Pronouced instability of tandem IU base pairs in RNA

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 con-taining tandem AU base pairs were the most stable in the ®rst two series (5¢XU3 ¢ and 5¢UX3¢), with an average melting temperature ~11oC higher than the helices with tandem 5¢GU3 ¢ base pairs and 25oC higher than the helices with tandem 5¢IU3 ¢ base pairs. For the third series (5¢XX3¢), the helix contain-ing tandem GG is the most stable, with an average melting temperature ~2oC higher than the helix with tandem AA base pairs and ~24oC 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-speci®c binding of magnesium ions to the inosine-containing RNA oligonucleotides