Properties of pseudouridine N1 imino protons located in the major groove of an a-form RNA duplex

Abstract

The exchangeable N1 imino protons of two pseudouridine (Ψ) bases located at adjacent Internal positions within an undecamer RNA duplex (5 AUA-CψψACCUG/3 UAUGAAUGGUC) can report on the environment of the major groove of an A-form double-stranded nucleic acid. The ψN1 Imlno protons of these residues (which are not involved in interstrand Watson-Crick hydrogen bonding) are protected from chemical exchange with the solvent water and thus are observable in the proton NMR spectrum in H2O (1). These protons will exchange readily at Increased pH values or upon thermal denaturation of the duplex. The longitudinal (T1) relaxation times of the ψN1 imino protons In 100 mM NaCI or in 10 mM MgCI2 and 100 mM NaCI are approximately two-fold faster than those of the ψN3 imino protons which are Involved in Watson-Crick base pairing. With the addition of spermkJine, the ψN1 imino protons become readily exchangeable at a temperature some 20°C below the melting temperature of the duplex. © 1992 Oxford University Press.