Modified nucleoside-dependent transition metal binding to DNA analogs of the tRNA anticodon stem/loop domain

Biologically active DNA analogs of tRNAPhe (tDNAPhe) were used to investigate metal ion interaction with tRNA-like structures lacking the 2'OH. Binding of Mg2+ to the 76 oligonucleotide tDNAPhe, monitored by circular dichroism spectroscopy, increased base stacking and thus the conformational stability of the molecule. Mg2+ binding was dependent on a d(m5C) in the anticodon region. In contrast to Mg2+, Cd2+ decreased base stacking interactions, thereby destabilizing the molecule. Since alterations in the anticodon region contributed to most of the spectral changes observed, detailed studies were conducted with anticodon hairpin heptadecamers (tDNAPheAC). The conformation of tDNAPheAC-d(m5C) in the presence of 1 mM Cd2+, Co2+, Cr2+, Cu2+, Ni2+, Pb2+, VO2+ or Zn2+ differed significantly from that of the biologically active structure resulting from interaction with Mg2+, Mn2+ or Ca2+. Nanomolar concentrations of the transition metals were sufficient to denature the tDNAPheAC-d(m5C) structure without catalyzing cleavage of the oligonucleotide. In the absence of Mg2+ and at [Cd2+] to [tDNAPheAC-d(m5C)] ratios of approximately 0.2-1.0, tDNAPheAC-d(m5C40) formed a stable conformation with one Cd2+ bound with a Kd = 3.7 x 10(-7) M. In contrast to Mg2+, Cd2+ altered the DNA analogs without discriminating between modified and unmodified tDNAPheAC. This ability of transition metals to disrupt higher order DNA structures, and possibly RNA, at microM concentrations, in vitro, demonstrates that these structures are potential targets in chronic metal exposure, in vivo.