride on duplex melting temperatures of deoxyoligonucleotides: resolution of a salt effect into specific and non-specific components

Abstract

Temperature-dependent uv spectroscopy has been used to determine the differential salt effect of tetramethylammonium chloride (Me4NCl) and sodium chloride (NaCl) on the thermal stabilities of a series of deoxyoligonucleotide duplexes that systematically differ in base composition and sequence. This approach has allowed us to resolve the AT-specific effect of Me4N+ from the more general, non-specific cation effects of Me4N+ versus Na+. Our results reveal that in the absence of AT-specific effects, Me4N+ (relative to Na+) significantly reduces the thermal stability of duplex structures. We offer an interpretation of this differential salt effect in terms of the influence of the condensed cation on water structure at the surface of the duplex. We also observe an AT-specific effect of Me4N+ which results in an increased thermal stability for AT-containing duplexes in Me4NCl relative to NaCl. This specific effect which is governed by mass action is found to be uninfluenced by base sequence and to be a linear function of the percent AT base pairs in the duplex.