PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure.
Pulsed electron double resonance (PELDOR) spectroscopy reveals a prearranged tertiary structure of the 27 nucleotides long engineered neomycin-responsive riboswitch. Measured distances between spin labels at positions U4-U14, U4-U15, U14-U26, and U15-U26 were unchanged upon neomycin binding which implies that the global stem-loop architecture is preserved in the absence and presence of the ligand. On the basis of our results, we infer that low-temperature PELDOR data unambiguously demonstrate the existence of an enthalpically favorable set of RNA conformations ready to bind the ligand without major global rearrangement.
Krstić
Ivan
I
Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany.
Frolow
Olga
O
Sezer
Deniz
D
Endeward
Burkhard
B
Weigand
Julia E
JE
Suess
Beatrix
B
Engels
Joachim W
JW
Prisner
Thomas F
TF
D000900:Anti-Bacterial Agents / Q000378:metabolism*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D009355:Neomycin / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012313:RNA / Q000032:analysis* / Q000378:metabolism; D013113:Spin Labels; D014529:Uridine / Q000032:analysis
D000900:Anti-Bacterial Agents; D013113:Spin Labels; D012313:RNA; D009355:Neomycin; D014529:Uridine