Effects of nucleotide bromination on the stabilities of Z‐RNA and Z‐DNA: A molecular mechanics/thermodynamic perturbation study

Abstract

The structures of Z_I- and Z_II- form RNA and DNA oligonucleotides were energy minimized in vacuum using the AMBER molecular mechanics force field. Alternating C-G sequences were studied containing either unmodified nucleotides, 8-bromoguanosine in place of all guanosine residues, 5-bromocytidine in place of all cytidine residues, or all modified residues. Some molecules were also energy minimized in the presence of H₂O and cations. Free energy perturbation calculations were done in which G8 and C5 hydrogen atoms in one or two residues of Z-form RNAs and DNAs were replaced in a stepwise manner by bromines. Bromination had little effect on the structures of the energy-minimized molecules. Both the minimized molecular energies and the results of the perturbation calculations indicate that bromination of guanosine at C8 will stabilize the Z forms of RNA and DNA relative to the nonbrominated Z form, while bromination of cytidine at C5 stabilizes Z-DNA and destabilizes Z-RNA. These results are in agreement with experimental data. The destabilizing effect of br⁵C in Z-RNAs is apparently due to an unfavorable interaction between the negatively charged C5 bromine atom and the guanosine hydroxyl group. The vacuum-minimized energies of the Z_II- form oligonucleotides are lower than those of the corresponding Z_I- form molecules for both RNA and DNA. Previous x-ray diffraction, nmr, and molecular mechanics studies indicate that hydration effects may favor the Z_I- conformation over the Z_II- form in DNA. Molecular mechanics calculations show that the Z_II–Z_I energy differences for the RNAs are greater than three times those obtained for the DNAs. This is due to structurally reinforcing hydrogen-bonding interactions involving the hydroxyl groups in the Z_II form, especially between the guanosine hydroxyl hydrogen atom and the 3′-adjacent phosphate oxygen. In addition, the cytidine hydroxyl oxygen forms a hydrogen bond with the 5′-adjacent guanosine amino group in the Z_II- form molecule. Both of these interactions are less likely in the Z_I- form molecule: the former due to the orientation of the GpC phosphate away from the guanosine ribose in the Z_I form, and the latter apparently due to competitive hydrogen bonding of the cytidine 2′-hydroxyl hydrogen with the cytosine carbonyl oxygen in the Z_I form. The hydrogen-bonding interaction between the cytidine hydroxyl oxygen and the 5′-adjacent guanosine amino group in Z-RNA twists the amino group out of the plane of the base. This may be responsible for differences in the CD and Raman spectra of Z-RNA and Z-DNA.