Do the 16 mer, 5'-GUGGUCUGAUGAGGCC-3' and the 25 mer, 5'-GGCCGAAACUCGUAAGAGUCACCAC-3', form a hammerhead ribozyme structure in physiological conditions? An NMR and UV thermodynamic study.
In a wide range of salt concentrations, 10-30 mM phosphate buffer containing up to 0.5 M Li2SO4 and 300 mM NaCl, 7.5 mM Mg2+, pH 5.5-7.5, a mixture of the 16 mer and the 25 mer RNA strands does not form a hammerhead in any amount detectable by NMR at 600 MHz. The imino-, amino-, aromatic- and anomeric protons in the NMR spectra of both the 16 mer and the 25 mer RNA have been assigned separately. Both the 16 mer and the 25 mer RNA both take up very stable hairpin structures, and when mixed together there is no major change of conformation in neither oligo-RNA.
Zamaratski
E
E
Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-751 23 Uppsala, Sweden.
Trifonova
A
A
Acharya
P
P
Isaksson
J
J
Maltseva
T
T
Chattopadhayaya
J
J
D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
D016337:RNA, Catalytic; C427204:hammerhead ribozyme