Thermodynamic data are reported revealing that pseudouridine (Psi) can stabilize RNA duplexes when replacing U and forming Psi-A, Psi-G, Psi-U and Psi-C pairs. Stabilization is dependent on type of base pair, position of) within the RNA duplex, and type and orientation of adjacent Watson-Crick pairs. NMR spectra demonstrate that for internal Psi-A, Psi-G and Psi-U pairs, the N3 imino proton is hydrogen bonded to the opposite strand nucleotide and the N1 imino proton may also be hydrogen bonded. CD spectra show that general A-helix structure is preserved, but there is some shifting of peaks and changing of intensities. Psi has two hydrogen donors (N1 and N3 imino protons) and two hydrogen bond acceptors because the glycosidic bond is C-C rather than C-N as in uridine. This greater structural potential may allow Psi to behave as a kind of structurally driven universal base because it can enhance stability relative to U when paired with A, G, U or C inside a double helix. These structural and thermodynamic properties may contribute to the biological functions of Psi.
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