Yong A. Shin

Interaction of metal ions with polynucleotides and related compounds. XX. Control of the conformation of polyriboadenylic acid by divalent metal ions

Abstract Divalent metal ions have profound effects on the conformation of poly A, as indicated by changes in optical rotatory dispersion and ultraviolet spectra, with different metal ions having distinctly different effects. At pH 6 and in the presence of 5 × 10 −2 M NaCl, two moles Ni(II) or Co(II) per mole of poly A residue stabilize the single helix; the same amount of Mg(II), Ca(II), Zn(II) or Mn(II) produce a mixture of double and single helix, while Cu(II) and Cd(II) induce the formation of a random coil structure. Under other conditions, these same metals have different effects, with the amount of added NaCl an important factor that can be used to control the way in which a particular divalent metal ion will induce the transition from a double helix to single helix or from helix to coil. The single helix is stabilized by metals binding to phosphate; the double helix is destabilized by metal ions binding to either phosphate or base, the former producing single helix and the latter random coil. The melting temperature of double helical poly A is diminished when metal ions bind to either type of site.

Some effects of metal ions on DNA structure and genetic information transfer

The reaction of metal ions with nucleic acids can lead to a variety of dramatic effects on nucleic acid structure, e.g., crosslinking of the polymer strands, degradation to oligomers and monomers, stabilization or destabilization, and the mispairing of bases. These effects have important implications for genetic information transfer. Metal ions are involved in many aspects of this transfer; we are presently concerned with the effect of metal ions on the orientation of the active site of RNA polymerase.Many of the effects of metal ions on nucleic acid structure involve changes in the conformation of the macromolecules. We have found that conditions that have been used to convert B DNA to Z DNA lead to at least two other conformational changes, and phase diagrams delineate the realms of stability of each of the forms. We have carried out a number of studies that demonstrate that the conversion of B to Z DNA is very closely correlated with a substantial decrease in the ability of the DNA to act as a template for RNA synthesis.

Changes of biological significance induced by metal ions in the structure of nucleic acids and nucleotides

We have previously shown that the action of metal ions on nucleic acids leads to a variety of perturbations in secondary structure, including crosslinking, mispairing, and degradation. We have demonstrated that metal ions also have a profound effect on the way in which nucleic acid molecules are packed together into highly organized aggregates [1]. These studies, along with those that reveal that metals also influence the enzymes that act on nucleic acids (such as cleavage enzymes and RNA polymerase) indicate how changes in cellular concentrations of metal ions can impact on cellular processes that depend on genetic information transfer. Many of the effects of metals on nucleic acids or other biomacromolecules involve conformational changes. We have recently been concerned with the ability of metal ions or complexes to induce interconversions among at least four nucleic acid conformers [2]. These studies were carried out with poly(dGdC)·(dGdC), which can exist in the Z-conformation, and we have discovered that conversion to Z-DNA can lead to further conversions to other DNA structures. These structures are all in equilibrium with each other, but each can be stabilized under appropriate conditions of nucleic acid and metal concentration. These conformational transitions are important because the biological activity of nucleic acids depends on their conformation. We have shown that different conformations of DNA have different activities as template for RNA synthesis. It has been reported that the progress of Alzheimers disease, the most prevalent form of senile dementia, is associated with the accumulation of aluminum in the chromatin of the brain [3, 4]. We have found that Al forms crosslinks between DNA strands and that Al binding to DNA in chromatin can be monitored by nuclear magnetic resonance (NMR). Al has also been implicated in dialysis dementia [5] through binding to ATP [6]. We have found by multinuclear NMR studies that Al forms four different complexes [7] with ATP. 27Al NMR is very sensitive to the chemical environment of Al and can be used in the identification of Al complexes in equilibrium with each other in a variety of systems of biological interest [8].

Recent Studies on the Effects of Divalent Metal Ions on the Structure and Function of Nucleic Acids

Metal ions are required for many of the processes in which nucleic acids transfer genetic information (Eichhorn, 1973). Thus metal ions are essential for the proper functioning of the genetic apparatus. Nevertheless the presence of the wrong metal ions, or even the essential ones in the wrong concentration, can lead to errors. Let me illustrate such errors in DNA, RNA and protein synthesis.

Metal complex induced changes in DNA conformation and template activity

Abstract It is now well-known that the interaction of metal ions with DNA leads to dramatic changes in nucleic acid structure [1] and recently it has become apparent that even the handedness of the double helix [2] and its compaction into aggregates [3, 4] is affected by such interaction. As recently demonstrated, DNA can exist in left-handed (Z) as well as the familiar right-handed conformations. The Z-structure is produced by DNA molecules containing alternating guanine (G) and cytosine (C) bases [poly(dGdC)· poly(dGdC) [5]. Compacted states have been known for some time to exist in vivo, and it is believed that these as well as left-handed conformations may be involved in the control of genetic information transfer. It is therefore important to understand how transitions between the DNA conformers take place, and whether such transitions affect the biological activities of DNA. We have addressed both of these problems. We have found that [Co(NH3)6]Cl3 brings about reversible transitions in the structure of poly(dGdC)· poly(dGdC) so that the right-handed B-form is first converted to Z-DNA and then to another structure that resembles A-DNA and finally to the highly compacted ψ-DNA [6]. The metal complex is thus able to induce three transitions among four conformers of DNA. By manipulating the concetrations of [Co(NH3)6]Cl3 and poly(dGdC)·poly(dGdC), as well as other factors such as reaction time and temperature, each of these conformations can be stabilized, and identified by its circular dichroism spectrum; or labilized and converted into another structure. We believed that the mechanism for these interconversions depends on the fact that increasing concentrations of the Co(III) complex stabilize conformations in which the phosphate groups of DNA are closer together. Conformational change in DNA, as demonstrated for the B → Z conversion leads to the biologically important consequence that the ability of the DNA to act as a template for RNA synthesis is affected. Figure 1 illustrates the correlation of the B → Z transition of poly(dGdC)·poly(dGdC) which occurs at ∼60 μM Co(NH3)63+, with a decrease in RNA synthesis to ∼ 1 2 the original rate, in the presence of E. coli RNA polymerase. A decrease in RNA synthesis also accompanies the conversion of a similar double helix in which the guanines are methylated, poly(dGdm5C)·poly(dGdm5C), from the B to the Z form, even though this transition occurs at a much lower (∼3 μM) Co(III) concentration. Clearly the metal complex has profound effects on the DNA conformation, and the DNA conformation affects the ability of the DNA to act as a template for RNA synthesis.