title: Does 29-mer RNA hairpin of the HIV-1 TAR RNA sequence bind magnesium? 19F-NMR and modelling studies.
abstract: 5-Fluorouridine residues have been introduced into functionally important bulge and loop regions of 29-mer HIV-1 TAR RNA hairpins I and II to study Mg2+ and Ca2+ binding using 19F-NMR spectroscopy. There was no substantial binding detected up to 20-molar excess in case of both cations, whereas association of argininamide, used as a reference ligand, could be detected at less than 1-molar excess. The deltadelta 19F value of 1.93 ppm observed for (F)U23 upon argininamide binding is in agreement with former NMR studies of TAR RNA/argininamide complex. However, obtained results do not confirm U38 x A27 x U23 base-triple formation. The unmodified HIV-1 TAR RNA hairpin resulted from 600 ps in aqua molecular dynamics simulation was subjected to a molecular mechanics modelling of Mg+ binding.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznañ.
authors.forename: A
authors.initials: A
authors.lastname: Fischer
authors.forename: Z
authors.initials: Z
authors.lastname: Gdaniec
authors.forename: M
authors.initials: M
authors.lastname: Olejniczak
authors.forename: L
authors.initials: L
authors.lastname: Bielecki
authors.forename: R W
authors.initials: RW
authors.lastname: Adamiak
mesh_terms: D001483:Base Sequence; D002118:Calcium / Q000737:chemistry; D003198:Computer Simulation; D005461:Fluorine; D015497:HIV-1; D008274:Magnesium / Q000737:chemistry*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D014529:Uridine / Q000031:analogs & derivatives
chemical_list: D012367:RNA, Viral; D005461:Fluorine; C001943:5-fluorouridine; D008274:Magnesium; D002118:Calcium; D014529:Uridine