Z‐RNA: The solution NMR structure of r(CGCGCG)

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Abstract
Left-handed double-helical Z-RNA has been studied using the ribohexanucleotide pentaphosphate r(CpGpCpGpCpG). One-dimensional proton nmr experiments were used to probe the structural details of the left-handed helix in concentrated sodium perchlorate solution. In 1M NaClO4 the RNA adopts the normal A-form double helix, and in 6M NaClO4 it is nearly all in the Z form. In 4M NaClO4 it exists as nearly equal parts of A form and Z form. Resonances corresponding to both A and Z form appear in the nmr spectrum, indicating that the duplex exchanges slowly between forms. Spin–spin coupling constants between protons in the ribose rings were used to determine the sugar-pucker conformations of the individual nucleotides. Quantitative nuclear Overhauser experiments were used to determine proton–proton distances within the nucleoside, and from these distances values for the glycosidic torsion angle were determined. The results show that the cytidines adopt C2′,-endo sugar puckers (S type) with pseudo-rotation phase values (P) of ∼ 165°. The bases are in the anti conformation, with χ values of ∼ − 140°. The internal guanosines adopt C3′,-endo sugar puckers (N type) with P ∼ 18°, while the 3′-terminal guanosine ribose exists in an equilibrium between S- and N-type conformations. All three guanosine bases adopt the syn conformation, with χ ∼ 70°. The results indicate that the solution structure of Z-RNA is very similar to that of Z-DNA.