Pronouced instability of tandem IU base pairs in RNA

• Published in: Nucleic acids research 2004-03, Vol.32 (5), p.1824-1828
• Main Authors: Serra, Martin J., Smolter, Patricia E., Westhof, Eric
• Format: Article
• Language: English
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkh501

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.