title: Preference for ribose over deoxyribose in loop-closing base pairs of extra stable nucleic acid hairpins.
abstract: We have investigated the effect of switching ribose to deoxyribose at the closing base-pair of an extra-stable RNA hairpin. Specifically, we studied the sequence 5'-GGAC(UUCG)GUCC, a dodecanucleotide that folds into a well-characterized, "extra stable" RNA hairpin structure. Recently, we showed that hairpins containing a 2',5'-linked (UUCG) loop instead of the native 3',5'-linked loop also exhibit extra-stability (Hannoush and Damha, J. Am. Chem. Soc., 2001, 123, 12368-12374). In this article, we show that the ribose units located at the loop-closing positions (i.e., rC4 and rG9) contribute significantly to the stabilization of RNA hairpins, particularly those containing the 3',5'-UUCG loop. Interestingly, the requirement of rC4 and rG9 is more relaxed for DNA hairpins containing the 2',5'-UUCC loop and, in fact, they may be replaced altogether (ribose--> deoxyribose) without affecting stability. The results broaden our understanding of the behavior of highly stable (UUCG) hairpin loops and how they respond to structural perturbation of the loop-closing base pairs.
authors.affiliation: Department of Chemistry, McGill University, Montreal, Quebec, Canada.
authors.forename: Rami N
authors.initials: RN
authors.lastname: Hannoush
authors.forename: Masad J
authors.initials: MJ
authors.lastname: Damha
mesh_terms: D020029:Base Pairing; D003855:Deoxyribose / Q000737:chemistry*; D009843:Oligoribonucleotides / Q000737:chemistry*; D012266:Ribose / Q000737:chemistry*
chemical_list: D009843:Oligoribonucleotides; D003855:Deoxyribose; D012266:Ribose