Two common assumptions are that duplex DNA structure shows little sensitivity to ionic conditions and that simple cations bind to DNA in a nonspecific fashion. Here we examine these assumptions using as a model ligand the inorganic cation Co(NH3)6(3+). We find, upon titration with Co(NH3)6(3+), that certain DNA oligonucleotides show pronounced changes in circular dichroism spectra. For oligonucleotides such as d(GGCCGGCC), with contiguous, same-strand guanines, the transition is toward A-DNA characteristics. For those oligonucleotides that manifest such large Co(NH3)6(3+)-induced changes in circular dichroism spectra, 59Co NMR relaxation measurements demonstrate that Co(NH3)6(3+) tumbling motions are greatly inhibited, so that the effective NMR correlation time approaches that of overall tumbling of the DNA oligomer. Very large upfield 59Co chemical shifts are observed for Co(NH3)6(3+) bound to such oligonucleotides. For another class of oligomers, which show no significant changes in the circular dichroism spectrum in the presence of Co(NH3)6(3+), the tumbling motions of bound Co(NH3)6(3+) are largely independent of those of the oligomer, and much more modest 59Co chemical shifts are observed. Oligomers in a third class cause significant rotational inhibition of bound Co(NH3)6(3+), and only modest changes in 59Co chemical shifts. Oligonucleotides in this class appear not to undergo large structural changes in the presence of Co(NH3)6(3+). Within these broad categories, a remarkable variability in 59Co NMR parameters, and in structural perturbations, is apparent for the 13 oligonucleotides that we have examined.

59Co NMR and CD measurements show for both stereoisomers of Co(en)3(3+) a similar trend in the sequence dependence of DNA recognition, as was reported previously for Co(NH3)6(3+). In particular, specific binding is evident to DNA molecules possessing runs of two or more same-strand guanine residues. The binding of either isomer to such sequences induces structural transitions toward A-DNA characteristics. Such measurements also show significant differences between the two stereoisomers in terms of how they recognize specific duplex DNA sequences. delta-Co(en)3(3+) binds more tightly than lambda-Co(en)3(3+) to right-handed, guanine-rich DNA, whereas lambda-Co(en)3(3+) binds more tightly than delta-Co(en)3(3+) to left-handed DNA. The two stereoisomers bind in an indistinguishable manner to AT-rich DNA.