title: Pronounced instability of tandem IU base pairs in RNA.
abstract: 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 approximately 11 degrees C higher than the helices with tandem 5'GU3' base pairs and 25 degrees 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 approximately 2 degrees C higher than the helix with tandem AA base pairs and approximately 24 degrees 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.
authors.affiliation: Department of Chemistry, Allegheny College, 520 N. Main St, Meadville, PA 16335, USA. mserra@allegheny.edu
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Serra
authors.forename: Patricia E
authors.initials: PE
authors.lastname: Smolter
authors.forename: Eric
authors.initials: E
authors.lastname: Westhof
mesh_terms: D020029:Base Pairing; D007288:Inosine / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D020871:RNA Stability; D013816:Thermodynamics; D014498:Uracil / Q000737:chemistry*
chemical_list: D014498:Uracil; D007288:Inosine; D012313:RNA; D008274:Magnesium