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Nucleic Acids Research, 1992, Vol. 20, No. 8 1883-1889
© 1992

CHEMISTRY

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

Kathleen B. Hall and Larry W. McLaughlin1

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine St Louis, MO 63110, USA 1Department of Chemistry, Boston College 140 Commonwealth Avenue, Chestnut Hill, MA 02167, USA

Received January 31, 1992. Revised March 19, 1992. Accepted March 19, 1992.

The exchangeable N1 imino protons of two pseudouridine ({Psi}) bases located at adjacent Internal positions within an undecamer RNA duplex (5 AUA-C{psi}{psi}ACCUG/3 UAUGAAUGGUC) can report on the environment of the major groove of an A-form double-stranded nucleic acid. The {psi}N1 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 {psi}N1 imino protons In 100 mM NaCI or in 10 mM MgCI2 and 100 mM NaCI are approximately two-fold faster than those of the {psi}N3 imino protons which are Involved in Watson-Crick base pairing. With the addition of spermkJine, the {psi}N1 imino protons become readily exchangeable at a temperature some 20°C below the melting temperature of the duplex.


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