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Nucleic Acids Research, 1994, Vol. 22, No. 15 3147-3150
© 1994

MOLECULAR BIOLOGY

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

Alan R. Wolfe and Thomas Meehan*

Division of Toxicology and Department of Pharmacy, University of California San Francisco, CA 94143, USA

*To whom correspondence should be addressed

Received March 31, 1994. Revised June 23, 1994. Accepted June 23, 1994.

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%).


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