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.
Banyay
Martina
M
Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, Stockholm SE-106 91, Sweden.
Sandbrink
Jessica
J
Strömberg
Roger
R
Gräslund
Astrid
A
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