The effect of sodium ion concentration on intrastrand base-pairing in single-stranded DNA.

The salt-induced formation of duplex structure (primarily hairpin loops) in denatured calf thymus DNA was monitored by measuring the decrease in absorbance at 260 nm as a function of increasing sodium ion concentration. It was found that this process was noncooperative and could be accurately described by the mass-action expression for the reversible formation of a binary complex: single strand (coil) + free sodium ion <==> hairpin (with associated sodium ion). The equilibrium constant for the transition was found to be 6 (M Na+)-1. The extrapolated absorbance at infinite salt concentration represents 11% hyperchromicity, which is one third of the hyperchromicity of denatured DNA in the absence of salt (36%).