Structure-Directing Properties of Na+ in the Solution Ordering of Guanosine 5'-Monophosphate. Stoichiometry of Aggregation, Binding to Ethidium, and Modes of Na+ Complexation

Article abstract of DOI:10.1021/ja00388a017

Tetramethylammonium has been found to be a structure-inert cation in the solution ordering of guanosine 5'-monophosphate (5'-GMP) at neutral or slightly basic pH.This finding has made it possible to study quantitatively by 1H NMR spectroscopy the stoichiometry of nucleotide ordering in the presence of Na⁺ as a structure-directing counterion.The dependence of the ordered-structures on total nucleotide concentration is consistent with the formation of octamers.Independent evidence for octamer formation is provided by the binding of ethidium to the ordered nucleotide.Two octamer-ethidium complexes are observed with octamer to ethidium ratios of 1:1 and 1:2.The dependence of ordered structure formation on Na⁺ concentration indicates the binding of four Na⁺ ions per octamer unit.The types of Na⁺ binding sites are inferred from mixed Na⁺-K⁺ experiments.One binding site is a highly Na⁺-specific structure-directing site.The second site is less Na⁺ specific, but it plays an important role in stabilizing the ordered structures.The replacement of Na⁺ by K⁺ at the second site dramatically stabilizes the Na⁺-directed self-structures.A model involving coaxial stacking of planar hydrogen-bonded tetramer units is proposed for the ordered structures.Normal and inverted tetramer stacking arrangement account for the presence of three NMR-observable isomers, provided that twisting about the C₄ symmetry axis is rapid.The hole defined by the four carbonyl oxygens of a tetramer unit is believed to be the highly Na⁺-specific binding site.Chelation of Na⁺ (or structure-stabilizing K⁺) by phosphate oxygens on adjacent tetramer plates is proposed as the less specific binding site.Model building studies suggest that interplate hydrogen bonding also may be involved in stabilizing the stacked tetramers.