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Published online 22 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 5 1824-1828

Pronouced instability of tandem IU base pairs in RNA

Martin J. Serra*, Patricia E. Smolter and Eric Westhof1

Department of Chemistry, Allegheny College, 520 N. Main St, Meadville, PA 16335, USA and 1 Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations and Simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes, F-67084 Strasbourg Cedex, France

*To whom correspondence should be addressed. Tel: +1 814 332 5356; Fax: +1 814 332 2789; Email: mserra{at}allegheny.edu

Received December 31, 2003; Revised and Accepted March 3, 2004

Optical melting was used to determine the stabilities of three series of RNA oligomers containing tandem XU base pairs, GGCXUGCC (5'XU3'), GGCUXGCC (5'UX3') and GGCXXGGC/CCGUUCCG (5'XX3'), where X is either A, G or I (inosine). The helices containing tandem AU base pairs were the most stable in the first two series (5'XU3' and 5'UX3'), with an average melting temperature ~11°C higher than the helices with tandem 5'GU3' base pairs and 25°C higher than the helices with tandem 5'IU3' base pairs. For the third series (5'XX3'), the helix containing tandem GG is the most stable, with an average melting temperature ~2°C higher than the helix with tandem AA base pairs and ~24°C higher than the helix with tandem II base pairs. The thermodynamic stability of the oligomers with tandem IU base pairs was also investigated as a function of magnesium ion concentration. As with normal A–U or G–U tandem duplexes, the data could best be interpreted as non-specific binding of magnesium ions to the inosine-containing RNA oligonucleotides.


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