title: Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes.
abstract: Molecular dynamics simulations of RNA molecules consisting of an antisense oligonucleotide forming a complex with a target strand thereby creating an internal bulge-loop with 3, 4, or 5 nucleotides have been performed with and without O2' methylation of the antisense strand. The methylation influences minor groove hydration, in particular near guanines but also around the methylated O2', and it also reduces the flexibility of both RNA strands. A G.U wobble pair adjacent to the bulge-loop is also found to increase the flexibility of the bulge nucleotides, compared to the situation with a standard Watson-Crick G-C base-pair in the same position.
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden.
authors.forename: Boel Nyström
authors.initials: BN
authors.lastname: Macchion
authors.forename: Roger
authors.initials: R
authors.lastname: Strömberg
authors.forename: Lennart
authors.initials: L
authors.lastname: Nilsson
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability
chemical_list: D016376:Oligonucleotides, Antisense; D012313:RNA