Characterization of an RNA bulge structure by Fourier transform infrared spectroscopy.
There may be several advantages associated with an antisense oligonucleotide that induces a bulged structure into its RNA target molecule. Many structures of RNA bulges are elucidated from single-stranded RNA models. However, a two-component system is the minimum requirement for a realistic antisense model. We have used Fourier transform infrared spectroscopy to investigate a single-stranded RNA oligonucleotide with known NMR solution structure, constructed to model a five nucleotide bulge, and its two-component oligonucleotide counterpart. The infrared spectra show A-helical base-paired stems and non-base-paired loops in both systems. The nucleosides are mainly in an anti-conformation. Both N-type and S-type of sugar puckers can be inferred from the infrared region sensitive to sugar conformations. The S-type of sugar pucker is likely to be associated with the nucleotides in the bulge. The FTIR results display an overall structural similarity between the two model systems.
Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Stockholm SE-106 91, Sweden.
Martina
M
Banyay
Jessica
J
Sandbrink
Roger
R
Strömberg
Astrid
A
Gräslund
D001483:Base Sequence; D002241:Carbohydrates / Q000737:chemistry; D002851:Chromatography, High Pressure Liquid; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000737:chemistry; D010710:Phosphates / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*
D002241:Carbohydrates; D016376:Oligonucleotides, Antisense; D010710:Phosphates; D012313:RNA