Detecting Ligand Binding to a Small RNA Target via Saturation Transfer Difference NMR Experiments in D2O and H2O

• Published in: Journal of the American Chemical Society Vol. 124; no. 45; pp. 13376 - 13377
• Main Authors: Mayer, Moriz, James, Thomas L
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 13.11.2002
• Subjects: Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Molecular and cellular biology; Molecular genetics; Transcription. Transcription factor. Splicing. Rna processing; Saturation transfer; Binding site; NMR spectrometry; RNA; Ligand
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja027526z

A small RNA motif is used as a target for ligand-based NMR-screening by saturation transfer difference (STD) NMR experiments. The prerequisites for using a small RNA target in STD experiments, such as saturation time, frequency, and pulses, are discussed. We also show that it is of advantage to use D2O as solvent instead of H2O due to the reduced R 1 relaxation rate in D2O. The 27-nucleotide model of the ribosomal A-site was known to bind the aminoglycoside paromomycin with high affinity. This binding interaction could be detected easily, proving the effectiveness of STD NMR experiments as a screening tool for RNA−ligand interactions.