Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling.
Site-directed spin labeling with continuous wave electron paramagnetic resonance (EPR) spectroscopy was utilized to characterize dynamic features of the kink-turn motif formed through a leader-linker interaction in the Vibrio cholerae glycine riboswitch. Efficient incorporation of spin-labels into select sites within the phosphate backbone of the leader-linker region proceeded via splinted ligation of chemically synthesized spin-labeled oligonucleotides to in vitro transcribed larger RNA fragments. The resultant nitroxide EPR line shapes have spectral characteristics consistent with a kink-turn motif and reveal differential backbone dynamics that are modulated by the presence of magnesium, potassium, and glycine.
Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States.
Jackie M
JM
Esquiaqui
Eileen M
EM
Sherman
Sandra A
SA
Ionescu
Jing-Dong
JD
Ye
Gail E
GE
Fanucci
D020121:5' Untranslated Regions / Q000502:physiology*; D004578:Electron Spin Resonance Spectroscopy; D005998:Glycine / Q000235:genetics* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding / Q000502:physiology; D012313:RNA / Q000235:genetics; D058928:Riboswitch / Q000502:physiology*; D013113:Spin Labels
D020121:5' Untranslated Regions; D058928:Riboswitch; D013113:Spin Labels; D012313:RNA; D005998:Glycine