title: The thermal stability of RNA duplexes containing modified base pairs placed at internal and terminal positions of the oligoribonucleotides.
abstract: The presence of various modifications within oligomers changes their thermodynamic stability. To get more systematic data, we measured effects of 5- and 6-substituted uridine on thermal stability of (AUCU(Mod.)AGAU)2 and (AUCUAGAU(Mod.))2. Collected results lead to the following conclusions: (i) 5-halogenated and 5-alkylated substituents of the uridine affect thermal stability of the RNA duplexes differently. Moreover, the 5-fluorouridine changes stability of the RNA duplexes opposite to remaining 5-halogenouridines; (ii) for oligomers containing 5-chloro, 5-bromo or 5-iodouridine stronger hydrogen bond formed between oxygen-4 of the 5-halogenated uracil and 6-amino group of the adenine is presumably responsible for stabilizing effect; (iii) placing of A-U(5R) base pairs closer to the end of the duplex enhance thermal stability relatively to oligomer with central position of this base pair; (iv) the effects of 5-substituents are additive, particularly for substituents which stabilize RNA duplexes; (v) 6-methyluridines (N1 and N3 isomers) as well as 3N-methyluridine present at internal position of A-U(Mod.) inhibit duplexes formation; (vi) 6-methyluridines (N1 and N3 isomers) as well as 3N-methyluridine placed as terminal base pairs stabilize the duplexes mostly via 3'-dangling end effect.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-704 Poznañ, Noskowskiego 12/14, Poland.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Ziomek
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Kierzek
authors.forename: Ewa
authors.initials: E
authors.lastname: Biała
authors.forename: Ryszard
authors.initials: R
authors.lastname: Kierzek
mesh_terms: D006358:Hot Temperature; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D009843:Oligoribonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics; D014498:Uracil / Q000737:chemistry*
chemical_list: D009692:Nucleic Acid Heteroduplexes; D009843:Oligoribonucleotides; D014498:Uracil; D012313:RNA