DIFFERENCES BETWEEN DNA-BASE PAIR STACKING ENERGIES ARE CONSERVED OVER A WIDE-RANGE OF IONIC CONDITIONS

Base pair stacking free energy parameters in a low ionic strength solv ent were determined from an analysis of DNA fragments using temperatur e gradient gel electrophoresis (TGGE). Transition midpoint temperature s (T-u) were determined for the first melting domain (52 +/- 4 bp) of 16, 339bp DNAs that differed from each other by single base pair subst itutions. The data were combined with previously obtained T-u data fro m 17 similar DNAs that had single base pair changes at different sites [Ke, S. H., and Wartell, R. M. (1995) Biochemistry 34, 4593-4599]. Th e T-u values were used to evaluate free energy differences (delta Delt a G) between 31 pairs of DNAs. Linear equations relating the delta Del ta G values to changes in base pair stacking were analyzed by singular value decomposition (SVD) to determine the 10 nearest neighbor free e nergy parameters. The order of stability of the parameters, TA < AT < AA < AG < GT approximate to TC approximate to TG < CC approximate to G C approximate to CG, was essentially the same as the hierarchy determi ned in 1 M Na+ [Allawi, H. T., and SantaLucia, J., Jr. (1997) Biochemi stry 36, 10581-10594]. The experimental free energy differences were i n good agreement with predictions made using nearest-neighbor paramete rs determined from several previous studies conducted in medium or hig h salt concentrations. Conversely the parameters determined in the cur rent study produced good predictions of free energy differences previo usly determined from 59 DNA oligomers in 1 M Naf. The results indicate that differences between base pair stacking energies are conserved ac ross a wide range of ionic conditions, and in both oligomer and polyme r DNA contexts.