Sequence-dependent effects of spermine on the thermodynamics of the B-DNA to Z-DNA transition

Spermine has been shown to bind to and stabilize a number of altered DNA conformations, including left-handed Z-DNA. Here, we have quantitatively studied the effects of spermine on the negative supercoil-induced transition from B- to Z-DNA. We have determined the intrinsic association constants for and the effective number of ligands that bind to both B- and Z-DNA. The intrinsic affinity of spermine for Z-DNA is similar to 10 times higher for d(CA/TG) (K-ZP = 1.2 x 10(8) M(-1)) than for d(CG) dinucleotides (K-ZP = 1.5 x 10(7) M(-1)), and both are greater than that for B-DNA (K-BP = 1.4 x 10(5) M(-1)). This accounts for the stabilization of Z-DNA by spermine. The number of spermine accommodated by Z-DNA (nz) is sequence-dependent [n(z) = 0.6 spermine per 18 d(CA/TG) dinucleotides and 2.3 for 12 d(CG) dinucleotides]. The value of n(z) of <1 was interpreted as evidence for negative cooperativity in spermine binding to d(CA/TG) dinucleotides. Thus, although d(CA/TG) sequences saturate at lower spermine concentrations, the ligand has an overall greater effect on the stability of d(CG) dinucleotides as Z-DNA. B-DNA accommodates more spermines per base pair than either sequence as Z-DNA. At higher concentrations (>10 mu M), spermine destabilizes Z-DNA. Using these parameters in a model for competitive spermine binding to B-DNA and Z-DNA, we can make predictions for how potential Z-DNA sequences found in the human genome are affected by cellular levels of superhelical density and spermine.