6GE1

Solution structure of the r(UGGUGGU)4 RNA quadruplex


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H NOESY2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride100% D2O0.06 M6.81 atm298Bruker AVANCE III 700
22D 1H-1H NOESY2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride100% D2O0.06 M6.81 bar333Bruker AVANCE III 700
32D 1H-1H NOESY2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride90% H2O/10% D2O0.06 M6.81 atm278Bruker AVANCE III 700
42D 1H-1H TOCSY2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride90% H2O/10% D2O0.06 M6.81 atm278Bruker AVANCE III 700
52D 1H-13C HSQC2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride100% D2O0.06 M6.81 bar333Bruker AVANCE III 700
62D 1H-31P COSY2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride100% D2O0.06 M6.81 bar333Bruker AVANCE III 700
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III700
NMR Refinement
MethodDetailsSoftware
molecular dynamicsAmber
simulated annealingXplor-NIH
NMR Ensemble Information
Conformer Selection Criteriatarget function
Conformers Calculated Total Number400
Conformers Submitted Total Number15
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementAmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2structure calculationXplor-NIHSchwieters, Kuszewski, Tjandra and Clore
3chemical shift assignmentSparkyGoddard
4peak pickingSparkyGoddard